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TurboMass Software User's Guide

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1. File I z jas Options Help Of mlale fee tl 21 El Source Diagnostics GC Interface Inlet Line Temperature 200 Source Parameters Election Energy h F FF Trap Emission po E Repeller 13 _ j _ Lens 1 E JES Lens2 551 S Source Temp C 180 Filament Curent com Source Current MS Parameters LM Res 18 2 HM Res fiat Jon Energy ia lon Energy Ramp 1 0 Multiplier V 75 0 7 131 0 219 0 502 0 see C Ready Vacuum OK Operate Vi Selecting Peaks 1 Select the number of peaks that you want to display by selecting the appropriate checkboxes in the top right panel of the Tune page For example if you want to display only the first and second tune peaks then select checkboxes 1 and 2 and deselect checkboxes 3 and 4 2 Click OR Select Peak Editor from the Tune Window menu Then for each active peak select the mass that you want to tune on the span and the gain 91 TurboMass Software User s Guide 92 NOTE Zooming or Unzooming a Peak Drag the mouse horizontally or vertically to define a larger area The peak is expanded to fill this area OR Click to return the peak to the original size To Change the Tune Mass Span or Gain e Edit the mass span or gain in the text fields above the peak display e Double clicking on the borders above or below the peak will increase or decrease the peak intensity
2. smetla Sample List Fom1 Fom1TIC Fom2 Fom3 Fom4 Fom5 Fom6 Form Fom8 SamplelD Sample Type File Name Matrix Level Vial Quantify Method Qualitative Method Submitter Task Analysis w 1 BFB Tune Eval B10040501 Water Mediu 8260b_Tutorial TiCsearch10 VOA_Tutori VOA_Tutori VOA iv 2 YOA STD 5ng Init Calib B10040504 Water Mediu 8260b_Tutorial TiCsearch10 VOA_Tuton VOA_Tutori YOA v 3 VOA STD 20ng Init Calib 810040505 Water Mediu 8260b_Tutorial TiCsearch10 VOA_Tutori VOA_Tutori VOA v 4 YOA STD 50ng Init Calib B10040506 Water Mediu 8260b_Tutorial TiCsearch10 VOA_Tuton VOA_Tutori YOA v 5 VOA STD 100n Init Calib B10040507 Water Mediu 8260b_Tutorial TiCsearch10 VOA_Tutori VOA_Tutori VOA v 6 VOA STD 200n Init Calib B10040509 Water Mediu 8260b_Tutorial TICsearch10 VOA_Tuton VOA_Tutori YOA v 7 MethodBlank Meth Blank B10040510 Water Mediu 8260b_Tutorial TiCsearch10 VOA_Tutori VOA_Tutori VOA v 8 SpikeDup1 Spike B10040511 Water Mediu 8260b_Tutorial TICsearch10 VOA_Tutori VOA_Tutori YOA v 3 SpikeDup2 Spike Dup B10040512 Water Mediu 8260b_Tutorial TICsearch10 VOA_Tutori VOA_Tutori VOA v 10 MethodBlank2 Meth Blank B10040513 Water Mediu 8260b_Tutorial TiCsearch10 VOA_Tutori VOA_Tutori YOA CBR 00123 Analyte B10040514 Water Mediu 8260b_Tutorial TiCsearch10 VOA_Tutori VOA_Tutori VOA W 12 00124 Analyte B1004
3. aK c 2 To display a window select Visible for that window 3 Edit the Library Display View dialog parameters for each of the Library windows and click OK Hits Window Header Specify how many hits 1 to 4 to display with the search spectrum in the No Hits drop down list Displays a header at the top of each window Clicking Header opens the Header Editor where you can edit the header information For more information about using the Header Editor see The Header Editor on page 54 Peak Label Threshold These parameters change peak labeling in the Hits Window and Delta Window Decimal Places None Full Scale Intensity Select 0 to 4 from the Decimal Places drop down list to specify the number of decimal places to which peaks are labeled You can set a threshold for labeling peaks with mass If selected TurboMass does not display mass labels for any peaks If selected this parameter sets a relative intensity threshold for peak labels If selected this parameter sets an absolute intensity Library threshold for peak labels Select Intensity and enter an intensity value 4 Use the Window menu commands to arrange the different Library windows Hit List Window 1 Eile Edit Display Process Window Help 18 xl 2 ala wle wo eale 1 H it Compound Name PIPERIDINE 1 NITRO THIOPHENE TETRAHYDRODIMETHYL 1 1 DIOXIDE PROPENAL DIMETHYLHYDRAZONE 2 PIPERIDINONE 1
4. ccccssceeseeeseeeteeeteeenes 121 Setting Data Acquisition Parameters c ccsccsscetecetsceteceeeeeeeeeseeeees 122 Setting Calibration Parameter c cccccccssecssecsteceteceteceteeeeeeeeeeeseeeees 123 Setting Automatic Calibration Check Parameters 0 ceseseeceetees 125 Setting Mass Measures c cccccecscessessseeseeseceseceseceseceseeseeeseeeeseeenseenaes 126 The Calibration Report ccccscccsscesscesscessceeeeeeeceeseeeseecsaecseecaecnaeenseenseeaes 128 Altering the Displayed Range c ccsccescsseceseceseceeeeeseeeeeeeeeseentees 129 Manually Matching Peaks ccccccecsseesceesteeeteceecnseceseceeeeeeeseaeeeaeens 129 Other Calibration Facilities eccececeesceseeseeesceseceeeeeeeseceaeeaeeeeeeaeeeeeeeeaes 130 Deleting the Instrument Calibration ec ececeeeeeceeececeeeeeecneeeeeeeees 130 Displaying a Calibration Graph ew eeeeccesecseeeceeececeeeeeeeceaeeaeeeneeaes 130 TurboMass Software User s Guide Displaying a Verification Graph ccccccesseceseceteceseeeeeeeeeeeeneeeeensees 131 Making a Calibration from a Data File eieeeeeeeeceeeeeteeeceeeeeeeeeees 131 Recalibrating a Data File cc cccecccesscesseeeneeeceeeeeeeeeeeesaeenseenseenaeens 132 Editing a Reference File ccccccsccssecsseceeceeeeeeeeeeseeeseecseeessecsaecnseenseenseenes 133 High Mass Calibration ccccssccsscssscssecessceeeeeeeeeeseeeseecseecsaecssecnseeeaeenseeaes 135 Performing a
5. cccccccecccsssecessceeseseeeeeseeeseeeeeeseeeneeenaes 431 Manipulating the Display cccsccesccesscessceeeceeeeeeseeeseecscecseeenseenseenseenseenes 432 Setting Magnified Ranges ss ssssseeseseeseseesseeresstssesseessesnsseesresese 433 Deleting Magnification Ranges cccceccseesseeseescecseeseesseceeeneenaeens 434 Changing the Range of Both Axes ssssssssssesseseesssssessessesseessesessresees 435 Restoring the Display cccccccscesseesseeteceeeeeecseeeeeeeeeseeeseeeseeesaeestees 435 Setting the Display Range Defaults cccccccescceseceeeeeeeeeeeeeeneeenes 435 Displaying a Spectrum as a List cccccesccesccessceeeeeeeeeeseeeseeeeeeeeensees 436 Controlling the Appearance of the Display s ssseseesesessseseseseresseeee 438 Controlling the Appearance of Peak Labels 0 ccceesesseeeteeeteeeteees 441 Removing Spectra from the Display ccccesceescceseeeseeeeeereeeteeetees 443 Real time Display of Spectra ccccceesccescesscessceeeeseeeeeseeeeeeeeeteeessees 444 Changing the Order of Displayed Spectra cccccccssecsesseeeteceteeeteeees 444 Adding Text to the Spectrum Display c cccccscesseeseeteesteeteeneees 444 Processing Spectra rea cous cavecsns ceuden dees saes seetes cide cieles n MR she a he eesst vee 446 Saving and Recalling Processed Spectra ccccesccesccesecessceeeeeeteeseeeees 446 IRR TON ARE R EE E TE EE AAEE AE 447 COMBINE slan e a a E a E E a 448
6. Warning i i The NIST EPA NIH MS Library NIST 02 and AMDIS setup is about to be launched After it completes it will leave important information From this installation covered and this install will not complete Please make certain that message is uncovered by closing or mimizing the other windows NOTE Be sure to close open windows on the desktop and watch for this prompt at the end of the installation 6 Click OK The next screen prompts to continue the install process Installation files are copied on the hard drive 710 Appendix B TurboMass Software Installation 4 NIST EPA NIH MS Library NIST 02 and AMDIS Setup NIST EPA NIA MS Library NIST 02 and A MDIS This setup program will install on your computer NIST EPA NIH Mass Special Lec NIST 02 and NIST MS Search Program ecu GC MS Analysis Program Automated Mass Spectra in Deconvolution end centcaton system AMBIS 1 HF SUD See eae AS Se ALY cs Dos before running this Setup progr Click Cancel to quit Setup and then close any programs you have futring Gick Nest to continue with the Setup program 7 Click Next gt to begin The NIST install splash screen is displayed and the install process begins The next screen prompts to finish the installation Information x The NIST EPA NIH MS Library NIST 02 and AMDIS setup has been launched After that installation has completed please click on the button below to complete
7. 10 Inthe LINK Configuration dialog click the Configure button next to the port selection The GC Configuration dialog is displayed GC Configuration PSIG gt Capilar mode 7 PPEB I Capilar mode B 722 Appendix B TurboMass Software Installation 11 To rename the GC to something other than its default name inst1 enter the new name in the Name text box This name will appear under the Name field in the Configuration Editor window 12 Click OK A check mark in the LINK Configuration dialog indicates that the GC has been configured LINK Configuration x Configuring LINK at port COM2 Instrument name gt LINK Ports and Instruments Instrument module pe Cl 500 GC with A I larus with Autosampler r Port A nst auTosts pa Eto ee etector mot 2 z Autosampler module ero ee Restart Reset lt Back Finish Cancel Configure the selected instrument 13 Click Finish When you first configure the GC the following message may display Configuration Editor xi 9 Check communication For Instrument insti at Port db2mkk11 COM 2 LINK Port 4 Lf Note it must be connected to the LINK box and turned on Tf you do not connect to the GC and check the Firmware revision the Modify Active Method In Run feature will be disabled 14 Ifthe GC is not turned on turn it on now and then click Yes OR If the GC is connected and turned on click Yes 72
8. Cancel 2 Select Static Calibration Scanning Calibration or Scan Speed Compensation as appropriate Usually all checkboxes should be selected 3 Optionally select Acquire amp Verify to acquire a calibrated mass spectrum of the reference compound 4 To automatically print a report of the calibration when the calibration is complete select Print Report If you choose not to print the report at this stage you can always print it from the calibration curve display later The report contains pictures of the calibration curves produced along with calibration statistics such as standard deviation 121 TurboMass Software User s Guide Setting Data Acquisition Parameters 1 Click Acquisition Parameters in the Automatic Calibration dialog to open the Calibration Acquisition Setup dialog Calibration Acquisition Setup x m Acquisition Parameters Scan From 2 amu Cancel Scan Io 620 amu Default Run Duration 0 32 mins Daat Data Type Centroid m Scan Parameters Static Span fao Static Dwell fo 0 sec Slow Scan Time B Fast Scan Time 0 2 sec Inter Scan Delay 0 05 sec 2 Specify the acquisition parameters Scan From and Specify the scan range for each calibration type Scan To Run Duration Specifies the data acquisition time for each calibration data file It is usually calculated by the software Data Type Specifies whether data will be acquired in centroid continuum or M
9. cccccsccssecscesseeseeeeeeeeseeeseeesceeseecaecnseenseenseenas 596 Report Generation Window Menu cccccsccsseescecsteestecsecneeneenseens 597 Contents S mple List Wc ieaiai ainn ira aa aa enni 604 Form 1 Tab Organics Analysis Data Sheet 0 cceeseseeeeeeeeeeeees 606 Form 1 TIC Tab Tentatively Identified Compounds cece 609 Form 2 Tab SMC Surrogate Compound Recovery ccceceeeeees 616 Form 3 Tab Matrix Spike Matrix Duplicate Recovery c6 618 Form 4 Tab Method Blank Summary cccccccsseesteesteeeteeeteeeaeens 620 Form 5 Tab Instrument Performance Check cceescesceeseerteentees 622 Form 6 Tab Initial Calibration Data cccccescesceeeeeeeeeeeeeessees 624 Form 7 Tab Continuing Calibration Check eceeceeseeeeeeeereeeees 627 Reassign Sample Type cccccccssccssecsteceseceseceseceeeceeeeeeseesseeeeeeeeeaaees 628 Form 8 Tab Internal Standard Area and RT Summary 0 629 Reassign Sample Type ricrea ei i a k 629 Error Messages and Warnings ccccccssssscessceeeeeseeeeeeeeceeessecseenseeeseenes 631 Error M ss SES onneen eani a eaa A AOA a 631 Warming Sencer roekan esnie a a AR eE i RAR E A F 633 Form Specific Checks cccccccssccesscesecesecseeeseeeseeeeeseeeseeeseeeseecsaeenseenseenseeaas 634 Report Method Usage s ceiccciscsevevccdivd veckecavecces ieee couse ti danseeteuat R a a e 640 Submitter Task Data Wind
10. 3 Use the mouse to move the outline of the image to the required position You can paste the contents of the Clipboard whether a bitmap a metafile or text into a spectrum window If in textual or metafile form you can rescale data using the mouse and there will be no distortion of the image However if you paste a bitmap rescaling is done by stretching the image which will cause some distortion To avoid this scale the image to the required size before you copy it to the Clipboard Removing pasted input from the display 1 Left click to select the item you want to remove 2 Press DELETE 457 TurboMass Software User s Guide 458 Manipulating Library Spectra Displaying a library entry l Select Get Spectrum from the Spectrum Edit Library menu If required select a new library by clicking File Enter an entry number in the Entry field You can add the library spectrum to the current spectrum window replace the current spectrum or be placed the library spectrum in a new window Click Add Replace or New as appropriate Click OK Once you have displayed a spectrum from a library you can browse the rest of the library by clicking EJ Appending the current spectrum to the current library 1 2 Select Append from the Spectrum Edit Library menu Click OK Adding the current spectrum to a new library is Select Append from the Spectrum Edit Library menu Click File Enter th
11. Ax Is Vt 1000 Dr _ Xs Vt 1000 Dr where Xs is TurboMass cot Area of the characteristic ion EICP for the compound to be measured from integration results Area of the characteristic ion EICP for the specific internal standard from integration results Amount of internal standard added in nanograms ng from appropriate Concentration column of the sample list as defined in the Quantify Method Average relative response factor from the heated purge of the calibration standard from calibration file Total volume of the methanol extract in milliliters mL Soil Extract Volume from sample list Volume of the aliquot of the sample methanol extract i e sample extract not including the methanol added to equal 100 uL in microliters uL added to reagent water for purging Soil Aliquot Volume from sample list Weight of soil sediment extracted in grams g Sample Wt from sample list Adjustment for dry weight basis 100 moisture 100 calculated from Moisture value in sample list Dilution factor The dilution factor for analysis of soil sediment samples for volatiles by the medium level method is defined as uL most conc extract used to make dilution uL clean solvent uL most conc extract used to make dilution from sample list Dilution Factor Dilution Factor from sample list 4 Xs is the target concentration amount This is calcu
12. Peak Detect 401 TurboMass Software User s Guide 402 The Join valleys parameter affects how baselines for partially resolved peaks are drawn The larger the value of this parameter the more peak baselines will be drawn up to the valleys between unresolved peaks The default value for this parameter is 30 and the normal operating range is 5 75 E File Edt Display Process Window Help 16 x S ale weloe elau Olaa Lal lelez da and mda TDASO922 SIR of 2 Channels Cl B 397 20 mg 2 21e6 Height E File Edt Display Process Window Help 16 x S ale weloe eau Alaaf Lal lelez da and mda TDAS0922 SIR of 2 Channels CH a 397 20 100 2 21e6 Height Reduce peak tailing and Raise baseline position the baseline end points In the example the pronounced tail on the peak at 5 42 min is reduced by decreasing the value of the reduce peak tailing parameter from 150 to 50 The default value for this parameter is 50 and the normal operating range is between 25 and 300 Chromatogram Chromatogram TDASO922 lolx E Fie Edt Display Process Window Help le x ale selaa elaj olala Aa lelle da and mda TDASO922 SIR of 2 Channels Cl 478 _ 397 20 4646324 4 73e6 Height 100 H 0 Time 5 38 5 40 542 5 44 5 46 5 48 5 50 S a E Fie Edit Display Process Window Help le x ala welle elaj Saef wal elele da and mda TDAS0922 SIR of 2 Channels C
13. Sorts the list in order of ascending Mass Deletes the list of Masses Left click a mass in the list and then click Delete to delete a single Mass Sample List 9 Sample List Top Level Menu The top level desktop includes menus and toolbar buttons that allow you to create and modify Sample Lists aii oe CeCe rT ECL Ea ee ee en ee ee ee 207 TurboMass Software User s Guide The TurboMass Menu Toolbar File Save As software Stop an acquisition View Spectrum View Spectrum Strip Functions 208 Sample List Tools MW Calculator Invoke Molecular Weight Calculator Help About TurboMass Display program information version number and copyright Edit Cut Cut the selection and put it on the clipboard Edit Copy Copy the selection and put it on the clipboard Paste the contents of the clipboard Samples Add Add samples to the Sample List Samples Insert Insert samples into the Sample List Samples Delete Delete samples from the Sample List Samples Field Invoke the Field Properties dialog Properties Samples Field Invoke the Customize Field Display Customize Display dialog Samples Field Remove Remove a field from the display Column Samples Fill Down Fill down Samples Field Align Align text to the left in the current Left column Samples Field Align Align text to the center of the current Center column 209 TurboMass Sof
14. The parameters required for the current analysis VOA SV or QA QC and current matrix water soil are displayed The controls are grouped in a way to allow efficient entry of sample specific data It also provides the ability to propagate changes made to one row to subsequent rows a command to update vial numbers and a command to update sample IDs including automatic incrementing of a numeric value The parameters are e Sample List e Analysis e Matrix e Concentration Level When you select an existing sample list the controls in the Analysis Matrix and Levels section are disabled and use the values in the last row of that sample list to indicate the nature of the sample list assumes all rows use same Analysis Matrix and Level settings If there are no entries for those columns for example if it was created prior to version 5 1 then the Analysis option will be set to QA QC and hence the other options will show no selection Sample List Existing sample list New sample list Analysis Volatiles Semi volatiles QA QC Sample List The Sample List section of the dialog provides you with the options of either selecting a new sample list or editing an existing sample list Select this radio button to edit an Existing sample list file When selected the lt sample list file name gt drop down list and Browse button are enabled All other controls in the dialog are be disabled i e Analysis Matrix and Lev
15. To insert multiple rows select the number of rows required and continue as for a single row Editing data in a cell Do one of the following to edit data in a cell 1 To select data for copying replacing data and other standard editing functions select the cell using the mouse or press SHIFT arrow key Sample List 2 To edit a single cell use the Cut Copy Paste and standard Windows editing commands in the usual manner or right click to display the following pop up menu Unde Cut Copy Paste Delete Select All Editing data in a column The following commands may be used to edit data in a column u Fill Down Select an area and click l or select Down from the Fill option from the Samples menu to fill the selected range with the first element in each column 237 TurboMass Software User s Guide Fill Series Select an area and click al or select Series from the Fill option from the Samples menu to fill the selected range with series data That is if the first cell in a column is viall the next will be vial2 vial3 and so on Insert Click or select Insert from the Samples menu to insert samples into the Sample List If a row has been selected a new row is inserted above the current one If more than one row is selected the same number of rows is inserted above the first selected row If a column has been selected the same number of rows as were originally in the column are inserted before the fi
16. Audit Log Viewer x Log View Time 13 29 08 Administrator Logon Logoff Successful log 13 29 17 Administrator Object Access Successful ob 13 29 22 Administrator Logon Logoff User logged ofl 14 09 48 Administrator Logon Logoff Successful log 14 10 27 Administrator Logon Logoff User logged ofl 14 10 29 Administrator Logon Logoff User logged ofl 14 11 19 Administrator Logon Logoff Successful log 14 35 44 Administrator Logon Logoff User logged ofl 14 36 00 Administrator Logon Logoff Successful log 14 36 18 Administrator Logon Logoff Successful log 14 37 06 Administrator Logon Logoff User logged ofl 14 37 32 Administrator Logon Logoff Successful log 14 37 58 Administrator Object Access Successful ob 14 38 05 Administrator Object Access Successful ob 14 38 25 Administrator Logon Logoff User logged ofl 14 39 37 Administrator Logon Logoff Successful log 14 41 30 Administrator Object Access Successful ob 14 41 37 Administrator Object Access Successful ob 14 41 46 Administrator Object Access Successful ob 07 Oct 1997 14 41 50 Administrator Object Access Successful ob gt gt The Audit Log Viewer displays the audit log that lists the date and time of each auditable event The Source column shows the type and a brief description of each event 2 Manage the audit log from the Audit Log Viewer dialog Log and View menus Log Clear All Events Select to completely
17. Matrix Spike e Ifa Spike Dup was located and its Sample ID ends with MSD look for the Spike sample with the same root Sample ID but ending with MS If this is not located look for the first Spike sample preceding the Spike Dup If one is not found look for the first Spike sample 635 TurboMass Software User s Guide 636 following the Spike Dup If no Spike can be located an error condition exists see below If a Spike Dup was located and its Sample ID did not end with MSD look for the first Spike sample preceding the Spike Dup If one is not found look for the first Spike sample following the Spike Dup If no Spike can be located an error condition exists see below If no Spike Dup was located look for the last Spike sample in the sample list If no Spike can be located an error condition exists see below Analyte If a Spike Dup was located and its Sample ID ends with MSD look for the Analyte sample with the Sample ID formed by removing the MSD i e same root no suffix If this is not located look for the first Analyte or Analyte Dup sample preceding the Spike Dup If one is not found look for the first Analyte or Analyte Dup sample following the Spike Dup If no Analyte or Analyte Dup can be located an error condition exists see below If a Spike Dup was located and its Sample ID did not end with MSD look for the first Analyte or Analyte Dup sample preceding the Spike Dup If one is not found look f
18. Save in E Acqudb 7 El c File name a 1110987654321 ipr a boo2 ipr a good ipr a 1234567891011 ipr a bounds ipr a heptacos ipr 1234567891011_2 ipr B centrold ipr rec ipr acqu ipr PS cold ipr test ipr Alripr a def ipr x tuneprm ipr autol ipr fa default ipr a TURBOMASS ipr Save as type Instrument Parameter Files ipr 7 Cancel H 89 TurboMass Software User s Guide 3 Click Save If the selected file already exists on disk you will be asked to confirm that you want to overwrite the existing information Click Yes to continue or No to enter a different file name NOTE Jfyou close the Tune page without saving any new settings the software will prompt you to save the file Restoring a Saved Set of Parameters l Click OR Select Open from the Tune File menu Open Tune File Look in E Acqudb z al cl E File name DEFAULT db Files of type Tune Parameters 7 Cancel 2 Select the tuning parameter set that you want to use either by entering its name or by selecting it from the displayed list 3 Click Open to open the Tune File dialog 90 Instrument Tuning Modifying the Peak Display The Tune peak display is modified using either the tune peak parameters or by using the mouse directly on the Tune Peak display EE TunePage c turbomass default pro acqudb default ipr
19. Window Choosing this option causes each subsequent trace to be added to those New Trace displayed in the current window Add Trace Getting Started Getting Help The TurboMass Help system contains detailed information on how to use TurboMass TurboMass Help can be accessed either from the TurboMass top level menu or from any of the TurboMass program windows If you enter Help from the TurboMass top level menu you will be given a general index of topics covering the whole of TurboMass If you enter TurboMass Help from one of program windows you will be given help on that particular topic For example if you select Help from Spectrum you will be given Help on Spectrum TurboMass Help also allows you to search for Help on a specific topic or keyword For more information on using Windows Help systems select Using Help from the Help menu on the TurboMass window This topic gives detailed instructions on how to use Windows Help systems The About Box The About TurboMass box gives you information about TurboMass including the version number 59 TurboMass Software User s Guide 60 TurboMass 3 Overview TurboMass Overview This chapter describes how to use the TurboMass data acquisition system It gives an overview of how to use TurboMass including mass spectrometer and GC setup method development data acquisition and data manipulation For specific information on how to perform your first run using you
20. specific Report Method is used EF Submitter Task Data Assign a report method to each form Submitter T ask Custom Compound List Report Methods Default CLP Like Default VOA_Tutorial VOA_Tutorial Project TUTORIAL_VOA PRO 650 Form Report Methods Description Volatile Organics Analysis Data Sheet VOA SVY Matrix VOA Both Report Method PKI1_VOA Semi volatile Organics Analysis Data Sheet Both PKIT_SV Volatile Organics Analysis Data Sheet Tentatively Identified Compounds Both PKIITIC_VOA Semivolatile Organics Analysis Data Sheet Tentatively Identified Compounds Both PKIITIC_SV Water Volatile System Monitoring Compound Recovery Water PKI2_VOA_water Soil Volatile System Monitoring Compound Recovery Soil PKI2_VOA_soil Water Semi volatile Surrogate Recovery Water PKI2_SV_water Soil Semi volatile Surrogate Recovery Soil PKI2_SV_soil Water Volatile Matrix Spike Matrix Spike Duplicate Recovery Water PKI3_VOA_Water Soil Volatile Matrix Spike Matrix Spike Duplicate Recovery Soil PKI3_VOA_Soil Water Semi volatile Matix Spike Matrix Spike Duplicate Recovery Click on the cell to activate the select report method butti Soil Semivolatile Matriz Spike Matrix Spike Duplicate Recovery Soil PKI3_SV_Soil Volatile Method Blank Summary Both PKI4_VOA Semi volatile Method Blank Summ
21. 1 Select the Detectors tab of the Instrument Control dialog Instrument Control x Autosampler Ovend nlets Carrie strument Timed Events Wetector NONE Detector B NONE Temp C Range fi Temp C Cl Range F z Time constant po z Adjust Doo Time constant o z Autozero M Gri Yalue fan Autozero M Gn Polarity Positive Negative Polarity Positive Filament Gn GF Shutdown Filament Gh r Gases m Gases None foo muy int None po Toric None bo mAn None po mmn None Doo min None m n INT en Attenuation oa Attenuation Offset On Offset 50 nv 2 Inthe Temp field enter a temperature value for the detector 3 Select a sensitivity setting for the detector from the Range drop down list This value is the gain level of the detector output The values depend on the instrument and detector type For example if you are using a Clarus with an FID the lower the Range setting the greater the detector sensitivity For a TCD the lower the Range setting the lower the detector sensitivity 170 GC Control 5 Select a Time constant This value sets the detector filter width in milliseconds which smoothes out the detector signal Higher values improve the signal to noise ratio but attenuate narrow peaks 6 Ifyou are using an FPD detector set the PMT This value is the percentage of the maximum photo multiplier voltage and sensitivit
22. 467 TurboMass Software User s Guide The following illustration shows part of a single scan from the raw and enhanced data files The background noise in the enhanced spectrum has been greatly reduced THOIR 384 32 667 10 0 THO 384 32 667 In the following illustration the lower trace is the raw data file the upper trace shows the same data file after it has been processed using Enhance to reduce background noise The original data file size of 41 2 MB has been reduced to 1 4 MB in the enhanced data file Scan ES TIC 1 23e8 Area 26 22 30 54 Creating a Clustered Data File The following describes how to create a clustered data file and provides examples 468 Strip and Combine Functions 1 Select Cluster in the Strip Datafile dialog 2 To change Input File or to select a subrange click Input Select input file and function using by choosing File to open a browser dialog Set the mass and retention time ranges if required 3 Ifthe default Output file name is not correct click Output and enter the required name 4 Select Cluster Datafile Options from the Strip Options menu to set the Cluster options 5 Click Process to start processing the data file The status bar at the bottom of the Strip dialog displays the progress of the current process The illustration shows the spectrum of a mixture of chlorinated and non chlorinated compounds The lower trace is the raw data file the u
23. Cascade windows Stack windows 371 TurboMass Software User s Guide 372 Adding buttons to the toolbar l 5 In the Available Buttons list select the button you want to add In the Toolbar Buttons list select the toolbar button before which you want to insert the new button Click Add to add the new button Steps 1 to 3 can be repeated as often as required Separators can be inserted between toolbar buttons to divide them into logical groups To add a separator repeat steps 1 to 3 selecting Separator in the Available Buttons list Click Close to exit and save changes Removing buttons from the toolbar 3 In the Toolbar Buttons list select the button you want to remove Click Remove to remove the button Steps 1 and 2 can be repeated as often as required Click Close to exit and save changes Changing the order in which toolbar buttons are displayed 3 In the Toolbar Buttons list select the button you want to move Click Move Up or Move Down to move the toolbar button Steps 1 and 2 can be repeated as often as required Click Close to exit and save changes Resetting the toolbar to default settings l Click Reset Chromatogram 2 Click Close to exit and save changes Displaying hiding the toolbar in the Chromatogram display gt Select Toolbar from the Chromatogram Display menu to display hide the toolbar in the display This command is a toggle A check mark will appear next
24. Communiqu Report Creator File Edt View Format Actions Tools Help MACAE TECNA ETETE EEN T y f Tools A g Qualitative Report 1 3 Header 35 Lab Name S TEXT4 TEXTS Bums TEXT3 ho Text2 2 Standard Footer 1 E TEXTI 5 3 Page Type 1 Eg Chromatogram Plot BL OBJECTFRAMI i Chromatogy iL 0 Pinea PUDSETIME Repor Pae pipageratg CHROMATOGRAM PLOT GRAPH HEADER BL TABLET TEXTE ooo Sees TEXT pe ee seo ee tonic ene eee 5 Abc TEXTS TEXT10 TEXT11 TEXTS 9 Peak nr L 3 Retention Timet 3 HeightDATA 9 Area DATA4S D Area DATAM D Nom ZDATA jameT ere 1 elven Beep min Tancer Tempe iB Met Data Objects Custom Obj Communiqu Reporting Modifying the Template To modify the template follow this procedure 1 Adda graphic by clicking Graphic in the Layout Tools toolbox A dialog similar to the following appears ii aK Look in a Precisely Logos z ace B gt intranet ico E he Precisely logo black bmp History Re Precisely logo greyscale bmp 74 he Precisely logo linear bmp he Precisely logo bmp Desktop Eu precisely ico LN Untitled ico My Documents My Computer 7 My Network P I Open as read only 2 Browse to the directory where the graphic is stored and select it by clicking on it 3 Move your cursor to the desi
25. Controlling the appearance of the Quantify Chromatogram display l To display a particular peak list entry in the Chromatogram window select the desired entry in the Summary window or the Peak List window entry To display a particular calibration standard peak select the desired calibration point in the Calibration Curve window This allows manual adjustment of integration results To control the appearance of the Chromatogram window select Chromatogram from the Quantify Display menu to open the Quantify Chromatogram Display dialog 297 TurboMass Software User s Guide 298 4 Edit your parameters Quantify Chromatogram Display x I Show Intemal Reference I Add to existing chromatograms Display Range integration x Cancel Show Internal Reference Add to existing chromatograms Show Edit Quantify Peak Dialog Display Range If selected the internal reference peak if specified will be shown with the current peak If selected each new chromatogram will be added to those already displayed If selected the dialog enables you to edit the Quantify Peak Can be set to Integration to use the integration range Keep Current to keep range currently displayed or Acquisition to use the acquisition range Quantify The Summary Window The Quantify Summary window gives a summary of the results of quantification The results in the Summary window can either be listed by compound or by samp
26. Eull Name Warren G Harding Description 2nd shift lab manager Password fe Confirm Password een Account Policies I User Cannot Change Password I Account Disabled Currently Assigned Rights Administer user accounts and groups Data Browser file delete Enter fonts and colors editor Customize TurboMass system globals Crea 4 Ifthe Password fields are available enter and confirm the new password 5 Ifthe Password fields are unavailable administrative privileges are required to change the password for the selected account Security Manager Toolbar The toolbar displayed at the top of the Security Manager dialog contains the tool buttons listed below The tool button functions are duplicated in the Security menus E Creates a new user e Creates a new group Copies the currently selected group or user account Ed Deletes the currently selected group or user account Edits the currently selected group account or user properties Eil Reviews the user account policy options EJ Reviews the group access rights E Reviews the audit policy options Setting up an Account Policy Appendix A TurboMass Security Before you create a user account or group you must specify an account policy to establish the password restrictions and the policy for individual user settings You can also enable or disable the TurboMass Security application 1 Select Account from the Policies menu Or Click to di
27. NOTE During the sample list processing associated with report generation processing from within the Quantify window View Results will be inaccessible to a user This is to prevent possible data file conflicts Context Menu Sample List Tab The following pop up menu appears when you right click on the Sample List tab i e the label area you click on to select the tab It allows you to quickly select and deselect Forms for printing v Form 1 Form 1 TIC Form 2 Form 3 Form 4 Form 5 Form 6 Form 7 Form 8 Form tab Remove This Form Removes the tab associated with the clicked on label from the Report Generation Window The associated Form will not be printed Report Generation Window Menu The following reporting controls are available from the Report Generation Window Menu Item Sample List Command Append Sample List Save As Exit Description Opens a data browser allowing the selection of a sample list file from the current Project only The selected sample list will be appended to the list already displayed in the window This command is only enabled when the Sample List tab is selected Opens a Save As dialog allowing you to enter a file name within the current Project Exits the Report Generation window 597 TurboMass Software User s Guide Menu Command Item Forms Print Assign Tentatively Identified Compounds Assign Header Sample Assign Analyte Assign Matrix
28. Run Duration mins 0 5 Scan Time s 0 2 Inter Scan Time s 0 05 Origin Multiple Samples The TurboMass top level window contains a Sample List Editor for defining multiple one or more samples that may be used together to perform a quantitative analysis The list of samples is set up using the spreadsheet style editor which can be tailored to suit different requirements 351 TurboMass Software User s Guide Starting a multi sample acquisition 1 Set up a Sample List as described on page 205 2 Select Start from the Sample List Run menu OR Click gt to display the Start Sample List Run dialog 3 Select the Acquire Sample Data checkbox Select Auto Process Samples to automatically process data with macros once it has been acquired Select Auto Quantify Samples to automatically perform quantification at the end of the sample list 4 Enter values in the Run From Sample and To Sample fields The default is all samples in the list 5 Click OK x Project C TurboMass TUTORIALQUANT PRO A IV Auto Quantify Samples bp I Qualitative Calculations Ea IV Generate Communiqu Reports J Preview Reports r Run Erom Sample f1 IoSample 3 Quantify Qualify and Generate Reports C After Each Run At End of Sample List r Process I Pre Run I Post Run Cancel 6 Repeat steps 1 to 5 as required Sample Lists will be added to a queue and will
29. Select Forms Dialog The Select Forms dialog provides you with the interface to select reports to be printed These reports are based upon templates or Forms defined by the US EPA ie Select Forms Sample List 8260_Tutorial spl Browse Select Forms to be generated V Form 1 Organics Analysis Data Sheet V Form 1 Tentatively Identified Compounds V Form 2 SMC Surrogate Compound Recovery V Form 3 Matrix Spike Matrix Spike Duplicate Recovery V Form 4 Method Blank Summary MV Form 5 Instrument Performance Check IV Form 6 Initial Calibration Data V Form 7 Continuing Calibration Check V Form 8 Internal Standard Area and RT Summary Help Cancel The exact format of the report you generate depends upon several selections you make within the Sample List or Sample List Wizard environments These include the following Sample Type Volatiles VOA Semivolatiles SV or QA QC Matrix Water or Soil Concentration SV only PerkinElmer provides two sets of reports one based on the US EPA OLM04 2 specification CLP Like and the other the default a format enhanced with 591 TurboMass Software User s Guide additional laboratory information and with a more attractive and convenient format PKI format The reports may optionally be defined by a configuration table set up by the TurboMass administrator This table maps the specified report to a Communiqu reporting template The table ap
30. must have an intensity greater than the specified Intensity Threshold Strip and Combine Functions Setting the Enhance processing parameters 1 Select Enhance Datafile Options from the Strip Options menu Window Ence _ Em Defaut fo Minimum Abundance feo Mass data points Scans i Intensity Threshold 2 Set the following parameters as required Mass data points Scans t Intensity Threshold Minimum Abundance Determines how many samples to look backwards and forwards along the mass scale The Mass parameter should not exceed half the number of samples that make up a peak Determines how many scans to look backwards and forwards respectively It should not exceed half the number of scans a chromatogram peak is present Defines an absolute intensity that a data point must exceed to be regarded as being significant For spectra with a high baseline this parameter will need adjusting so that its value is approximately equal to the intensity at the top of the noise The larger this value the more likely that information will be discarded as being noise Determines the minimum percentage of neighboring samples examined whose intensity must be above the specified threshold for the current sample not to be rejected as noise The larger this value the more likely that a sample will be discarded 3 To set the parameters to their default values
31. p Cancel jf posie Default T Use Second Mass Difference Centroid Second Mass Diff p oo amu Second Ratio p oo hc oe ee a Mass Tolerance 0 05 amu Ratio Tolerance fao oo Time Window 0 00 min Threshold 5 00 I Use Intensity Ratios Strip and Combine Functions 2 Set the following parameters as required First Mass Diff and First Ratio Second Mass Diff and Second Ratio Mass Tolerance Ratio Tolerance Time Window Determines the requested separation and intensity ratio of the first pair of peaks The intensity ratio is calculated as intensity of low mass peak intensity of high mass peak The requested intensity ratio may be less than 1 Intensity ratio comparison may be deselected using Use Intensity Ratios if not selected then no ratio comparison is attempted and peaks are selected purely on the basis of mass difference Determines the mass difference between and intensity ratio of the first and third peaks in the triplet note not the first and second The second mass difference can be calculated by selecting Use Second Mass Diff if not selected then examination is restricted to pairs of peaks only not triples Specifies a window for each of the maximum of two specified mass differences Pairs or triples of peaks are detected if the corresponding peak s lay at the specified mass difference the specified mass tolerance Specifies the maximum mismatch betw
32. r Project C TurboMass QUANTIFY PRO 353 TurboMass Software User s Guide The Quantify Samples dialog allows you to automatically process data files once they have been acquired To integrate samples calibrate standards quantify samples and print quantification reports select the appropriate checkboxes For more information on automated sample list analysis refer to Quantify on page 247 Integrate Samples Calibrate Standards Quantify Samples Print Quantify Reports Project Quantify From Sample n To Sample n 354 Integrates all the sample data files named in the Sample List Uses integration results to form Quantify calibration curves Uses integration results and Quantify calibration curves to calculate compound concentrations Prints the results of integration and quantification Displays the project into which data will be acquired If you want to change the project into which data will be acquired you can cancel the acquisition and create a new project by selecting Project Wizard or open an existing one by selecting Open Project from the Sample List File menu Note that this means that data may only be processed from one Project at a time Make sure that all data files you might want to process at the same time are acquired to the same Project Sets the range of samples in the Sample List that will be analyzed Data Acquisition Monitoring an Acquisition Acquisition sta
33. 50 When a new version of TurboMass is opened all files which are no longer compatible with the new version are stored in subfolders called Old For example old method files will be in the Old subfolder of the MethDB folder These files can still be used with older versions of TurboMass but should not be used with the new version Data File Structure Data acquired from the mass spectrometer are saved into data files on the computer s hard disk These data files may contain more than one acquisition function and may also contain processed data derived from the original raw data for example refined spectra All files are acquired to the data directory of the current project For example if the file name is specified as test2 then the data files are stored in the directory c TurboMass currentproject data test2 If the data file contains 2 acquisition functions and 2 sets of processed data then the directory listing will be as follows _Header txt Data file header information _Funcs inf Information on MS functions acquired _history inf Information on how data has been processed _expment inf Experimental record information _Func001 dat Data file for first function one for each function _Func001 idx Data file index for first function _Func002 dat Data file for second function _Func002 idx Data file index for second function _inlet inf Information on GC method _proc001 dat First processed data file one for each process _proc001 id
34. 546 Defining User Elements You can define a user element by specifying its name symbol average and monoisotopic masses l N In the Molecular Mass Calculator dialog click User elements to display the User definable elements dialog D Deuterium OK Name Deuterium Cancel Avg Mass jaca Delete Mono Mass jns Update Enter the parameters and click Add to add the group to the list You can add up to 10 elements isotopes or molecules to the list To edit a particular element or group click Update To remove a selected group click Delete Click OK to save the list and return to the Molecular Mass Calculator dialog Click Close to exit the Molecular Mass Calculator Report Method Editor 1 9 NOTE Report Method Editor About the Report Method Editor The Report Method Editor is an extension to the TurboMass software It enables you to specify a collection of report definitions Communiqu report templates and related parameters that are printed sequentially The Report Method is a dataset that you can specify in each row of the Sample List It defines the reports to be generated following the analysis data or at the end of the Sample List The Report Method will consist of a list of report templates and associated parameters namely 1 When the report will be generated for all runs for runs of a specific type for only the last run in the sample list 2 The output destination s of the report print s
35. C New window Next to File is the name of the currently selected TurboMass raw data file Select from the drop down list the GC detector data channel A or B to display Enter an Offset positive or negative to be applied to the GC detector chromatogram display to help align it with the mass spectrometer chromatogram For example a positive offset of 0 15 minutes would cause the plot to start at 0 15 minutes on the time axis If the X axis display is changed to scans the previous offset in minutes will continue to be used for the GC detector trace Select one of the following NOTE Chromatogram e Add trace A radio button that indicates the new chromatogram will be added to the current window in stacked or overlay mode e Replace trace A radio button that indicates the new chromatogram will replace the active chromatogram in the current window e New window A radio button that indicates the new chromatogram will be displayed in a new window If necessary select anew TurboMass raw file by clicking the File button If a new file is selected the File name displayed will be updated and the Channel control will also be updated appropriately Aligning GC Detector Traces Data from the GC detector may be slightly out of phase with data from the mass spectrometer as there may be a time lag between analyte arrival You can specify an offset to the time axis of each GC trace to allow you to manually align
36. Peak lists Sample lists Quantify methods Quantify calibration curves Tuning files Scanning methods Instrument calibration files Inlet methods Projects are created and selected from the TurboMass top level File menu See Getting Started on page 23 for instructions on how to create or open a Project Creating a Quantify Method A Quantify Method must be created before Integration or Quantification can be performed The Quantify method describes how a data file is processed to produce calibration curves and quantitative information Details must be entered into the method for each of the compounds being used in the analysis The Quantify Method specifies information for performing the following tasks Integration of a chromatogram trace to obtain peak information Location of the chromatogram peak relating to a specific compound from the list of detected peaks Calculation of a response factor for the located peak Formation of a Quantify calibration curve Environmental calculations 257 TurboMass Software User s Guide Quantify Method Editor The Quantify Method Editor creates new methods and modifies existing ones A method selected from within the Method Editor will become the current system method file and is used when performing Quantify operations Changes made to the method are not made permanent until they have been saved to disk Consequently the method must be saved before it can be used to perfor
37. SUDMACE ste senaera o EE A dees A e OS 450 Smooth eer sabe ere e r secede aE EE r E Er fee EE N EA 451 Center irrar Angecgcant eae btanreed dee itee sneer aed ain ee iti eee 453 Copying to and from the Windows Clipboard ccccesccesseesseeereeereeeneeeees 456 Manipulating Library Spectra ccccccesccesecesscessceeeceeeeeeeeeeseeeseeeeeneeeaeenes 458 Strip and Combine Fumctions scccssccsccscssssscsssscssccsssccesssseesseseesees 461 Stap PUNCH ONS 555 sid evel ors a a a a eaae vat cegss ede deenenwacersgceweens 463 Creating a Subtracted Data File ccecccessceesceeseeeecstecsteceteenteeneenes 464 Creating an Enhanced Data File cceecceeceeseeeseeeeeeeeeteeeseeeteenseeees 467 Creating a Clustered Data File cccccceceesceeceeeeeeeeeeeeneeesseeteeneenes 468 Creating a CODA Data File cece cecccecseeseeeteeeneeeeeeeeesaeeneeneenseenes 469 Selecting a Data File to Process ccccscecsseesseeeteeeeceeceeeeeeeceeeeeeeeenes 470 Selecting a Data File and Subrange to Process 471 Contents Selecting a Background Data File cccccecsccessceseceseeeeeeeeeeeeeeeeseennes 472 Selecting an Output Data File ccceccseecseesteceteceteceteceeeeeeeesseeeees 472 Setting Enhance Datafile Options cccceescceseceseceseeeeeeeeeeeeeeesneeenes 474 Setting Cluster Datafile Options cccccesccescessceseeeeeeeeeeeeeesteeseeeeees 476 Setting Cluster Centroid Options ccccccccessceseceseces
38. See Appendix E LIMS Import File Example The imported file contains one line per sample list row and each line will consist of some or all of the functional parameters that can be defined in a row The text file 225 TurboMass Software User s Guide 226 NOTE NOTE NOTE contains a definition of which fields columns the text file is defining for each sample list row The names used in this list will be the database field names for the columns Text items that contain the defined separator character e g commas must be enclosed in quotes If quotes are to be included in a string enclosed in quotes they must appear twice e g This string contains not only a comma but also quotes within it The import operation appends the sample rows defined in the text file to the currently displayed sample list However if the current sample list is blank following a File New command the imported sample list will overwrite the blank line and append subsequent lines For the purpose of determining a blank sample list the fact that the File Name cell is empty will be sufficient To import a Sample List from LIMS The key thing to remember is that each Sample List file must have two sections The Variable Parameter List and the Variable Parameter Data The Number of Parameters in the Variable Parameter List must equal the number of values in the Data string For example if the NumberOfParameter
39. Spike Matrix Spike Duplicate Recovery Environmental Reporting Selecting this check box indicates that Form 1 Tentatively Identified Compound TIC report is to be generated for each applicable sample in the sample list Form 1 TIC shows library search results for the largest typically 10 to 30 non target peaks in the Each is assigned an estimated concentration based upon its response compared to the Total Ion Current of the nearest internal standard compound TurboMass qualitative processing prior to entering the Select Reports window will initially generate a list of several potential hits from the NIST library search You must choose one of these hits for each unidentified peak enter an alternative text e g long chain hydrocarbon or delete the TIC peak from the report Until you have performed this task the qualitative results will be marked in the qualitative data file as Pending The data file be marked Complete only after you have reviewed the data for each peak and accepted the default compound identification or selected a different one Form 2 reports the recoveries of the specific analytes defined as System Monitoring Compounds SMC also called surrogates It flags any compound whose recovery is outside of Quantify Method specified limits The sample to be used as the source of the header information for the report is indicated by the data source item Header Sample Index This defaults to the first c
40. The chromatograms in each chromatogram window share a common time axis To display chromatograms on different time axes you must put them in separate windows Chromatogram The Chromatogram Toolbar The toolbar is displayed at the top of the chromatogram window and allows you to perform some common operations by clicking the appropriate toolbar button The default Chromatogram toolbar contains the buttons listed below It is also possible to customize the toolbar and add additional buttons for other Chromatogram operations Ee Opens a data file Prints the current window in portrait format S Prints the current window in landscape format Sends a picture of current window to the Clipboard Copies a list of points in the chromatogram to the Clipboard Ba Copies a list of detected peaks to the Clipboard Pastes the contents of the Clipboard onto the display Selects a mass chromatogram a Performs peak integration Combines spectra scans across a chromatogram peak Compares BFB and DFTPP spectra to US EPA method criteria EN Performs automatic library searches 369 TurboMass Software User s Guide 370 Select to process all traces in the current window Writes text onto a chromatogram E Toggle to display each subsequent chromatogram or chromatogram process in a new window or to add to the current one E Click to cause each subsequent chromatogram or chromatogram process to E is unavailable whe
41. and hence Communiqu templates to be used in generating the EPA Forms for an existing Submitter Task 1 Choose Submitter Task Data from the Environmental Configuration submenu under the Tools menu in the Sample List window Select the appropriate Task for the Submitter Select the Report Methods tab Review the table displaying Forms to 8 and their variants together with the associated report method 651 TurboMass Software User s Guide 5 Where necessary select the appropriate report method to be associated with each Form When the mapping of Forms to report methods is correct choose the File Save command 652 Environmental Reporting Custom Compounds Tab It is possible to define a subset of the compound list from a Quantify Method and associate it with a Submitter and or Task name one list per Task These subsets can be used for three purposes 1 During quantitative processing to ensure only the specified compounds are reported and are identified as target compounds for qualitative processing 2 During qualitative processing to eliminate from the search for Tentatively Identified Compounds only those peaks that are identified as targets for that particularly Task The Custom Compound Lists also enable you to define a reporting limit for each compound i e set the J flag if the compound is between the Method Detection Limit and the Reporting Limit or the U flag if it is below both on t
42. but has not yet been physically removed from the library file Edit 4 Select gt Enty No 1of3 Library Name VOAs nme ooon Soe cas 6766 3 Formula C Molat fue Restore Entry Test Specumfomstandad voas OSOS Vawel 00 vaez 0 00 s i DELETED 521 TurboMass Software User s Guide 522 Using the Library Locator The Library Locator can be used to look through a library Filters can be set up and searches performed to select certain classes of compounds Locating one or more library entries 1 Select Locate from the Library Process menu The Locator dialog is displayed 4 Select gt Enty No 5328 of 62235 Library Name NIST pz R Name PIPERIDINE 1 NITRO CAS 7119 94 0 Formula C5H1002N2 Molwt 130 Text Value 1 Value 2 Flags Fites The Library Locator dialog contains the following information about a library entry Library Name Entry No Compound Name CAS Number Formula Molecular Weight Mol Wt Spectrum and Structure User Libraries may also contain Values 1 and 2 and User Flags The Locator dialog can be used in two different ways to select a particular entry for examination or to set filter parameters that control the entries displayed by the Locate process 2 Search the library Manually Use the scroll arrows to page through the library entries one at a time or click Select enter the desired Entry No and click Update OR Library Using filters Click
43. called the Bayesian method requires two parameters This method characterizes each mass channel as a set of up to its first four moments The first moment represents peak position the second peak width and the third asymmetry The program can be restricted to use less than four moments by reducing the Max no of moments parameter Reducing this value will decrease the run time of the process It is also possible to reduce the number of mass peaks used for comparison This value is represented by the Max no of masses parameter Decreasing this parameter will also result in reduced run time The Bayesian method is based on a rigorous probabilistic analysis The output value loosely represents the natural logarithm of the probability that the peak is pure Therefore to calculate the probability that a peak with purity value x is pure evaluate exp x This implies that the maximum score 100 probability pure is 0 409 TurboMass Software User s Guide 410 Unleaded gasoline Bayesian Method Simple Method 3 33e6 88 99 Calculating the peak purity index for a Total lon Chromatogram 1 Display the chromatogram range of interest in a chromatogram window 2 Integrate the chromatogram remembering to disable smoothing 3 Select Purity from the Chromatogram Process menu to open the Peak Purity dialog 4 Select the purity method either Simple or Bayesian For the Bayesian method opt
44. click Default 475 TurboMass Software User s Guide 476 Setting Cluster Datafile Options Cluster operates on both centroid and continuum data For continuum data a special fast centroid process is used See Setting Cluster Centroid Options on page 478 The centroid process works by examining each pair or triple of peaks in each spectrum to determine if they are separated by the correct mass difference s and if their intensity ratios lie in the correct range s If Time Window is set to a value other than zero then neighboring scans within that time window are examined For example using the values in the Cluster Analysis Options dialog mass difference 1 22 0 Da mass difference 2 33 0 Da both intensity ratios 1 0 mass tolerance 0 5 Da ratio tolerance 30 time window 0 00 min threshold 0 01 Triplets will be detected with the mass difference between the first two peaks being 21 5 22 5 Da and between the first and third peaks 31 5 32 5 Da The intensity ratios of the peaks must lie in the range 0 7 to 1 3 low mass peak high mass peak and the peaks must lie in the same scan The peaks must be more intense than 0 01 times the most intense peak in the function Setting Cluster processing parameters 1 Select Cluster Datafile Options from the Strip Options menu to open the Cluster Analysis Options dialog Cluster Analysis Options Mass 1 z First Mass Diff 1 00 amu First Ratio 1 00 p E
45. fields click in the field and then enter a value The Temperature and Hold fields are disabled until you set the Rate You can also adjust the Temperature and Hold values by dragging the corresponding points on the curve to the desired position 1 Select the Oven Inlets tab of the Instrument Control dialog GC Control Instrument Control x Autosampler Oven Inlets Carrier Detectors Instrument Timed Events r Program time min Oven 2000 440 390 Inj A PSSI 20 00 220 IME NONE man 110 Dataendtime 20 00 0 0 0 5 0 100 150 200 250 300 r Cryo Coolant of x Cut in temp C 60 Timeout min 999 Heated zone setpoints C r Oven Injector amp On Aurian 00 Max temp C 350 Injector B fi Equil time min 2 0 From the available program tabs beneath the table select the tab for the temperature program that you want to edit The curve for the program that you select appears as a solid line The curves for all other programs appear as dashed lines In the Initial Temp field of the table set the temperature for the start of the run In the Initial Hold field enter the amount of time that you want to hold the initial temperature To hold the temperature until the end of the oven program enter 999 Set the Rate Temp and Hold values for the other ramp levels The time value under Program time changes to reflect the time that is required to complete the
46. gt Left click at one corner of the region of interest and drag the mouse vertically to the diagonally opposite corner As you drag the mouse TurboMass will indicate the region you have selected do not go beyond the bounds of the axis When the mouse is released the selected region will be redisplayed to fill the current window This operation can be repeated as often as required Restoring the Display gt Toggle EJ to restore the display to its previous state or to the default range OR Toggle the Default command in the Spectrum Display Range menu to restore the display to its previous state or to the default range These operations do not remove magnification ranges Setting the Display Range Defaults The display range default settings specify both the effect of clicking and adding a new spectrum to the display Changing the default display 1 Select Range Default from the Spectrum Display menu 2 Make any changes 3 Click OK poet range ca graph a Current 435 TurboMass Software User s Guide Default range Only relevant to Centroid mode acquisitions Specifies whether the mass axis will range from the first peak in the scan to the last peak in the scan Data or over the range you requested when the acquisition started Acquisition Default graph If there is more than one spectrum in the same window this option specifies whether the default mass range for that window is made large en
47. interest and drag the mouse horizontally to the other end As you drag the mouse TurboMass will indicate the range you have selected When the mouse is released the selected range will be redisplayed with an initial magnification factor of 2 Hold down the SHIFT key and left click and drag across the region of interest To expand the spectral range of interest left click and drag the mouse and click as many times as required to achieve the desired magnification Click E to restore the original spectral range Create single or multiple magnification ranges using the Magnify menu command 1 Select Magnify from the Spectrum Display Range menu or double click the magnify range indicators of an existing magnified range to open the Spectrum Magnify dialog 2 Enter the range you want to magnify in From and To Enter the magnification factor you want to apply in By 3 To define more than one magnification range select a new range in the Range field and repeat step 2 4 You can define up to five different magnified regions of the spectrum 5 Click OK to exit The spectrum is redisplayed with the data in the selected regions magnified by the requested factor The magnified regions are displayed in a different color and labeled with the magnification factor 433 TurboMass Software User s Guide 434 Magnifying the range of the intensity axis using the toolbar Use one of the following tool buttons to magnify the intens
48. m Data Storage IV Store all data from run I Store run log Data Points 618 Delay time min Run time min Collect data from channel 4 only Cancel Zol 2 Under Data Channel select channel A B Dual or None 3 Under Source select the appropriate additional signal source for the data channel s 158 7 GC Control Under Set Data Rate to set the rate at which the GC will sample its detectors either select By peak width at base and then enter the number of seconds in the text field With this option TurboMass acquires data in terms of the width at its base of the narrowest peak that you expect to occur in the run If you enter a peak width TurboMass calculates the optimum sampling rate for that peak width collecting at least 20 data points across the peak OR Select By sampling rate and then enter or select a rate With this option TurboMass acquires data from the GC using the number of data points per second that you explicitly set or the nearest available rate to that value Under Data Storage either select Store all data from run to store all the data from a run This option is useful if you don t know the run time because you have not entered the GC oven program OR Deselect Store all data from run to store only the data collected in a given time window You must specify the relevant times In the Delay time field enter the number of minutes that you want to
49. or select Previous to save the change and select the previous compound Choose Save from the File menu to save the new Custom Compound List Environmental Reporting Generic TIC Names Dialog This dialog enables an administrator or other person with appropriate access permission to edit the list of generic compound names that appears in the Tentatively Identified Compounds dialog This dialog displays when you choose Generic TIC Names from the Environmental Configuration submenu of the Tools menu or clicks the New Name button in the Form 1 TIC Assign Tentatively Identified Compounds dialog Generic TIC Names Unknown Adol Condensate Unknown Alcohol Unknown Aldehyde Unknown Alkane Unknown Alkene Unknown Amide Unknown Amine Unknown Aromatic Unknown Hydrocarbon Unknown Ketone Unknown PAH Unknown Phthalate Delete Unknown Cancel Parameter Description lt list gt A list displaying the currently defined generic names in alphabetical order lt edit box gt An edit box that enables you to edit an existing name or enter a new name 657 TurboMass Software User s Guide 658 Add Click this button adds the current contents of the edit box to the list as a new entry Modify Click this button to set the currently selected item in the list to the current contents of the edit box Delete Click this button to delete the selected item from the list To create edit a list of generic compound names To create a l
50. right click on a peak in the spectrum generates a chromatogram centered around the nearest peak The vertical height at which the mouse is clicked is also taken into account The peak chosen will be the nearest peak of equal or greater intensity A right click and drag operation generates a chromatogram for the selected range Displaying the same mass chromatograms for a new data file 1 Select Open from the Chromatogram File menu to load the Chromatogram Data Browser 2 Select the new data file you want to display 3 Select Replace All to replace the existing data file and also any mass chromatograms that are on display 4 Click OK TurboMass Software User s Guide TIC and BPI Chromatograms The Total Ion Current TIC chromatogram is the default chromatogram displayed when you start the chromatogram module or when you select a new data file using the File Open command The intensity plotted at each point in the TIC is the sum of all the intensities in that scan You can also obtain the TIC by selecting TIC from the chromatogram toolbar A BPI Base Peak Intensity Chromatogram plots the greatest intensity at each scan whereas the TIC is the sum of the noise and the sum of signal at each scan The BPI chromatogram exhibits a greater apparent resolution and signal to noise but will only contain contributions from the most intense components Therefore it is possible that some peaks in the TIC chromatogram may not be visible in th
51. start an acquisition The simple function list shown might contain only one function for example a centroided mode full scan between 50 and 550 amu using EI ionization Immediately above the function bar display is a time scale that shows when the function will be active from and for how long it will run In this case the function starts after 5 minutes and then runs for 35 minutes terminating after a total elapsed time of 40 minutes gt To open this dialog open the MS Method from the Sample list OR Click in the MS panel in the TurboMass main window 193 TurboMass Software User s Guide 194 Scan Functions c turbomass tutorialreports pro acqudb default exp 0 x File Edit Options Toolbars Functions Solvent Delay Solvent Delay One Solvent Delay olslals atl alv ee wsscan ep sk Total Run Time sale oj eee etl E 10m e a e a TE Delay 1 Start 0 00 min End 2 00 min A MS Scan Time 2 00 to 10 00 Mass 50 00 to 300 00 El Figure 7 Function list showing a single function The currently selected function is highlighted If the display shows more than one function you can select a new function either by selecting it or by moving to it using the up or down arrow keys on the keyboard A more complicated function list might have four SIR functions running sequentially for 10 minutes each Function List Editor Scan Functions c turbomass tutorialquant pro acqudb standard_1
52. that do not appear on the Main Data Browser Add The data are added to data currently displayed as a new trace in the same window Replace The data replace existing data in the window New The data are displayed in a new window Window The Chromatogram Data Browser has an additional parameter that does not appear on the Main Data Browser Replace All Ifyou are displaying the mass chromatograms for a number of selected masses and select this parameter when the new file is opened traces will be replaced by traces at the same masses 39 TurboMass Software User s Guide Data Browser Fields File Name Directories Drives Information Sample Description Acquired Function History 40 Lists data files in the current directory and provides a field where you can enter or select a file name The file name may include a path if required Lists the directories available on the current drive Lists the other available drives These will include floppy disk drives and network drives when available Contains information relevant to the currently selected data file Contains the sample description text obtained from the header of the currently selected data file This will be information such as compound name and concentration that was entered during acquisition Contains the date and time of data acquisition Displays the acquisition function currently selected The function description gives the function typ
53. the calibration curve is fitted These transformations are useful with very wide dynamic range data to prevent all the low concentration data points from being visually complressed together on the calibration curve Axis transformations cannot be used with RF type curves curves that use point weighting or curves that include or force the origin 266 Quantify 8 Ifrequired set the Concentration Units parameter The value set here will be used on the concentration axis of calibration curves and in the concentration column header in the Summary Report Mapping of Retention Time to Relative Retention Time When Retention Time is the selected Peak Location mode and the compound has an Internal Reference defined then the software will calculate the appropriate value for the Relative Retention Time field and display it in that disabled field to 3 decimal places The calculated value will be RT Current Compound RR _ RT Internal Reference When you enter a new value for RT the displayed RRT value will be updated when focus leaves the RT field Similarly if Relative Retention Time is the selected Peak Location mode and the compound has an Internal Reference defined then the software will calculate the appropriate value for the Retention Time field and display it in that disabled field The calculated value will be RT RRT current compound x RT Internal reference When you enter a new value for RRT the disp
54. to this menu item when it has been selected 373 TurboMass Software User s Guide 374 Displaying Chromatograms You can display various types of chromatograms in the Chromatogram Window mass chromatograms TIC and BPI chromatograms You can also display chromatograms in several ways Adding or Replacing Chromatogram Traces TurboMass gives you a number of options for displaying any new chromatogram traces New chromatogram traces can be generated by e Opening anew file e Processing chromatogram traces subtract smooth integrate etc e Selecting mass chromatograms with the mouse or by using the Display Mass menu command To display each new chromatogram trace in a new window click E To cancel this mode and display new traces in the same window click again When new traces are displayed in the same window you can choose whether to add the new trace to the traces currently displayed or to replace the current trace with the new trace Click to replace the currently selected trace with each subsequent chromatogram or chromatogram process Click a second time to add each subsequent chromatogram or chromatogram process to the traces on display Up to 16 chromatogram traces can be displayed in one window NOTE is unavailable when is chosen Chromatogram Mass Chromatograms The following procedure describes how to display a summed mass chromatogram 1 Click OR Select Mass from the Chromatogram Display
55. will begin to mass calibrate Refer to Chapter 6 Mass calibration for details If you selected Evacuate reference Gas in the UltraTune Setup dialog UltraTune turns off the Reference Gas and the pumps out the reference gas NOTE You can verify if it has been done by selecting Reference Gas On from the Gas menu to remove the check mark and selecting Pump Out Reference Gas from the Gas menu and wait about one minute as the reference gas is pumped away Select Pump Out Reference Gas from the Gas menu again to remove the check mark and stop pumping the gas File lonMode Calibration MEER Options Help Reference Gas On Pump Out Reference Gas Cl gas on 8 Select Exit from the File menu Edit Calibrate Process View Help Open Save Save As 97 TurboMass Software User s Guide Running UltraTune Custom AutoTune TurboMass can automatically tune the mass spectrometer using UltraTune Custom with an EI ion source UltraTune Custom ramps the settings for the tuning parameters until they are optimized to give good intensity resolution and peak shape NOTE The goal of UltraTune Custom is to give a satisfactory library searchable spectrum not to achieve maximum sensitivity Running UltraTune Custom 1 Click OR Select UltraTune followed by Custom AutoTune from the Tune page Options menu Fie IonMode Calibration Gas Help Ca a UltraTune gt 98 Readbacks
56. 638 640 642 644 646 648 650 Scan El 629 42 631 35 1 09e3 633 21 648 39 Thee AB0010 2 0 128 Cm 1 18 AB0000 2 0 128 Cm 1 18 622 52 624 626 636 63 639 31 643 23 Scan El 648 58 1 65e3 636 95 639 81 643 54 646 77 645 47 Dale 628 630 632 634 636 638 640 642 644 646 648 650 Figure 4 Effect of increasing lon Counting Threshold on noise in Heptacosa The value of the lon Counting Threshold should be set such that background noise is removed without significantly reducing the intensity of the smallest peaks of The following example shows the effect of increasing the lon Counting Threshold on a part of the spectrum that contains a low intensity peak As the lon Counting Threshold is increased beyond a certain value the peak becomes narrower and its 77 TurboMass Software User s Guide intensity is reduced as the thresholding rejects part of the genuine signal In this case an lon Counting Threshold value of 4 would be suitable Baseline 0 lon Counting 4 Data Storage Compressed AB0250 2 0 128 Sm SG 2x1 00 Cm 1 18 Scan EI 1 lon Counting Threshold 25 AB0060 2 0 128 Sm SG 2x1 00 Cm 1 18 Scan El in 614 06 1 53e4 lon Counting Threshold 6 AB0040 2 0 128 Sm SG 2x1 00 Cm 1 18 Scan El 100 6 2 84e4 lon Counting Threshold 4 625 Baseline 0 lon Counting 2 Data Storage Compressed AB0020 4 0 232 Sm SG 2x1 00 Cm 1 18 Scan El 614 06 3 98e4
57. ARMEI ERS Text Data Format Continuum X M ni ae el Run Duration mins jas Scan Time s jaz End M 504 ea Inter Scan Time s p 05 Close Origin Start Mass 500 2 Make any required changes to the settings Data File The name of the data file to which acquired data will be Name written The filename can be up to 128 characters If the file exists you will be asked if you want to overwrite it Text A text area that is used to enter the sample description The description can be displayed on any output of the acquired data and has a maximum length of 80 characters 110 Data Format Start Mass End Mass Run Duration Scan Time Inter Scan Time Instrument Tuning The type of data that will be collected and stored on disk It can be Centroid Continuum or MCA Specifies the mass at which the scan will start The Start Mass must be lower than the End Mass Specifies the mass at which the scan will stop Length of the acquisition measured in minutes Specifies the duration of each scan in seconds Specifies the time in seconds between a scan finishing and the next one starting During this period data is stored on the PC 3 Click Start Acquisition 111 TurboMass Software User s Guide 112 Mass Calibration 6 Mass Calibration Introduction TurboMass provides a fully automated facility for calibrating the mass scale of an instrument To open the
58. Allow A4 Letter page resizing option in each template s description page should be selected and in all cases the Paper drop down list on the template description page should always be set to Letter so that the page size appears properly in the template editor Bile Format OAA T L E z Default Header L Default Footer L Page Type 1 MEFEAEEREETIO A Letter 8 1 2 x 11 in Default Margins Default orientation Number of page types _ 0 25 inches I Display grid T Snap to grid E Layout Tools Mi a Abc Portrait Landscape Data Objects Custom Objects 2 Drag a Text Block into the Header Label it Qualitative Report Testl Then format the text as follows Highlight text and right click to select Format a b Select Font tab Click OK moe o 572 Set to Blue 20 pt Ariel Bold Set Paragraph tab alignment Horizontal Center Resize the Text Block so that you can see the text Communiqu Reporting 3 Click on Footer in the Layout toolbox on the left of your screen The footer appears 4 From the Data Objects toolbox left click DateTimeReport Layout Tools H S 3 Data Objects Global Project amp System Miscellaneous PagexofY PageNo NumPages Communiqu s oftwareVersion OperatingS ystemU s
59. Amount of internal standard injected in nanograms ng from appropriate Concentration column of the sample list as defined in the Quantify Method Vi Volume of the concentrated extract in microliters uL Concentrated Extract Volume from sample list Vi Volume of the extract injected in microliters uL Injection Volume from sample list Ws Weight of sample extracted in grams g Sample Wt from sample list GPC GPC factor derived from setting in sample list GPC Y N GPC 1 0 if water sample was not subjected to GPC GPC 2 0 if water sample was subjected to GPC RRF Average relative response factor from calibration file D Adjustment for dry weight basis 100 moisture 100 calculated from moisture value in sample list Df Dilution factor The dilution factor for analysis of soil sediment samples for semi volatiles by the medium level method is defined as follows uL most conc extract used to make dilution uL clean solvent uL most conc extract used to make dilution X is the target amount in nanograms which assumes that the internal standard amount is entered as nanograms in the Sample List If the internal standard amount is entered as a concentration then the user must enter a user multiplier to make the necessary correction 762 Index Index A account policies 674 acquisition from Tune 110 GC status 183 MS status 357 Acquisition stop 360 an
60. By The table may be sorted by retention time compound name internal reference standard or the quantify trace ion Report Type The Compact format displays the compound data in paragraph format taking as many lines for the compound as required The Extended format displays one compound per line Compound Select Current to display the current compound Select All to display all compounds OR Select Range and enter the compound range in the text field 3 Optionally enter text for the headers and footers on the report 4 Select Page Numbers to add page numbers to the report Editing the Compound Format in the Quantification Method Report Selecting which fields will be displayed in the Quantification Method Report gt Select Edit Compound Format from the Quantify Edit menu to display the Report Format dialog 290 Quantify The fields present in the Method Report are shown in the Displayed Fields list in the Report Format dialog Other fields that can be added to the Method Report are displayed in the Available Fields list The Method Report will display up to the maximum number of columns that will fit on one page To include more columns print in landscape mode instead of portrait mode Appending new fields to the Method Report 1 Select the field you want to append in the Available Fields list box 2 Click Append 3 Repeat steps 1 and 2 as required 4 Click OK to save the changes Inserting new fields in the Meth
61. CSV file in a Communiqu Section object All items enclosed in the Section should have the Down from Top property set to zero 0 Also all items should have the same Height value set as the Section itself 574 Communiqu Reporting 1 Click on Chromatogram Active X in the Project gt Samples directory of the Data Objects toolbox Graphic Data Objects have a small red x as their icon Data Objects 3 Global 3 Project i Y Project Name Project Directory Project Date Time Samples a Sample ID 3 Concentrations 3 Conditions 3 Sample Description 3 Task Description 3 Sample Type 3 Submitter 3 Vial Number 3 Injector B Inject Volume 3 Process 3 Process Options amp Process Parameters 3 Spare 1 3 Spare 2 a Spare 3 a Spare 4 3 Spare 3 Job 3 User Name 3 User Divisor 3 User Factor 1 3 User Factor 2 User Factor 3 amp Chromatogram Active gt le 575 TurboMass Software User s Guide 2 Left click on Chromatogram ActiveX move the cursor to the center of the design page then left click and hold the mouse as you drag the mouse to expand the box The box displays as CHROMATOGRAM PLOT GRAPH HEADER Se ee ee O a Qualitative Report Test 1 ae CHROMATOGRAM PLOT GRAPH HEADER 3 From Layout Tools left click on Table then move your cursor to the page and left click A four column by two row table appears 4 Select the tab
62. D Sample and Compound Table Output Fields Appendix D Sample and Compound Table Output Fields Compound and Sample Report Output Fields The following table describes each output field and format The two columns on the right specify whether the field is available in the Compound Report C and or Sample Report S a CE ee a Se Eo ee PT Concentration found in Blank which is O subtracted from final Concentration pee ooe Ce a Calibration File Name of Quantify Calibration file used to ae quantify peak excludes extension omnia emma o prerana mas gt Trace QUAN_TRACE C40 Raw datafile chromatogram integrated to produce peak A chromatogram description can consist of TIC BPI mass or mass range To add or subtract chromatograms use and operators Concentration error from standard concentration Deviation 100 Conc StdConc StdConc Pk Flags PK FLAGS C4 Peak integration description flags 1st character baseline start 2nd baseline end b starts ends on chromatogram curve v starts ends as valley dropline between two peaks starts ends as a shoulder dropline between two peaks t perk was not detected within the retention time window M manually defined by user Found Peak Scan a Scan number of the peak apex TurboMass Software Guide Injection Volume INJ_VOL N 19 9 Injection volume of sample currently set up to 1 Set during Quantify Locate processing otherwise is 0 IS Compound Compound refe
63. Data File oseeneeeeeeeessseesesseseeeeseese 532 Mapping part of the data file of interest ese eeeeeeeeeeeteceeeeneeees 532 Manipulating the Display cccccccesccesscessceeseeeeeeeseeeseecseeeseeeaecsaeenseenseenes 534 Changing the Map Intensity Scaling 0 0 ccceccseesseesteesteceteceeeneenes 535 Controlling the Appearance of the Display csecceecceseeeeeeeeeteeeees 537 Displaying the Status Bar and Toolbat eceeeesceseeeceeceeteeneeeneeeees 539 Selecting the Current Cursor Position ccccccssesceseceeeeeeeeeeeeeeseeenes 540 Editing the Header Information cccccesceessceeeeeeeeeeeeeeeneeeteeensees 540 Printing from Map cccccccesseesseceteceneceeceeeseeeeeeeeeseeeseeeseecsaecsaecnseenseenseenas 541 Copying to the Windows Clipboard 0 cccccccssecsteeseceesceeeeeeseeeseeseeeneeenaes 542 Molecular Mass Calculator sccccccsscsssscssscssscssscssscssssnsssnesencssssseosees 543 Calculating the Molecular Mass cccccccscessseesseeseeeeeeeseecaeceaecnseenseeeeeennes 545 Defining User Eleminten e E 546 Report Method Editor e seossessseosseosseossoossoessocssoossoossoossoossoosssosssosssosssse 547 About the Report Method Editor ccc cccccsseeseeseeseeseeesecnaecnecneeeseeees 549 Report Method Editor Toolbar 0 ccccecccecscesseseceeeneeeneeeseecssecsaecseeneenseenes 551 Selecting an Existing Template 0 ccccccccsscceseceneceeeceeeceeeeeeseesseeeseeee
64. High Mass Calibration cccecsseesceeecereeeeetecneeeeeeeees 135 Saving and Restoring Calibrations c ccccccesscessceseceeeeeeeeeeseeeseeeeeeeeesaes 137 Saving a Named Calibration cccccccccsecsseeseceseceseceeeeeeeeeeeeeseeeeseeenes 137 Restoring a Saved Calibration ccccccccssessecesceeseeeeeeeseeseeeseeeeeensees 137 GE Comtr ol oociececcccesssccicsccuesscesensscuceedsecsaceeetecceticesscdesessesceetaseesesesesacsecsseeees 139 Overview of TurboMass GC Control 0 ec ececeecceceeeeeeecesecteeeeesecneeeneeeees 141 PREG MCN recisi iate en e EEEE EEEE 141 THEGC Status BOr Ea aa A E 141 The GC Editor Toolbars and Status Bars ceccecceseereeseeeeeeeeeeeeees 142 Configuration iness naa a E o A an O RE 143 Configuring TurboMass for GC Control cccecceesseesseeeteeeteceteeeeenes 144 Initial GC Configuration cccccccccsecssecsceeseceecesecseeeeeseeeseeeeeeneeesaees 144 Reconfiguring the GC ccceccccsseeseceseceseceeeeeeeeeeeseeeeeneeeseeeseeeeeenaees 149 Changing the Instrument Configuration ecccesecceeeceteeteeeeeeeeeaeees 150 Changing Your Acquisition Port ccccccesscssseesseeseesecsteesteenteeneeees 150 Configuring TurboMass without GC Control eeeeeeseeneeeeeeteeeeees 151 Configuring User Options cccccccesccessceeceeeseeeseeeeeceeesaeenseenaeenaeens 151 Printing Configuration Information eeceeseeseeseceeeneeeeceeeteeneeaes 155 GE Method Editors sesecessesxc
65. IONIPASS L TRUE if within the limits 5 0 ION2MASS N 10 2 Qualifier Ion 1 Mass 5 0 ION2RT N 8 3 Qualifier Ion 1 Mass Chromatogram Peak Top Retention Time 5 0 ION2AREA Qualifier Ion 1 Mass chromatogram Integrated Peak Area ION2HEIGHT Qualifier Ion 1 Mass chromatogram Integrated Peak Height ION2_ST_RT Qualifier Ion 1 Mass chromatogram Integrated Peak RT of Baseline Start ION2_EN RT Qualifier Ion 1 Mass chromatogram Integrated Peak RT of Baseline End Qualifier Ion 1 Mass chromatogram Integrated Peak Height of Baseline ION2_ST_HT Start Qualifier Ion 1 Mass chromatogram Integrated Peak Height of Baseline ION2_EN_HT N12 End 5 0 ION2RATIO N 19 9 Qualifier Ion 1 Ratio 5 0 ION2LOWLIM N 19 9 Qualifier Ion 1 Ratio Low Limit 5 0 ION2HIGLIM N19 9 Qualifier Ion 1 Ratio High Limit 5 0 ION2PERTOL N 19 9 Qualifier Ion 1 Percent Tolerance 5 0 ION2PASS L TRUE if within the limits 5 0 ION3MASS N 10 2 Qualifier Ion 1 Mass 5 0 ION3RT N 8 3 Qualifier Ion 1 Mass Chromatogram Peak Top Retention Time 5 0 ION3AREA N 16 3 Qualifier Ion 1 Mass chromatogram Integrated Peak Area 5 0 ION3HEIGHT N 12 2 Qualifier Ion 1 Mass chromatogram Integrated Peak Height 5 0 ION3_ST_RT N 8 3 Qualifier Ion 1 Mass chromatogram Integrated Peak RT of Baseline Start 5 0 ION3_EN_RT N 8 3 Qualifier Ion 1 Mass chromatogram Integrated Peak RT of Baseline End 5 0 Qualifier Ion 1 Mass chromatogram Integrated Peak Height of Baseline ION3_ST_HT N12 Start 5 0 Qualifier Ion 1 Mass chrom
66. Library 1 Select Range From from the Library Display menu 2 Enter new mass axis From and To values and click OK Restoring the displayed mass axis range gt Toggle the EJ tool button to restore the display to its previous mass range or to the default mass range OR Select Range Default from the Library Display menu to display the default mass range Delta Window at Library Delta olx amp Fie Edit Display Process Window Help lej x 2 ala we ala eee 2 100 The Delta window shows the difference between the search spectrum and the currently selected hit Positive peaks are those that are more intense in the search spectrum than in the hit spectrum Negative peaks are those that are more intense in the hit spectrum than in the search spectrum The 100 annotation point of the intensity axis refers to the base peak intensity of the spectra before subtraction The mass axis of the Delta window is always the same as that of the Hits window and cannot be changed independently Structure Window 509 TurboMass Software User s Guide 510 2f Library Structure OY x C Eile Edit Display Process Window Help lej x 2 ala we ala eee 2 The Structure window shows a graphical representation of the chemical structure of the currently selected hit The structural pictures are derived from structure data supplied by the United States National Institute for Standards and Technology NIST
67. METHYL SYDNONE 3 4 DIMETHYL N NITROSO 2 METHYL OXAZOLIDINE BORON TRIHYDRO N METHYLMETHANAMINE T 4 N HEXYLMETHYLAMINE DIHEXYLAMINE N NITRO xj The Hit List window gives a text listing of the best 20 hits resulting from the library search These hits are listed in order of either reverse or forward fit depending on which order was selected as the Ranking parameter in the Library Search Parameters dialog You can format the Hit List window to include the following about each hit e Hit number e Compound name e Forward fit value e Reverse fit value e Chemical formula e Molecular weight e Library entry number 505 TurboMass Software User s Guide 506 e Library e CAS number The current hit is that selected in the Hit List window It is the first hit that is displayed in the Hits Delta and Structure windows You can make any other hit the current hit by selecting it in the Hit List window Modifying the fields displayed in the Hit List window 1 Select Format List from the Library Edit menu to open the Format DB List dialog at Cancel Update Justification Format Hit Compound Name Henove Remove All Fields list type l Brief list Hormalllist Full list The Format list contains the fields currently displayed in the Hit List window The Fields list contains additional fields available for display To change which fields are displayed
68. MS Scan to open the MS Scan Function Editor 2 Enter the scan function parameters 199 TurboMass Software User s Guide 200 WARNING m Mass m z r Method Start jo lonization Mode M End eoo Data Centroid he Scans To Sum gt Time Mins Scan Duration secs Start B Scan Time 0 2 End fi 0 Inter Scan Delay 10 01 Cancel Start Mass End Mass lonization Mode Specifies the mass at which the scan will start The Start Mass must be lower than the End Mass Specifies the mass at which the scan will stop Both the start and end masses can be selected directly from a spectrum displayed in the Spectrum window If you right click and drag the mouse across a spectrum TurboMass will automatically enter the start and end mass values for the selected mass range Specifies the ionization mode and polarity that will be used during the acquisition Do not select El if a CI ion source is installed The filament will not regulate properly Data Specifies the type of data to be collected and stored on disk Centroid Stores data as centroided intensity and mass assigned peaks Data are stored for every scan Almost always used for GC MS Continuum Data are not centroided into peaks Instead the Scans To Sum Start Time Function List Editor signal received by the interface electronics is stored regularly to give an analog intensity picture of the data being acquire
69. Monitoring Data ACQUISITION ccccccesseesteceteceeceeceseeeeeeseeeeeeeeeneesaes 65 Manipulating your Data cccecccccsseesseessecseceeceseeeseceseeeeecseeeeeeeeeneenaes 65 Reporting your Data cccccccccecsseesseesseeseessecesecesecnsecsseeeeeseeeeeeeseneenaes 65 Instrument Data Thresholds scssccssscssscssscsssssssessssessessescssscssssssees 67 Selecting the Inlet Systema renar a cues cena EE A E 69 Setting Instrument Data Thresholds ccccecccecseeeceeeneeeseeeeeesseesseenseenaeens 70 Setting Data Thresholding Parameters 0 c ceccesceesceseeeeeeeeeeecneeeeeeeees 70 Changing Lab and User Information ccccccccesccessceeeeeeseeeeeeeteeeeeeseeeseees 79 Communications Status and Diagnostics ccccesccessceeeeeeeeeeeteeeeeeseesees 80 Communications Status ce cceecceceeceeeeceseeseeeeceaecaeeeeeeseceeeeeeaecnaeeaeeeees 80 DA QNOSTICS iecere a a A E EA AT 80 istrument Tuning s sssssscssocssscsoosssistoeorioss osovi vecs so osooso satone otes sesoonse 81 The Tune PASC re oe e as delved saneer tes seeestes T e A N a 83 The Tune Page Toolbar roreicsegirria e 85 Changing Tune Parameter Settings c cccsccesccssecessceeeeeeseeeseeeeeeeeeeeestees 86 Printing Tune Information cccceseeseceseceseceeeceeeceeeeeeeeeeeeeeseeeseeeeeeaeesaees 87 Experimental Record issiron anae irn an a a 88 Saving and Restoring Parameters cccccesccesseeeeeeeeeeeeeeeeeeesseesseenseenseees
70. NOTE Quantify Quantify Sample Report Graphically displays all located chromatogram peaks and tables quantification results Report is grouped by sample The Chromatogram application is opened when producing the report The Quantify Toolbar The Toolbar is displayed at the top of the Quantify window By choosing the toolbar buttons you can perform some common operations Prints the current Quantify window display in portrait format Prints the current Quantify window display in landscape format Shows the previous peak in the Summary window Shows current peak in the Summary window Shows the next peak in the Summary window Arranges the windows in a tiled view Arranges the windows in a cascaded view Arranges the windows in a stacked view Selects the current entry Decrements the current entry in the Summary window Increments the current entry in the Summary window Restores the default display range EH HERO BRB eEe 255 TurboMass Software User s Guide 256 A Step by Step Guide to Quantification Creating a Sample List The first thing that you must do when using Quantify is to create a list of samples that you want to use to perform the analysis These samples can be acquired manually but more often they will be acquired automatically using an autosampler The Sample List Editor has various columns such as Filename vial or bottle Number and Sample Type that can be filled in for each sample Each
71. Optional processing then allows three options Ignore Worst5 The 5 of scans that have the greatest deviation from the of Scans mean are disregarded in the noise signal Ignore Scans Those scans whose deviation from the mean is greater than Outside 1 SD one standard deviation are disregarded in the noise signal Ignore Scans Those scans whose deviation from the mean is greater than Outside 2 SD two standard deviations are disregarded in the noise signal 411 TurboMass Software User s Guide 412 Options and 3 are expected to give roughly equivalent results Option 2 should give an RMS value of about double that of the other two options If one of these three processing options is selected then the mean and RMS deviation of the noise are recalculated disregarding the appropriate points E Fie Edit Display Process Window Tools Help l x Eee PN el Aea elel S N RMS 3 7 41 Calculating the signal to noise value for a Mass Chromatogram 1 Display the chromatogram range of interest in a chromatogram window 2 Select Signal to Noise from the Chromatogram Process menu 3 Enter Signal and Noise ranges Either enter values or right click at one end of the Chromatogram region of interest and drag the mouse horizontally to the other end TurboMass indicates the range you have selected The dialog will be updated to show this range 4 Select the Noise Processing and Display methods required 5 Click OK Chromatog
72. Processed spectra can be subtracted enabling averaged spectra to be used as background Both centroid and continuum type files can be subtracted different 463 TurboMass Software User s Guide 464 types cannot be mixed Enhance Removes noise from continuum data files It examines each data point and its close neighbors to determine if it is noise or part of a real feature Data points not considered to be valid are removed from the output data file Enhance can significantly reduce data file size Cluster Detects pairs or triplets of peaks separated by a specified mass difference Parameters specified are mass differences and expected intensity ratios both with tolerances together with a time window and a global threshold The resulting data file will contain only these peaks Again Cluster will significantly reduce data file size CODA COmponent Detection Algorithm essentially removes mass chromatograms that represent background from the dataset Each raw mass chromatogram is compared to a smoothed standardized mass chromatogram and masses in which the background is high or in which spikes are present are rejected Creating a Subtracted Data File The following section describes how to create a subtracted data file and provides examples 1 Select Subtract in the Strip Datafile dialog 2 To change Input File or to select a subrange click Input Select Input File and Function by clicking File to open a browser dia
73. Quantify Calculations Linear Calibration Curve Amounts are calculated using a linear calibration as follows Amount Peak Response Intercept Gradient Where Peak Response is the response value calculated for a peak Intercept is the intercept calculated for the linear calibration Gradient is the gradient calculated for the linear calibration Quadratic and Higher Order Calibration Curves Amounts are calculated by solving the following equation using the Newton Raphson Method Peak Response P Amount Where Peak Response is the response value calculated for a peak P is the polynomial function calculated for a set of calibration points User Parameters User parameters can be used to multiply or divide the final quantitation results These factors are entered per sample in the Sample List If a factor is not specified of zero it is assumed to be one Final Amount Amount Dilution Factor Extract Volume User Factor Initial Amount Injection volume The User Peak Factor is entered per compound in the Quantify Method Final Amount Amount User Peak Factor 737 TurboMass Software User s Guide 738 Calibration Curve Statistics Coefficient of Determination The coefficient and determination is calculated for a regressed calibration curve In the case of a linear unweighted curve it is equivalent to the square of the correlation coefficient and is reported as such Correlation coefficients ar
74. Raw Data File ChA The full name of the current raw data file for each Ch B or both active channel This information appears only if data are being saved from a Clarus detector Analysis Information Instrument Method The name of the current method used for instrument control Run Time The total length of time the current cycle is to run Delay Time The amount of time between the start of the run and when data will be analyzed Sampling Rate The number of data points acquired per second Viewing Detailed Instrument Information The Details window displays information about the state of the GC Current GC Control This section summarizes some of the more important current values I F Status Status of the interface For more information refer to Understanding GC Status Messages on page 185 Elapsed The amount of time in minutes that the current cycle has been Time running Aux Current flow pressure Carr A B Current carrier flow pressure Inj A B Current injector temperature Oven Temp Current oven temperature Program Length of time to run the oven program Time Zones The setpoint Init Set for all zones might change during a run if you have set any timed events The column will indicate Ready Not Ready Alarm or N A Injector Temp Init Set Setpoint temperatures for injectors A and B Actual Current actual temperatures of injectors A and B Ready Whether or not the injector is ready Detector Tem
75. Remove Programs gi Currently installed programs Show updates Change or Remove Programs s 0 Snagit 6 Al Spyware Begone 5 15 fe TurboMass er5 2 0 Add New Programs o change this program or computer click Change Rem 8 Windows Installer 3 1 KB893803 E Wireless G Notebook Adapter with 7 am Add Remove Windows Components Size Size ve it From your Size 13 85MB 5 20MB 9 12MB _ Y On the Add or Remove Programs dialog select TurboMass Ver5 X and click on Change Remove The Uninstall shield loads Do not click Cancel unless you want to halt the unistallation 685 TurboMass Software User s Guide InstallShield Wizard 4 Click on OK to start the software removal The following appears Confirm Uninstall 5 Click on OK a second time to confirm The following appears ILD Then the LCD Stops if running and the following appears 686 Appendix B TurboMass Software Installation Setup Status Uninstall continues this may take several min The following appears Shared File Detected 6 Click the check Box and Click on Yes The following appears 687 TurboMass Software User s Guide information S Please remember to remove J Communiqu MatLab Runtime Components 7 Click on OK The following appears TurboMass Maintenance Complete InstallShield Wizard has finished performi
76. Select All Samples Add check marks to all boxes thereby selecting all samples How to Generate a Report To generate a set of environmental reports follow this procedure IMPORTANT fyou change the quantitative results at the report generation time for example you select a different method you must reprocess otherwise the qualifier flag assignments may be invalid 1 Choose the Environmental Reports command from the Tools menu of the Sample List window or press the icon on the Sample List icon bar 2 Use the default sample list the one displayed in the Sample List window or select a different one 3 Select the set of Forms to be generated 4 Review the displayed sample list and any global errors or form specific errors identified by the TurboMass software e Correct any global errors if possible by changing the rows selected for processing in the sample list e Correct any form specific errors if possible by adjusting sample assignments associated with Form 602 Environmental Reporting 5 Open the Tentatively Identified Compounds dialog if a Form 1 TIC has been selected or else skip to step 8 and review the default compound assignments for each reported peak 6 As appropriate compare the spectra of the alternate search hits with the peak spectrum and change the TIC assignment if necessary 7 Close the Tentatively Identified Compounds dialog when all peaks have been reviewed 8 Choose the Pri
77. Shutdown Shutdown can be run in either of the following ways e Select Shutdown from the TurboMass Run menu e Inthe Sample List Run menu select Edit Shutdown In the Shutdown dialog select Shutdown from the Control List menu Editing the Shutdown parameters 1 Select Edit Shutdown from the TurboMass Run menu to display the Edit Shutdown dialog Data Acquisition ShutDownE _ACE acl Shutdown Diem S 2x 2 Select the appropriate checkboxes to enable startup before and or shutdown after a batch run or on error Enter the time in minutes when shutdown should start after a Sample List batch run NOTE Selecting a shutdown time that is too short could cause premature shutdown 3 Set up an Auto Control Task timetable ShutDownE _ACE acl Shutdown Diem S 2x C AMIpnx3 s NOTE The original parameters are carefully selected Be cautious about changing them 361 TurboMass Software User s Guide Task Pre Delay Post Delay lon Mode File Name Control Tasks 362 A drop down list of all the tasks that can be controlled from this page The list of Tasks will vary depending on the system configuration lon Mode Source Gas Off Source Gas On Time in seconds to wait before this task is run Time in seconds to wait after this task is run A drop down list of Ionization modes Enabled when lon Mode is selected from the Task list Enabled when Tune File is selected from the T
78. Spike Sample Assign Matrix Spike Duplicate 598 Description Queues the selected sample list rows for reprocessing Opens the Tentatively Identified Compounds dialog Enabled when the Form 1 TIC tab is selected and no Form 1 TIC errors exist Assigns the selected row as the source of report header information for Form 2 Displays Header in the Status column for that row Assigns the selected row as the Analyte to be treated as the sample which gets spiked to produce the MS and MSD samples for Form 3 Displays Analyte in the Status column for that row and displays the row in the Analyte color Enabled when the Form 3 tab is selected Assigns the selected row as the Matrix Spike sample for Form 3 Displays Spike in the Status column for that row and displays the row in the Spike color Enabled when the Form 3 tab is selected Assigns the selected row as the Matrix Spike Duplicate sample for Form 3 Displays Spike Dup in the Status column for that row and displays the row in the Spike Dup color Enabled when the Form 3 tab is selected Menu Item Command Assign Method Blank Assign Tune Evaluation Sample Assign Continuing Calibration Environmental Reporting Description Assigns the selected row as the Method Blank sample for Form 4 Displays Meth Blank in the Status column for that row and displays the row in the primary data color Enabled when the Form 4 tab is selected Assigns the selec
79. String dialog NOTE Chromatogram Processing Chromatograms Three processes are available for use on chromatograms polynomial background subtraction smoothing and integration Background subtraction and smoothing help you improve the presentation of the data Integration locates peaks positions baselines and calculates peak statistics for quantitative work Processing Multiple Chromatograms The background subtract smooth and integrate processes can be performed automatically on all the chromatograms within the current window To enable this operation click g or select Process All Traces from the Chromatogram Process menu the menu item will have a check next to it To turn off multiple processing reselect the toolbar button or menu item You can choose to add the processed trace to the current window or replace the current trace with the processed trace Toggle to cause each subsequent chromatogram or chromatogram process to replace the currently selected trace or to add chromatogram process to be added to the display is unavailable when is selected Subtract Background Subtract fits a smooth curve through the noise in the chromatogram and then subtracts this curve from the chromatogram leaving the peaks on a flat baseline Polynomial order Bo Below curve fioco Cancel Tolerance fono I Flatten edges I Make graph of fitted polynomial 393 TurboMass Software User s Guide 394 Polynomial Ord
80. The following procedures describe how to alter the mass and intensity axes Changing the range of the mass axis To change the range of the mass axis do one of the following e Left click at one end of the region of interest and drag the mouse horizontally to the other end TurboMass will indicate the range you have selected do not go beyond the bounds of the axis When the mouse is released the selected range will be redisplayed to fill the current window e To expand the spectral range of interest left click and click ey as many times as required to achieve the desired magnification Click EJ to restore the original range Repeat this operation as often as required e Change the range of the mass axis from the menu 1 Select Range From from the Spectrum Display menu 2 Enter new From and To values for the mass axis 3 Click OK Changing the range of the intensity axis Left click at one end of the region of interest and drag the mouse vertically to the other end TurboMass will indicate the range you have selected do not go beyond the bounds of the axis When the mouse is released the selected range will be redisplayed to fill the current window This operation can be repeated as often as required Spectrum Setting Magnified Ranges You can set magnification ranges in several ways Creating magnification ranges using mouse and menu commands If you have a three button mouse middle click at one end of the region of
81. User s Guide Process Pre Run Post Run Quantify the Data Specify the name of the process that will be run before the acquisition of files in the Sample List Specify the name of the process that will be run after the acquisition of files in the Sample List To quantify data after it has been acquired select Process Samples in the Sample List Quantify menu 1 Select the options required and click OK to start the analysis Quantify Samples x Ga r z V Quantify Samples e T Print Quantity Reports Integrate Samples Calibrate Standards Quantify Samples Print Quantify Reports 242 Project Takes QUANTIFY PRO Quantify From Sample 7 To Sample E Method TutorialQuant Browse Curve TutorialGuant Browse cms Integrates all the sample data files named in the peak list Uses Integration results to form Quantify calibration curves from all the data files in the Sample List Uses Integration results and Quantify calibration curves to calculate compound concentrations from all the data files in the Sample List Produces hard copies of the results of integration and quantification Sample List Report Preview Window This window displays when the Preview Reports option has been checked in the Start Sample List Run dialog and a Communiqu report has been generated as part of data reprocessing Only one report is available at a time in the preview
82. UserName T TEXTS l ihraru Caarsh Chramatanrami ICnastrum Dannart TEA TEXT3 File 23 Full Filename Printed 33 DateTimeReport 5 TEXT2 ami io es Barapa Desenhe Page 34 PagexofY amp Instrument Type E 2 Standard Footer 1 Mise into e conditions D Instrument Name TEXTI 3 Inlet Interface Tyr S a Page Type 1 3 LabName i Chromatoaram Plot a pect S OBJECTFRAM 3 Project Name amp Chromatogr Project Digg Si TABLE a Project Date Time der P amp 3 Sone CHROMATOGRAM PLOT 3 Sample ID TEXTS GRAPH HEADER TEXT10 100 E 9 Concentratior TEXT11 A 3 Conditions TEXTS z 3 Sample Desc 9 Peak Number 0 0 Time 3 Task Descrip 3 Retention Timel 000 20 00 40 00 60 00 80 00 100 00 S Sample Type bl Hela 3 Submitter real Te ZIDATAMI 3 VielNumber If d Nom Z DATAd e e m ees arenae norm Pinan 3 Inject Volume 9 Process E 3 Process Optic 3 Process Para 3 Spare1 3 Spare 2 3 Spare 3 3 Spare 4 3 Spare 5 3 Job 4l gt Position 0 5 3 Width 7 25 Height 1 78 3 User Name seep i ame gt Custom Objects Click on Project Name move your cursor to the designer page the click where you want the Project Name to appear and drag it to the desired size Click on Layout Tools to display the Layout Tool selections click on Text Block move your cursor to a position on the designer page click and drag to put the text block on the page Position the cursor on an edge of the Text Block and hold the left
83. a Ad Top J Date Format F Use Date DD MMMM YYYY 7 Time Format Use Time Localtime HH MM tt ZZ C Orignal time Selected zone I 24 hour chock GMT SirdedTing Layout C Oge Time C Time Date Co c Tue Time Date Preview 24 September 2003 11 45 Eastern Dayot Time The default Communiqu setting for Date Time Data Objects is Local time In order to ensure that the correct time is reported on your computer right click the Date Time Object in your template select Object Properties from the pop up menu and in the following dialog select Original time to set the Time Format then click OK 579 TurboMass Software User s Guide NOTE When setting the Numeric Data Object Properties in your Communique template increase the number of significant figures from the default of 4 to 6 in order to see the reported number with no rounding applied Otherwise Communiqu doesnot report 6 figures but instead applies rounding 13 Select Save from the Communiqu Report Creator File menu and name the file for example Mod Qualitative Report K Communiqu Report Creator Fie Edit View Format Actions Tools Help a Print preview Bri Close Template W Ext 14 Close Communiqu Report Creator by clicking Exit from the File menu Select the Template in the Report Method Editor After closing the Communiqu Report Creator the Report Method Editor appears 580 Communiqu Reporting Modity Move U
84. a tentatively identified compound as well as for a positively identified target compound Blank contaminants are flagged B only when they are detected in the sample This flag identifies compounds whose concentrations exceed the upper level of the calibration range of the instrument for that specific analysis If one or more compounds have a response greater than the upper level of the calibration range the sample or extract shall be diluted and reanalyzed 607 TurboMass Software User s Guide D Ifasample or extract is reanalyzed at a higher dilution factor for example when the concentration of an Analyte exceeds the upper calibration range all reported concentrations on that Form I are flagged with the D flag This flag alerts data users that any discrepancies between the reported concentrations may be due to dilution of the sample or extract A This manually applied flag indicates that a tentatively identified compound is a suspected aldol condensation product X Other specific flags may be required to properly define the results If used the flags should be fully described Section of the Window Description Sample List view The spreadsheet displays selected information from the Sample List Column widths can be changed in the standard way by dragging the header divider The selected columns can be changed using the Options Customize Display Deactivate Q flags This Form includes one unique feature it contains reporting f
85. ae ic cee Opening an existing method You can open an existing method from two places From the Method Editor gt Select Method Editor from the GC menu to open the Startup dialog In the Startup dialog select Load method stored on disk or select Load recently edited method and select the desired method From the Sample List gt Right click the Inlet File cell in the Sample List that contains the GC method you want to open and select Open from the drop down menu OR Select Open from the TurboMass Edit menu 157 TurboMass Software User s Guide Setting Data Channels The Data Channels command in the Instrument menu control how TurboMass acquires analog and digital data by letting you set the channel or channels for data collection the data sampling rate and the analysis run time Some of the options available on the Data Channels tab depend on the type of instrument that you are using If not select None NOTE Setting data channels applies only if you have additional conventional detectors installed on the GC If not choose None Setting channel options for the GC 1 Select Data Channels from the GC Method Editor Instrument menu to open the Data Acquisition dialog Data Acquisition x Data Channels m Data Channel Dual CB C None Source Channel Det Channel B fp etB 4 X m Set Data Rate C By peak width at base s By sampling rate pts s
86. agreement Use the scroll bar to view the rest of this agreement Copyright c 2006 by PerkinElmer LAS Inc All rights reserved PerkinElmer LAS Inc Software License Agreement IMPORTANT Read the terms and conditions of this Software License Agreement Agreement carefully before installing the Programs This Agreement represents the entire agreement between Licensee as defined below and PerkinElmer LAS Inc and its Affiliates collectively PerkinElmer concerning the Programs and the accompanying Documentation Select Yes to accept the agreement Select No to cancel the setup After clicking Yes the Confirm Instrument dialog displays Verify that the software will work with one of these two mass spectrometers Confirm Instrument This software is for use with the Clarus 500 MS or TurboMass Gold Mass Spectrometers from PerkinElmer only These spectrometers can be recognized from the nameplates shown below PerkinElmer PerkinElmer If your spectrometer is one of these click Next to continue with the installation Click Next to proceed with the installation The Install Shield Welcome dialog displays 693 TurboMass Software User s Guide Setup Installing TurboMass VYer5 2 0 Welcome to the InstallShield Wizard for TurboMass The InstallShield Wizard will install TurboMass on your computer To continue click Next 6 Click Next The Destination Location screen appears Setup Installing TurboMa
87. and are their copyright Not all NIST Library entries have associated structures If the currently selected hit has no associated structure the message No structure found appears in the Structure window If the Structure window is blank it may be because it is too small to contain the structure As a quick check try maximizing the window Structures are associated with library entries by their CAS number If you create a user library and enter the correct CAS numbers you can view the structures for the entries The mass spectral structures library is stored in the Structdb sub directory in the TurboMass installation directory Printing the Results of a Library Search You can print the library search results displayed in currently selected Library window Printing the library search results gt Click or to print in portrait or landscape format respectively Library OR Select Print from the Library File menu You can choose whether to print all windows or only the current window Copying To and From the Windows Clipboard The Windows clipboard can temporarily store information that is being transferred from one application to another You can use the Clipboard to move data out of a window as a picture and in some cases as a text list Copying a picture to the Clipboard 1 Set up the picture you want to copy in its window and select the window 2 Click OR Select Copy Bitmap from the Edit menu The displayed
88. are used to specify certain criteria that a library entry must meet in order to appear in the Hit List If you have the molecular weight and elemental formula of a compound you can use these filters to refine the search For example if you know that the search compound contains at least one chlorine atom you can specify this information in the search filters If you know that its molecular weight falls within a certain range you can specify this information in the search filters Specifying library search filters 1 Select Filters from the Library Edit menu to display the Filters dialog p Elements _ F Min Reverse fo p Mowi p m In ir ir Active h 1200 E i L User Values a Min Ma mnei fa minez im oo clude Other Elements Plym User fleas T Apply evact Cancel Reset 2 Change the library search filters as required by setting the following parameters Fit Specifies a Minimum Forward and or a Minimum Reverse 498 Mol Wt Active Min and Max Elements Min Max Active Library Fit value that a library entry must have in order to appear in the Hit List To make the filter active select the checkbox next to it and enter a value between 0 and 1000 into the relevant field These parameters specify a range within which the molecular weight of the library entry must fall in order to be included in the Hit List To make the filter acti
89. be measured in the calibration standard 757 TurboMass Software User s Guide Soil Sediment Samples Low Level Concentration g kg SED PS where Xs is TurboMass concentration is RRF Ws D Ws D where Ax Area of the characteristic ion EICP for the compound to be measured from integration results Ais Area of the characteristic ion EICP for the specific internal standard from integration results ls Amount of internal standard added in nanograms ng from appropriate Concentration column of the sample list as defined in the Quantify Method RRF Average relative response factor from the heated purge of the calibration standard from calibration file D Adjustment for dry weight basis 100 Y moisture 100 calculated from Moisture value in sample list Ws Weight of sample added to the purge tube in grams g Sample Wt from sample list Df Dilution factor This is not included in the EPA equation but is being included here for consistency and to avoid the need for special cases in the software Xs is the target concentration amount This is calculated based on a concentration entered for the internal standard in the Sample List 758 Concentration ug kg Appendix F Environmental Reporting Calculations Soil Sediment Samples Medium Level where Ax Ais RRF Vt Va Ws Df Ais RRF Va Ws D Va Ws D
90. better than the Moving Mean However Savitzky Golay does tend to produce small artifacts on either side of the real peaks Noise Reduction is optimized for single GC peaks in the signal to noise range of 3 1 to 200 1 A window containing multiple GC peaks may lead to a loss of GC peak resolution Smoothing a chromatogram and or reducing noise 1 Select Smooth from the Chromatogram Process menu to open the Smooth chromatogram dialog 397 TurboMass Software User s Guide W Smooth chromatogram E xj m Method Window size scans E OK Number of smooths 2 a Cancel C None C Mean Savitzky Golay T Noise Reduction 2 Set the Window size parameter The number you specify is the half width of the smoothing window in scans This parameter can be set automatically by right clicking and dragging the mouse across a chromatogram peak at half height 3 Select a Smoothing method Mean or Savitzky Golay 4 As required adjust the number of times the smooth is repeated by changing the Number of smooths parameter Increasing this parameter gives a heavier smooth 5 Select Noise Reduction to apply noise reduction to a chromatogram NOTE Ifyou only want to apply Noise Reduction without applying smoothing select None and then select Noise Reduction 6 Click OK 398 Chromatogram E File Edt Display Process Window Help le x 2 ala slala wla Lalefe Of Le lelez Prepared standard 50 STAND
91. button as well as a definition in the status bar at the bottom of the window The toolbar is displayed by default You can hide the toolbar by selecting Toolbar from the View menu in both GC Editors A status bar appears at the bottom of each GC editor that displays a short Help message explaining the function of the command you highlight in a menu or the button that the mouse is positioned over The status bar is displayed by default You can hide the status bar by selecting Status Bar from the View menu in both GC Editors GC Control Configuration When you open the Configuration Editor the screen displays information defined during configuration Configuration Editor BIB sei ele a Name Type Acq Port LINK Port Configured Your name for the GC The GC model or type The physical data acquisition port to which the 600 Series LINK Interface is connected The physical port to which the GC is connected Displays Yes if you have provided all the information TurboMass needs to configure the GC Otherwise the status is No 143 TurboMass Software User s Guide 144 IPM Shows whether or not the Instrument Personality Module IPM for the GC has been downloaded The first time you open this window the IPM will not have been downloaded Once configuration is complete the area below the Configuration Editor Summary list displays key GC information On the left is information about the LINK inte
92. by Sample in the Summary section and then click OK 287 TurboMass Software User s Guide 4 5 CAUTION Select the data file of interest by pressing the left or right arrow icons Remove any undesired peaks by double clicking on the peak name and pressing DELETE and then click OK When you are ready to update the Quantification method with the retention times in the list select Update Retention Times from the Process menu The update is immediate and irreversible Creating a new Quantify method Select New from the Quantify File menu The editor parameters are set to default values and the Compound list is empty The name of the current method in the editor title bar is set to Untitled Add the desired compounds as described below Select Save As from the Quantify File menu Enter the name of the new method into the Save As dialog Selecting an existing Quantify method Select Open from the Quantify File menu Select the required method file from the file selection dialog and click Open The compounds within the method appear in the Compound list The first compound in the method is selected Propagating general parameters to all compounds gt To use the same integration parameters for all compounds in the method select 288 Propagate General Parameters from the Quantify Method Editor Edit menu Quantify A check mark will appear next to this option and the general parameters will be copie
93. by sample I Calibration curves T Quantify samples Cancel Format 5 Quantify Choose the reports you want to print by selecting the appropriate checkboxes Click OK to save changes and open the Print dialog Set the print and print setup parameters as required The Quantify Report margins can be changed by clicking Margins Click OK to print the Reports Changing the format of the Quantify reports l To open the Quantify Report Format dialog either select Report Format from the Quantify File menu OR Select Print Report from the Quantify File menu to open the Quantify Reports dialog and then click Format Quantify Report Format x eooo c a Sample Report Summary by compound Portrait 7 Horizontal graphs fi Summary by sample Portrait 7 Vertical graphs Ja Calibration curves Portrait z I Display Table Quantify samples Portrait bd r Page Header S l M Page Numbers Footer Cancel Enter the required text in the Header and Footer fields to create a customized header and or footer that will appear on each page of the Quantify Reports Select or deselect Page Numbers to turn page numbering on or off as required Set the Sample Report parameters to specify the number of Horizontal graphs and Vertical graphs you want to display on one page of the Sample Report 317 TurboMass Software User s Guide 318 5 7 If you want to print out a summary table of
94. can be set to High Medium or Low Annotating a particular peak e Hold down the CTRL key and right click the peak you want to annotate with the mass label e To remove the mass label from the peak hold down the CTRL key and right click the peak a second time Removing Spectra from the Display You can remove the currently selected spectrum by pressing the DELETE key A dialog will ask you to confirm the deletion Clicking OK will remove the spectrum from the display This operation does not affect the data stored on disk You can also remove traces using the Remove Spectra dialog This is a faster method if you want to remove more than one spectrum Removing multiple spectra from the display 1 Select Remove from the Spectrum Display menu 2 The spectra in the current window are listed in the order in which they appear on the display You can select one or more spectrum by clicking in the list Clicking again on a selected item will cancel the selection You can select all the spectra by clicking All 3 Click OK to exit r Ca ae 3 GAS2 Scan El 1644 Combine 2 GAS2 Scan El 1394 443 TurboMass Software User s Guide 444 Real time Display of Spectra You can display each new spectrum as a data file is being acquired by clicking or by selecting Real Time Update from the Spectrum Display menu Each spectrum window has a separate real time update switch You can see the state of the switch for a parti
95. can define up to five different magnified regions of the chromatogram Click OK to redisplay the chromatogram with the data in the selected region magnified by the requested factor The magnified regions are displayed in a different color and labeled with the magnification factor Magnifying the range of the intensity axis using the Toolbar gt Click Q to increase the magnification of the current range The current magnification factor is multiplied by 1 5 and rounded up to the nearest even number to give the increased magnification factor If the initial magnification factor is 2 this will give subsequent magnification factors of 4 6 10 16 etc Click cy to decrease the magnification of the current range The current magnification factor is divided by 1 5 and rounded down to the nearest even number to give the decreased magnification factor If the initial magnification factor is 16 this will give subsequent magnification factors of 10 6 4 etc Changing the magnification of a particular range gt Double click the magnification description of the magnification range to display the Chromatogram Magnify dialog Enter the new magnification factor and click OK to exit Deleting magnification ranges 1 To delete a single modification a select the magnification description that appears above the range and click to indicate the currently selected range The description will change color to red 383 TurboMass
96. change the hold time duration of a level select the point that represents the time and drag it horizontally If you selected capillary mode during instrument configuration set the Length and Diameter of the column under Column Turn on the Vacuum compensation for the column If the instrument is configured with auxiliary pneumatics enter the Auxiliary Pneumatics setpoints for any auxiliary zones Under Split Control select a split control mode If you select Ratio enter a split ratio in the Ratio field OR If you select Flow enter a split flow in the Flow field GC Control Setting GC Valves You can use the Instrument Timed Events tab of the Instrument Control dialog to enter the initial settings for any valves installed on the GC 1 Select the Instrument Timed Events tab of the Instrument Control dialog The Valves group reflects the system configuration Instrument Control i SEU One Gf 2 MONE Si S NONE e nE 4 NONE an of 2 NONE Sih SP is 6 RONE SLi 2 Under Valves set the Initial Setting buttons to On or Off for each valve 169 TurboMass Software User s Guide Setting GC Detector Parameters NOTE These parameters apply only if you have additional conventional detectors installed on the GC You can use the Detectors tab of the Instrument Control dialog to control the sensitivity of detection during the analysis as well as the magnitude of any optional analog output from the GC
97. chromatogram and select Scan or Time as the horizontal axis unit from the Chromatogram Display menu 3 To display the new spectrum in the Library Hits window click Update 4 Click OK Library Selecting a new search spectrum from a different data file 1 Click OR Select Open from the Library File menu to open the Library Data Browser dialog Library Data Browser x File Name Directories 50STD630 RAW c turbomass data 8270 50SDB630 RAW cv ca 5O0STD630 RAW E TurboMass ISTD7114 RAW amp pata Help STD6274 RAW gt 8270 z TNMX7104 RAW Experiment fh Delete Drives cS z Network r Information Sample 50 ng 8270 Mix Description Acquired 30Jun 1997 11 04 22 Eunction Scan 35 500 El x History Raw Data 2 Select the new data file from the File Name list 3 To select a processed spectrum that is the result of Combine or Refine processes click History 4 Click OK The Hits window is updated to show Scan 1 of the new data file which becomes the current search spectrum 495 TurboMass Software User s Guide 496 Selecting a new search spectrum from the Spectrum window gt Select a new spectrum by using the Data Browser by clicking EJ or Display Spectrum Ifyou initiate the Library search from the Spectrum window the spectrum currently displayed in the Spectrum window is used as the search spectrum For more information see Spectrum on
98. clear the audit log Do this periodically because a very large audit log may slow TurboMass processing View Newest First When selected displays the most recent event first Oldest First When selected displays the events in order of occurrence the first event in the list is the oldest Detail Displays detailed information about a selected Audit Log entry 678 Appendix A TurboMass Security Event Detail Refresh Reopens the Audit Log 679 TurboMass Software User s Guide 680 Appendix B TurboMass Software Installation Appendix B TurboMass Software Installation TurboMass Software Installation NOTE The computer must have Windows XP with Service Pack 2 installed as the operating system The TurboMass software is preloaded on your system by your Service Engineer however there may be a time when you need to reinstall the software or upgrade from a previous version This procedure describes how to upgrade or reinstall the TurboMass software If you have any questions or you need to re configure the Ethernet communications to the mass spectrometer please contact your local PerkinElmer Service Representative During the installation you will be prompted to do the following e Confirm the installation directory e Confirm your setup options e Confirm your instrument pre configuration options IMPORTANT Before installing TurboMass v5 2 first uninstall the existing TurboMass Commu
99. compounds mix Enabled if the Analysis type is Volatiles or Semi volatiles Vol surrogate added An edit box that indicates the volume of surrogate standard added to the sample This field is enabled if the Analysis type is Volatiles or Semi volatiles ISTD lot no A text field allowing identification of the lot number of the internal standard compounds mix Enabled if the Analysis type is Volatiles or Semi volatiles All concentration calculations for target compounds are made relative to an internal standard Sample List gt Click the Lab Information tab and enter the Lab Information for this sample Lab information displays for each Sample ID in the Sample List These values typically do not change on a per sample basis so they have been put in this second tab to simplify the user interface amp Sample List Wizard Sample List Sample Information Row Sample ID il Sample Rows Concentrations Add Cone A Conc B Cone C Cone D Cone E Cone F 0 0 0 0 0 0 Insert gt Sample Tracking Delete Submitter Task Job Contract EPA Sample No Case No ENEN List File SAS No SDG No Save Lab code Save s Files GC Method MS Method Quantify Method Calib Curve Qualitative Method lel lel Le Le Le Concentrations Display The concentrations grid with a horizontal scroll bar contains cells for you to enter standa
100. control is not available for internal standards MDL Soil An edit box to indicate the MDL minimum detection limit for the selected compound in soil samples Concentrations below this value will not be reported This control is not available for internal standards For the purposes of environmental reports the term MDL is used to indicate the threshold value for the U qualifier flag Values below this threshold value will flag the compound with a U in the Form 1 report and no concentration value will be printed When using a Minimum Detection Limit MDL and Reporting Limit values the TurboMass software handles the calculations for a straight dilution by using a dilution factor However if you modify the samples e g volumes or weights then you should refer to the EPA equations specified in OLM04 2 or SOM11 to adjust the MDL and or Reporting Limits for differences between the nominal specified in the method and the actual sample volumes and weights Quantify Response Factors For each target and surrogate compound you can define Minimum RRF An edit box that defines the minimum acceptable RRF Relative Response Factor to the internal standard for this compound 0 0000 to 9999 9999 or left empty in initial and continuing calibrations IMPORTANT f you change the Minimum RRF value Maximum RSD value and or Maximum Difference value you must reprocess recalibrate the sample list for this new value to be
101. delete and edit user accounts Create delete and edit groups Assign access privileges to groups Group rights policy Set the account policy Disable Security Set the audit policy View and manage the audit log TurboMass Security and TurboMass cannot be run simultaneously Close TurboMass before opening the Security application If Security is enabled when TurboMass is opened the user is required to log on to TurboMass by entering a username and password into the Login dialog Logging on to TurboMass with Security enabled l Double click the Security icon in the TurboMass program group to open the Security Manager dialog 665 TurboMass Software User s Guide 666 TurboMass Security Manager User Policies Tools View Help elel Ee Fale Description TurboMass Administrator Built in account for administering TurboMass cmon Members Can fully administer TUOM ASS nnn If security is enabled TurboMass displays the Login dialog TurboMass Login x Type a logon name and password to log in Logon Name Administrator Cancel Password If the following message is displayed verify the password and username TurboMass could not log you on Make sure your username is correct then type your password again Passwords are case sensitive so please make sure that Caps Lock is not accidentally on If the message remains verify that the user has a valid account with Security Make sure that
102. displays the number of the current page and the number of pages in the report Either side of the text are buttons that display from left to right e The first page in the report e The previous page in the report e The next page in the report e The last page in the report Displays a single page of the report in the preview area Displays the drop down palette from which a multi page layout can be selected Selection of a multi page option will change the display in the preview area to that format assuming the report contains sufficient pages A drop down list that enabled the user to select a zoom factor for the report display Displays a standard Windows Save As dialog enabling the user to save the current Communiqu data source as a file which may later be loaded into the Communiqu Designer as preview data when editing templates Sample List Report Preview Action Toolbar Control Print Current Print All Cancel All Reports Next Preview Description A command button that prints the current report where print is defined within the Report Method and closes the preview window The next report from the sample list if any will be previewed A command button that prints the current report enables printing for all future reports from the sample list where print is defined within the Report Method and closes the preview window Future reports will not be previewed A comma
103. downloaded method l Select Modify Active from the GC menu or double click the GC portion of the system icon in the Acquisition Control Panel OR Right click the active method in the Inlet File cell in the Sample List The GC method in use appears in the Modify Active Method Editor window In the Modify Active window select a command from the Instrument menu to modify the parameters associated with that command Save your changes after editing method parameters Note that the Save As command is not available because you cannot save the changes as a new method Close the Modify Active window The GC Status field will display different messages based on the instrument you are using While you are modifying the method the instrument state will be Paused It will change to Resumed when you close the Modify Active window Function List Editor 8 Function List Editor Introduction The Function List Editor is used to set up the function s that the mass spectrometer will use to scan the instrument during an acquisition A function list can be a mixture of different scanning techniques that can be arranged to run either sequentially or concurrently during an acquisition Typical uses for mixed function acquisitions are to acquire different SIR groups over different retention windows and the ability to switch MS scan mass ranges during an acquisition A function list is produced saved on disk and then referenced by name when you
104. drive or directory 5 Click OK to exit the Map Data Browser dialog 6 Alter values as required in the Create Datafile Map dialog and click OK A status bar at the bottom of the map window will keep you informed of the progress of the Map process Stopping the Map process before it has been completed gt Click OR Select Stop Process from the Map Process menu 529 TurboMass Software User s Guide 530 About the Map Display The Map display has three parts The top trace shows a mass chromatogram of the currently selected mass The lower trace shows the spectrum for the currently selected retention time The middle trace shows the map display of mass against retention time for the data file Each block of color represents the intensity of a particular mass at a particular retention time You can select a mapping mode and color scheme for the map display using the Display Scale options The currently selected mass and retention time can be changed by moving the cross hairs cursor over the display Moving the cursor in the vertical direction changes the current mass Moving the cursor in the horizontal direction changes the current retention time The current cursor position is shown on the right side of the status bar at the bottom of the display Double clicking on the mass chromatogram will open the Chromatogram window with that mass chromatogram displayed Double clicking on the spectrum will open the Spectrum window
105. edit these two lists 2 To add a field select the field you want to add from the Fields list and click Append 3 To remove a displayed field from the Hit List window select the field you want to remove from the Format list and click Remove 4 To insert a new field between two currently displayed fields select the field you want to insert from the Fields list then in the Format list select the field before which you want to insert the new field and click Insert 5 To modify the justification for any fields select the field for which you want to change the justification from either the Fields or Format lists click Library Justification to open the List Field Justification dialog select Left Right or Center justification modify the Field Size Width Significant Figures SF and Decimal Places DP as required repeat as required and click OK to return to the Format DB List dialog List Field Justification Cancel Field Name CAS hd Field Size al Justification Width cs ils Left C Centre C Bight 6 Repeat steps 2 5 as required for each change you want to make to the Hit List window fields 7 To view the results of your changes without exiting the dialog click Update 8 Click OK Hits Window The Hits window displays the search spectrum with up to four of the hits spectra The header above each hit spectrum shows the hit number fit value the library name
106. elapse between the start of the run and when data analysis starts In the Run time field enter the number of minutes for which you want the interface to collect data Note that the run time must always be greater than the delay time Select Store run log to upload the run log at the end of each run When you select this option TurboMass prints the GC run log as part of the report Store run log is available even when there are no additional detectors installed on the GC To save your work and close the dialog click OK Setting Control Options 159 TurboMass Software User s Guide 160 The Control Options command in the Instrument menu opens a submenu that has additional commands for controlling your instruments When you select a command from this submenu TurboMass opens the Instrument Control dialog which contains tabs for each major control command Setting control options parameters Select Control Options from the Instrument menu and select a command from the cascaded menu The Instrument Control dialog opens to the tab corresponding to the command that you selected Select the tab for each control option that you want to complete or edit Make any changes to the values in the dialog To save your work and close the dialog click OK To save your work without closing the dialog click Apply To close the dialog and discard your changes since the last time you clicked Apply click Cancel The following sections desc
107. enter a new name into the File Name field and click Open Click Exit Appending a single peak to the current Peak List Select Peak List Write from the Chromatogram Edit menu to display the Edit Peak List dialog Select the peak you want to append either from the Peak Tops list or by right clicking the peak in a chromatogram trace Click Append The contents of the Peak List list will be updated to include the new peak 415 TurboMass Software User s Guide 416 4 To append all the peaks in the Peak Tops list click Append All Deleting a single peak from the current Peak List 1 Select Peak List Write from the Chromatogram Edit menu to display the Edit Peak List dialog 2 Select the peak you want to remove from the Peak List list 3 Click Delete 4 To delete all the peaks in the peak list click Clear All Reading a Peak List into a Chromatogram Use the following procedures to select a peak list file and read a single peak or the entire peak list into the currently selected chromatogram Selecting a Peak List file 1 Select Peak List Read from the Chromatogram Edit menu 2 Click File to display the File Open dialog 3 Select a file from the list and click Open 4 Click OK Reading a single peak into the currently selected chromatogram 1 Select Peak List Read from the Chromatogram Edit menu 2 Select a peak from the Peak List list 3 Click OK Chromatogram Reading a whole peak list into t
108. exp 10 x File Edit Options Toolbars Functions Solvent Delay One Solvent Delay olslals ata y g scan g SIR Total Run Time 45 00 gt t Eri Now type e ine 1 Solvent Delay 1 Start 0 00 min End 5 00 min Ef SIR of 3 masses Time 5 00 to 15 00 El Z SIR of 3 masses Time 15 00 to 25 00 El ZF SIR of 3 masses Time 25 00 to 35 00 El E SIR of 3 masses Time 35 00 to 45 00 El Figure 8 Function List showing multi functions Up to 32 functions may be created in the function list A more advanced technique Selected Ion and Full Ion Scanning SIFI has a mix of MS scan and SIR functions As an example it may have a single full MS scan method that runs for the entire chromatogram and multiple SIR functions timed for the elution of specific compounds This allows both the universality of full scan analysis with the ability to library search and the higher sensitivity of SIR 195 TurboMass Software User s Guide 196 Function List Editor Adding a New Function A new function can be added either by clicking one of the function buttons at the top of the editor or by selecting MS Scan or SIR from the Functions menu The editor for the function type selected will be displayed showing default values Make any changes required to the parameters and click OK to add the new function Modifying an Existing Function An existing function can be modified by double clicking on the function in the function
109. feo o0 e Median p Centered spectrum Ca Heights _ Strip and Combine Functions 2 Set the following parameters and click OK Peak width at base amu Baseline threshold Top Centroid Median Specifies the expected width of the continuum peaks at baseline It has two purposes first it determines the amount of smoothing that is applied to the continuum spectrum prior to centroiding proper and second it determines how close together two sticks must lie in order to be grouped into a single stick that is it controls the multiplet resolution For smoothing the width at half height of the peak is estimated as half the specified width at baseline and it is this estimated value that is used in the smooth For multiplet resolution peaks closer than the specified Peak width at base distance together will be regarded as a singlet Specifies the minimum signal level in the spectrum above which a peak will be considered significant These parameters allow a selection of peak Top peak Centroid and peak Median methods to be made This functions as for the standard centroid software see Center on page 453 Similarly selection of peak areas or heights is the same as in Spectrum Setting CODA Options CODA operates on both centroid and continuum data It works by standardizing and smoothing each mass chromatogram in the dataset and then comparing the smoothed standardized mass chromatogram with
110. ff Files of type Sample Lists SPL x Cancel 2 Select a data file and click Open Creating a Sample List Using the Sample List Wizard The TurboMass Sample List window is in a spreadsheet format which allows easy editing of multiple samples but this becomes unwieldy when there is a lot of information required for each sample The Sample List Wizard is a forms format equivalent display It allows for easier editing of the large amount of per sample information required of environmental and QA QC samples The Sample List Wizard enables you to select an existing sample list or create a new one Only the parameters required for the current type of analysis VOA SV or QA QC and current matrix water soil are displayed The controls are grouped in a way to allow efficient entry of sample specific data It also provides the ability to propagate changes made to one row to subsequent rows a command to update vial numbers a command to update sample IDs Several fields have automatic incrementing of numeric values and there are commands to insert delete and add sample rows Sample List NOTE All environmental reporting users should use the Sample List Wizard to ensure that all sample information is entered You can enter or modify all of your environmental and QA QC sample list parameters using the Sample List Wizard You can still edit directly from the Sample List The recommended approach to using the Sample List Wizard is to cre
111. focus Selecting an item prepares it for an action for example when you select text it appears in reverse video When you select a dialog option you activate the option but the function is not carried out until you click OK which closes the dialog and sometimes completes another operation Enter or select When you use the File Select or File Open dialog to open a file the phrase enter or select is used to refer to the actions you can take to open that file When you enter a filename you type it in the File Name field exactly as it exists When you select a file you browse for it on your computer or your network When you select a file you will not introduce typographical errors Unless otherwise indicated the values in the illustrations of this manual are examples only They are not intended to indicate the exact values you will see or to suggest the values you should use for a specific application Getting Started 2 Getting Started Getting Started Starting TurboMass To start TurboMass Double click the desktop shortcut OR Use the Windows Start menu If TurboMass Security is enabled the TurboMass Login window opens Enter your Logon Name and Password and click OK The TurboMass menu bar will appear at the top of the display If you have trouble starting TurboMass there may be a problem with your Security setup See Appendix A TurboMass Security on page 659 Quitting TurboMass To terminate a TurboMass se
112. for each selected calibration type 117 TurboMass Software User s Guide 118 Overview Of The Calibration Process Check the Instrument Tuning The mass spectrometer should be in Operate mode with Reference gas on Check that the peak shape and intensities are correct Set the Calibration Parameters 1 Select the appropriate reference file for the calibration reference sample that you are going to use typically HEPTA REF 2 Ifrequired set the automatic calibration checking parameters in the AutoCal Check Parameters dialog These parameters control how closely the recorded data must match the reference file 3 Ifrequired set the Peak Match and Curve Fit parameters in the Calibration Parameters dialog These parameters control the location of reference peaks in a calibration spectrum and the drawing of a calibration curve to correct the resulting mass differences 4 Ifyou are calibrating continuum or MCA data types you should set the Mass Measure parameters These parameters control peak detection in continuum and MCA data There is no need to set these parameters if you are using centroided acquisition the typical GC MS data acquisition mode Start an Automatic Calibration 1 From the main Calibrate dialog click Calibrate Start Acquisition to open the Automatic Calibration dialog 2 Select the types of calibration you want to perform 7 Mass Calibration Usually all checkboxes should be selected S
113. for the Analysis type Form 6 The data for Form 6 will be taken from the Calibration file referenced by most of the rows in the sample list The general checks will have ensured that only one Calibration file is referenced This Calibration file can be taken from any sample row other than the Tune Eval which is ignored The first Analyte or Analyte Dup row found in the selected rows of the sample list will be marked as the source of the header information for Form 6 The file name of this sample will be displayed on the Form 6 tab The user can change this assignment if necessary Errors No errors specific to Form 6 Warnings No warnings specific to Form 6 Form 7 Primary data for Form 7 will be taken from a Cont Calib sample The default Cont Calib will be the last Cont Calib sample row selected in the sample list Errors If no Cont Calib sample was located in the rows selected for processing according to the rules given above then an error message will be displayed Form 7 Error No continuing calibration sample identified Warnings No warnings specific to Form 7 Environmental Reporting Form 8 Primary data for Form 8 will be taken from a Cont Calib sample which may be the Mid Level of an Initial Calibration with summary information from other samples types other than Tune Eval Cont Calib or Init Calib types The default Cont Calib to be used as the primary data set will be determined as follows e Ifthe selected
114. fs Erom fi To fi Browse Eea iji Cancel Select the Static Scanning or Scan Speed Compensation calibration type Use the default or click Browse and select a file The default files are STAT RAW for the static file SCN RAW for scanning and FAST RAW for scan speed compensation Optionally enter a range of scans to combine From and To 131 TurboMass Software User s Guide 5 Click OK Recalibrating a Data File This option allows the current calibration to be applied to a previously acquired data file 1 Select Recalibrate Data File from the Calibration Process menu to open the Display Calibration Graphs dialog 2 Click Browse and select the data file you want to recalibrate 3 Click OK 132 Mass Calibration Editing a Reference File The table below lists the contents of the file Hepta ref that is the standard reference for EI calibration Calibration reference files consist of two columns of numbers separated by any number of spaces or TAB characters The first column contains the reference peak masses the second column contains the reference peak intensities The reference peak intensities are not at present used by the calibration software and so can be set to a nominal value of 100 However you may wish to enter realistic values here to improve the appearance of the reference spectra 49 99379 0 73 68 99518 100 00 99 99358 6 31 118 99199 7 80 130 99199 36 31 149 99039 1 29 16
115. if you add an autosampler to a GC you must reconfigure the LINK and GC as you did when you initially configured your GC As you are starting with a configured LINK and GC you must first disconnect the GC from TurboMass control and clear the LINK configuration l In the TurboMass top level window select Release Control from the GC menu to release TurboMass control of the GC Releasing the GC from TurboMass control lets you control the GC from the keypad The GC front panel display changes from External TurboMass to Method control where Method is an internal GC method 149 TurboMass Software User s Guide 150 2 Make the required changes from the GC keypad 3 To update your GC configuration in the TurboMass Configuration Editor select Configure from the Instrument menu to open the GC Configuration dialog and either click Query Inst for Config to obtain your updated parameters from the GC then click OK OR Enter your changes in the GC Configuration dialog and click OK to update your GC configuration For more information on setting the GC parameters see Setting the GC configuration options on page 147 Changing the Instrument Configuration 1 Select your instrument in the Configuration Editor 2 Select Disconnect from the Configuration Editor Instrument menu respond to the confirmation message that appears and click OK TurboMass clears your LINK port and GC configuration information 3 T
116. it with another A different time offset can be applied to each of the GC detectors acquired Only the display is affected the data on disk remain unchanged This only works if the horizontal axis is displayed as time and not scans Aligning two chromatograms 1 Select a chromatogram 2 Select Align from the Display Range dialog 3 Enter the Offset time that is required to line up the two chromatograms and click OK 379 TurboMass Software User s Guide 380 Manipulating the Display You can alter the displayed ranges of the horizontal and vertical intensity axes and set the magnification ranges Altering the Horizontal Axis Do one of the following to alter the range of the horizontal axis Altering the range of the horizontal axis zoom e Use the mouse Left click at one end of the region of interest and drag the mouse horizontally to the other end A line appears across the range you have selected Do not go beyond the bounds of the axis When you release the mouse TurboMass redisplays the selected region to fill the current window Repeat this operation as often as required e Use the menu 1 Select Range From from the Chromatogram Display menu 2 Enter new From and To values for the horizontal axis 3 Click OK Centering the display around a point on the horizontal axis 1 Select either Range Center On Scan or Range Center On time from the Chromatogram Display menu Only one of these items wil
117. less storage space is required The disadvantage of MCA is that as there is only one scan it cannot be used for time resolved data For MCA scans this defines the number of scans to sum to create a spectrum Specifies the retention time in minutes at which this function will become active that is data acquired and stored 201 TurboMass Software User s Guide 202 End Time Specifies the retention time in minutes at which this function will cease to be active that is data acquired and stored Scan Time Specifies the duration of each scan in seconds Inter Scan Specifies the time in seconds between a scan finishing and the Delay next one starting During this period data is stored but not acquired The total time for a scan Scan Time Inter Scan Delay Scan rate Start Mass End Mass Scan Time Da sec Scans sec 1 Scan Time Inter Scan time Setting Up an SIR Function The SIR Selected Ion Recording technique is typically used in those situations where only a few specific masses are to be monitored during an acquisition Since most of the data acquisition time is spent on these masses the SIR technique is far more sensitive than full scanning The signal to noise ratio increases with the square root of the dwell time The SIR editor is used to enter the masses that you would like to monitor and their respective dwell time span and inter channel delay time When possible we try to monitor ions c
118. likely to differ for each mass chromatogram E File Edit Display Process Window Help Noise Com 2 Lo Be Laja u 4 Peseta 26784 00 Cancel da and mda TDAS0992 iad Smooth Enable smoothing Copy 100 Peak detect Paste Threshold 7 00 i i 11 00 Retention time window 0 26 11 29 11 55 Enable You can choose to smooth the chromatogram before integrating smoothing by selecting Enable smoothing The parameters for the smooth can be examined and altered by clicking Smooth For more information see Smoothing Chromatograms on page 397 Threshold Small peaks can optionally be removed by setting one of the four available threshold parameters Click Threshold to open the Response Threshold dialog where you can examine or modify these parameters 400 Chromatogram Response Threshold Relative height Removes peaks whose height is less than the specified percentage of the highest peak Absolute height Removes peaks whose height is less than the specified value Relative area Removes peaks whose area is less than the specified percentage of the largest peak area Absolute area Removes peaks whose area is less than the specified value You can examine and modify the parameters that control the positioning of baselines and separation of partially resolved peaks by verticals droplines by clicking Peak detect in the Integrate chromatogram dialog to display the Peak Detect dialog
119. list This will bring up the appropriate editor for the function type and allow you to change the function information When you have finished editing the function the function list display will be updated to show any changes Removing a Function You can remove a function by selecting it and then selecting Delete from the Edit menu Changing a Function s Start and End Times You can change the start and end times of a function by going into its editor as described in Modifying an Existing Function on page 196 The Total Run Time field in the Scan Functions window shows the total run time for all the functions Entering a new value in the Total Run Time field and clicking will set the maximum retention time for the experiment The ratio of the functions defined will be maintained For example if two functions are defined one from 0 to 5 minutes and the other 5 to 10 minutes then a Total Run Time of 10 minutes will be displayed If this value is changed to 20 and is clicked then the first function will now run from 0 to 10 minutes and the second from 10 to 20 minutes Function List Editor Setting a Solvent Delay A solvent delay can be set for a function list using the Solvent Delay Time control No data is stored during the solvent delay period which means that solvent peaks that would normally be seen eluting at this time on the TIC chromatogram of the acquired data will no longer be seen The filament in the source is turned off
120. main calibration dialog select Calibrate Instrument from the Calibration menu on the Tune page 115 TurboMass Software User s Guide 116 How A Calibration Ils Formed A mass spectrum of a reference compound a calibration file is acquired and matched against a table of the expected masses of the peaks in the reference compound that are stored as a reference file Each peak in the reference file is matched to a corresponding peak in the calibration file The mass differences between the reference peaks and calibration peaks are the calibration points A calibration curve is fitted through the calibration points The vertical distance of each calibration point from the curve is calculated This distance represents the remaining or residual mass difference after calibration The standard deviation of the residuals is also calculated This number is the best single indication of the accuracy of the calibration Mass Calibration Calibration Types TurboMass requires up to three calibration curves e A static calibration is used to accurately park the quadrupole mass analyzer on a specific mass of interest in Tuning and SIR for example e A scanning calibration enables peaks acquired in a scanning acquisition to be mass measured accurately e A scan speed compensation calibration compensates for lag time in the system when the instrument is scanned rapidly A separate mass spectrum of the reference compound is acquired
121. mouse button down and drag the edge to the proper size Click in the Text Block and type for example Project Name Highlight the text and right click to display the text formatting options nuniqu Report Creator File Edit View Format Actions Tools Help Communiqu Reporting x MACAE TEEME EEEE mils z n Qualitative Report 1 3 Header TEXT4 TEXTS TEXT3 TEXT2 2 Standard Footer 1 TEXTI E a Page Type 1 Acquired Sample ID Mise Into 23 Full Filename 24 Creation Date Time 25 Sample Description 28 Conditions Project Name DATAAB Printed 33 DateTime Page 34 PageX TEXTS Peak Number Retention Time CHROMATOGRAM PLOT GRAPH HEADER Area DATA45 Area DATAA D Nom Z DATA E GRAPHIC Project NamefDAT TEXT12 a 3 D Height DATA4 a 3 E23 Chromatogram Plot E L OBJECTFRAM amp Chromatoay S E TABLET Texts TEXT TEXTS TEXT10 TEXT E Position 3 1 75 Width 1 96 Height 0 4 wee Dew wo ww 7 Click Save As from the File menu name and save your file 8 Exit the Report Designer Layout Tools Data Objects User Name Software Version Instrument Type Instrument Name Inlet Interface Type Lab Name oject Project Name Project Directory Project Date Time Samples 3 Sample ID Concentrations Conditions Sample Description Tas
122. neve ain ade eae exladind Poa clnivens niet 30 Changing Colors and Fonts cccccccscsssscesseeeeeeeeeeeeeeeseeeseeeseeeaeeeaeenaees 31 TurboMass System Global Parameters ccccccsessecsseeeeeeeeeeseeeeneeenes 34 PLOCESSES mongira eane ee E A EAA E a TETE 35 Mass Defect Correction cccsceeceseseeeeseesecceeceesecaecaeeaeeeeeaecaeeeneeaeenee 36 TURBOMASS IN ction neeaae a n a E AE 37 Selecting and Viewing Data cccccccccescesscesseeeeeeeeeeeseeeseecseeeseeesseenseeeaeens 38 The Data Browsers eerte aa a eE a aae Saa Eaa 38 Experimental Record ccccccccecsseesseesceeseessecssecnsecnseceseeneeeeeeeeeeeseneenses 41 Deleting a Raw Data File 0 eeccecccecsecseeeneeecceeseceseceeeeeecseeeeseeeeneenaes 42 History Selector sss scccseccasssdssin sets da rina PA a ees E O iA e RAe 42 Processed Data Labels ccecccecscesseesseesecsecesecesecnsecnseeeeeeseeeeneeeeneenaes 44 Using Explorer to work with Multiple Data Files 0 00 eeeeeeereeeeees 45 PHOJOCUS N ssh E E gcdoads sadedude Taaedaa stabbed T 47 Directory Structures steciei ecsecadscel cached sdaesstus Bidets dab eesti aani ida weve cats 49 Data Prle Structure eer hein dantied ck ative wants 50 Displaying Spectra ccccccsccesscsecesseeeseessecsseceseceseceseceseeeeeeseeeseeeenneeeaes 51 Displaying Chromatograms cccccccscecssecsteceseceneceeceeeeeeeseeeeeeeeeneenses 52 The Header Editor srcima e ee os taceeucs e singel des Geese 54
123. new group name appears in the list of groups Deleting a user account or group 1 To delete a user account or group select the user or group from the relevant list in the Security Manager dialog and select Delete from the User menu 2 Click OK to confirm the deletion Security removes all traces of the user account or group If you create a subsequent user or group with the same name TurboMass treats it as a new user account or group For example you will need to set up group rights and group membership for the new group NOTE The Administrator user account and the Administrators group cannot be deleted Assigning group rights 1 Select Group Rights from the Policies menu OR 674 Appendix A TurboMass Security Click to open the Group Rights Policy dialog Right Administer user accounts and groups Grant To Administrators Assign The dialog lists the group s that have access to the currently selected right Right A group of access privileges that can be granted to groups The Administer User Accounts and Groups right refers to the various tasks performed within the Security Manager any group granted this privilege can modify user accounts and groups and perform policy changes such as changing group rights This right should only be assigned to groups that require administrative privileges Grant To The list of groups that have the currently selected right From the Right drop down list selec
124. new printer in the Printers dialog under 389 TurboMass Software User s Guide 390 a custom name and select this printer as your default Purge the print documents when done as described above Annotation Threshold Parameters Annotation Allows you to specify a minimum intensity for a peak to be labeled Threshold Full Scale Allows you to set a threshold as a percentage of the base peak intensity Intensity Allows you to set an absolute intensity threshold All Peaks Annotates all peaks regardless of intensity Level Determines the amount of labels that appear on the chromatogram The Level parameter can be set to High Medium or Low Removing Chromatograms from the Display You can remove the currently selected chromatogram trace by pressing Delete A message will ask you to confirm the deletion Clicking OK will remove the trace from the display This operation does not affect the data stored on disk You can also remove traces using the Remove Chromatogram dialog This is a quicker method if you want to remove more than one trace Removing multiple chromatogram traces from the display 1 Select Remove from the Chromatogram Display menu to display the Remove Chromatogram dialog Remove Chromatogram xl Chromatogram 2 The traces in the current window are listed in the order in which they appear on the display You can select one or more traces in the list Clicking again on a selected item will cancel the select
125. oP fo Right Change the Field Name to show the heading you want to display above the column Select the Justification setting to Left Center or Right as required Edit the Field Width Significant Figures SF and Decimal Places DP as required Click OK to update the Peak List window Changing the Current Peak List file gt To view another Peak List select Peak List from the File menu to display the 310 File Open dialog and select a peak list Quantify Displaying Peak List Chromatograms gt To display the chromatogram and peak associated with a Peak List window entry double click on the desired entry Manually Changing Quantify Results Although TurboMass can perform a complete automated quantification analysis from setting up a Sample List and acquiring data to printing Quantify Reports it is also possible to repeat individual Quantify processes and to manually edit results including e Manual editing of peak baselines e Editing calibration curves to exclude erroneous calibration points e Performing Quantify Locate compounds Calculate calibration curves or Quantify compounds processes Manual Peak Integration If the automated peak detection is not determining peak baselines satisfactorily it is possible to define the baselines manually This can be achieved by modifying the peak information held in the Peak Lists or by creating them from scratch 1 To display an integrated peak in Chromatog
126. of its own if the k Spectrum toolbar button is activated 51 TurboMass Software User s Guide 52 Removing spectra and document windows To remove a particular spectrum select the spectrum to make it the currently selected spectrum and press DELETE Click OK to confirm the deletion To close a particular Spectrum window click the Windows close button EX Displaying Chromatograms Like spectra there are several ways in which you can display the Chromatogram window The two most common ways are selecting Chromatogram from the TurboMass View menu and double clicking the Spectrum window Selecting chromatograms from Chromatogram Select Chromatogram from the View menu The chromatogram displayed will be the Total Ion Current TIC chromatogram of the current data file If the Chromatogram window is already on display it becomes the current window If whole rows are selected in the Sample List editor Chromatograms from the data files represented by these rows will be displayed Selecting chromatograms from Spectrum gt Double click the spectrum at the mass of interest The chromatogram displayed will be the mass chromatogram of the mass indicated by the click If the Chromatogram window is already on display the selected chromatogram will either be added to the one currently on display OR Will replace the one currently on display if the Chromatogram toolbar button is activated Getting Started OR Wi
127. of specifying a threshold Full Scale Intensity Allows you to set a threshold as a percentage of the intensity of the largest peak in the spectrum Allows you to set an absolute intensity threshold The threshold parameters are not applicable to continuum mode data 439 Style Overlay Graphs Fill Trace Graph Header Process Description Spectrum If selected multiple traces in the same window will be superimposed on the same axis If deselected the traces will be drawn on separate axes arranged vertically When spectra are overlaid only the currently selected trace is annotated If selected the area under the spectrum trace will be colored This option only applies to continuum type not centroid data Allows you to turn off the header information normally displayed at the top of the spectrum in order to produce data for publication If selected the header will be displayed if deselected the header will not be displayed Each process performed on a spectrum adds a summary of its parameters to the spectrum s header The Process Description option allows you to turn off only the process information and leave the remainder of the header on the spectrum Graph Header over rides Process Description That is if the Graph Header is turned off the Process Description will be as well Split Axis Is enabled when Overlay Graphs is selected Split Axis allows you to change the aspect ratio of the spect
128. on nominal masses for elements For example H is and Cl is 35 Formula and Mol Wt are compared within an entry and you are warned if there is a discrepancy Any text to a maximum of 30 characters Any positive or negative integer no decimal point or decimal point value These values can be used when setting filters for library searches or in the Process Locate dialog A string of one or more characters representing user specific information You can enter any characters you like including spaces to a maximum of eight characters The order and case of the characters are significant These values can be used when setting Filters for library searches in the Process Locate dialog or when selecting the Flagged Entries parameter in the Edit Library dialog Repeat step 2 as necessary Each time you select a new entry you are prompted to save the changes you have made Click Close and click Yes to save changes Indexing a User Library Before you can use a new or newly appended user library for searching you must index the library to create a Presearch file for it The Presearch file contains each library spectrum reduced to its eight most intense mass weighted peaks Indexing a library requires a lot of processing and may take considerable time depending on the size of the library The Library Reindex dialog displays an estimate of the time required to index the library Each time you add new entries to the library you need t
129. perform the analysis These samples can be acquired manually but more often they will be acquired automatically using an autosampler The Sample List Editor has various columns such as Filename vial or bottle Number and Sample Type that can NOTE Qualitative Method be filled in for each sample Each sample is displayed as one row in the Sample List The Sample List Editor is part of the TurboMass top level menu You need to tell TurboMass everything that it needs to know about the samples in the list in order for it to perform a complete analysis You must describe to the system what each of the vials in the autosampler contains i e whether it contains a standard an analyte a blank or a QC sample how to acquire it its concentration s if it is a standard or has internal standards In addition you must specify the name of the file in which to store the data You may also want to add some management information such as Sample ID the submitter s name or a sample description and the Report Method template used i TurboMass TUTORIALQUANT Untitled ioj x File Edit Samples Run View Quantify Configure GC Tools Help alela S a gt fmm an Waa taaa e lee e alll S12 Ee 7 Conditions Quantify Method Calibration Curve Qualitative Methoc Loo Gc File Name MS Method GC Method Vial Injector Sample ID m Oven Temp oc General Status For more information on how to create a Sa
130. picture is transferred as a bitmap to the Windows clipboard Copying the current hit list to the Clipboard gt Click to copy the current hit list to the Clipboard Retrieving data from the Clipboard Many Windows applications have an Edit Paste or similar command to read data in from the Clipboard Consult the documentation for more information You can use the Edit Paste command to copy bitmaps into the Spectrum and Chromatogram applications 511 TurboMass Software User s Guide 512 Refining the Search Spectrum The Refine process is used to identify only those masses that contribute to a specific peak in the TIC In this way Refine Search removes small peaks that are the result of background noise and can therefore improve library search results You supply two parameters for the Refine process Window Size and Noise Threshold The refine algorithm generates the summed mass chromatogram over a range of 1 Da centered on each integer mass in turn It examines these chromatograms for a number of scans equal to the window size around the peak top scan If a peak is present in this range for which the topmost point is within one scan of the peak top scan and more intense than the noise threshold value then this mass appears in the refined spectrum To refine the search spectrum 1 Specify new Refine parameters by choosing Refine from the Library Process menu to open the Refine Spectrum dialog Refine Spectrum Ea Window
131. range is 50 100 404 Chromatogram E Fie Edit Display Process Window Help la x aja wene wla eao o La lels da and mda TDAS0922 SIR of 2 Channels CL too 1464 397 20 419439 5 77e5 1580 Height 302840 9 1510 162576 E Fie Edt Display Process Window Help le x e alaj wene aju eaa O AAL ne 53 da and mda TDASO922 SIR of 2 Channels Cl 100 1464 _ 397 20 419439 1580 5 77e5 isee 304548 1603 Height 5 242538 isin 284696 2 164309 163 o 129240 1678 112122 Detect Shoulder peaks is selected in the Peak Detect dialog and is used optionally to attempt to detect completely unresolved peaks or shoulders The algorithm will detect a shoulder if the slope of the shoulder top is less than the specified percentage of the steepest slope on the peak Therefore to make shoulder detection more sensitive increase the value of this parameter The default value is 30 and the normal operating range is 20 90 Integrating a chromatogram 1 Display the chromatogram range you want to integrate 405 TurboMass Software User s Guide 406 2 3 Select Integrate from the Chromatogram Process menu Enter a value for Noise Peak to peak amplitude To calculate this value display a section of the chromatogram that contains only background Right click at one end of a section that contains background noise and drag the mouse to the other end of the noise section When the mouse
132. rather than from a button in the compound list 283 TurboMass Software User s Guide section of the Method Editor since all items in this dialog are global to the method and not compound specific To set QA QC Limits 1 From the Method Editor select QA QC Limits from the Edit menu QA OC Limits Internal Standard Area Lower Limits Internal Standard Area Upper Limits Internal Standard AT Limits mint 2 Make the following entries then click OK Internal Standard Area Lower Limit The value from 0 to 100 that defines the acceptable lower limit of the area measured for each internal standard peak in a sample compared to that in the most recent continuing calibration or mid level of the initial calibration if no continuing calibration has yet been performed Internal Standard Area Upper Limit Enter a value from 0 to 100 that defines the acceptable upper limit of the area measured for each internal standard peak in a sample compared to that in the most recent continuing calibration or mid level of the initial calibration if no continuing calibration has yet been performed Internal Standard RT Limits min Enter a value from 0 00 to 999 99 that defines the acceptable limits for the actual retention time of each internal standard peak in a sample compared to that in the most recent continuing calibration or mid level of the initial calibration if no continuing calibration has y
133. sample rows contain Cont Calib rows then the primary data set will be last Cont Calib sample row selected in the sample list e Ifthe selected sample rows do not contain a Cont Calib row but contain one or Init Calib rows then the middle row of this set will be marked in the Status column as the Cont Calib If an even number of Init Calib rows are selected then the closest row past the mid point will be flagged as the Cont Calib If only one Init Calib row exists then that will be chosen Errors If no Cont Calib sample was located in the rows selected for processing according to the rules given above then an error message will be displayed Form 8 Error No continuing calibration sample identified Warnings If no rows selected for processing are of sample type other than Tune Eval Cont Calib or Init Calib then a warning message will be displayed Form 8 Warning Sample list contains no sample types reported in Form 8 summary 639 TurboMass Software User s Guide Report Method Usage The following report methods specify templates designed for use from the TurboMass environmental report generation window only To use these report methods they must be specified in the Submitter Task Data window s Report Method tab Examples of these reports in PDF file format are found in the directories C TurboMass Tutorial_ VOA pro C TurboMass Tutorial_ SVOA pro IMPORTANT Using these report methods in a sample list Report Method column f
134. set the Time Window parameter as described in step 7 b If Relative Retention Time is selected set it to the time at which the compound is expected to elute relative to the compound specified in the Internal Ref field The value specified here is a multiplication factor that is applied to the time at which the internal reference compound elutes This can be used to handle situations where some drift may occur in the time at which compounds elute but their relative retention times remain constant If you selected Retention Time set Time Window to specify by how much the compound elution time may vary The Time Window is applied either side of the predicted retention time to give a valid window The Time Window also defines the chromatogram range that will be integrated Set Peak Selection to specify which peak should be located where more than one peak is detected within the time window By default the peak Nearest to the specified retention time will be selected Other retention time based options that can be selected are Largest peak and First peak or Last peak in the specified time window NOTE The setting for the Peak Selection control will determine the appearance of the lower part of the window 262 e Select Spectrum for the best match to the reference spectrum and specify the Rev Fit Threshold to do a reverse search test in peak selection Only Quantify peaks above the specified Rev Fit Threshold value are considered f
135. showing that spectrum Map The Map Toolbar The Map toolbar at the top of the Map window allows you to perform some commonly used actions by clicking a button Ej Selects a data file Prints current window in portrait format A Prints current window in landscape format Sends bitmap of current window to the Clipboard K Stops the current map process ci Edits intensity scaling for map display E Toggles to restore the previous display range or to display the default display range You can toggle the toolbar display on off by selecting Toolbar from the Map Display menu When the toolbar display is selected a check mark will appear next to it in the Display menu 531 TurboMass Software User s Guide 532 Selecting a Range to Map from the Data File By default the Map program will create a map for the whole file covering the full range of retention time and mass Reducing the mass and retention time ranges will require less memory and the map process will take less time You may find this useful for large data files It is also possible to reduce the resolution used for the mass and retention time axes Reducing the resolution will reduce memory requirements and may also enhance features in the data The Map program will sum all masses in a window equal to the mass resolution to create the map display For example if the mass range is set to 50 amu to 350 amu and the mass resolution is set to 1 amu a point
136. spectra These spectra can come from raw data files or from existing libraries Creating a User Library The steps involved in setting up a user library are as follows e Run the Spectrum application and select the first spectrum that you want to add append to your library e Select Library Append from the Spectrum Edit menu e Click File and enter the name for the new library Click OK When prompted click Yes to create the new library Click OK to add the first spectrum e Using the TurboMass Spectrum application select spectra one at a time to put into your library e For each selected spectrum use the Library Append command from the Spectrum Edit menu to add to your library e Inthe Library application select Edit Library and set up the text data for each entry e Use the Index Library command from the Library Process menu to create the Presearch file for the new user library Once you have created a user library you can add new spectra to it at any time by repeating these steps Creating a new user library 1 Open the Spectrum application 515 516 TurboMass Software User s Guide 2 Display the first spectrum you want to append to the library by doing one of the following To add spectra to an existing user library display the spectrum you want to append to the library OR To add spectra from a different library to an existing user library display the library entry that you want to append t
137. spectrum After clicking this button point to where text is required and left click The Edit Text String dialog appears for text input When OK is clicked the text is written to the Spectrum display Selecting once causes each subsequent spectrum to appear in a new spectrum window rather than being added to the current window Selecting a second time cancels this mode 427 TurboMass Software User s Guide 428 NOTE Selecting once causes each subsequent spectrum or spectrum process to replace the currently selected trace Selecting a second time causes each subsequent spectrum or spectrum process to be added to the traces on display E is unavailable when is clicked fe Toggles real time spectrum update on and off cy Increases magnification of current range cy Decreases magnification of current range tad 2 Deletes current magnification range Selects a new scan from the current data file e Decrements the currently displayed scan gt Increments the currently displayed scan EJ Click once to restore the previous display range click again to use the default display range Customizing the Spectrum Toolbar The Spectrum toolbar can be customized to add other buttons for the operations that you use most frequently remove buttons you do not require and determine the order in which the toolbar buttons are displayed In this way you can customize the TurboMass display to suit the way you work To cu
138. tab Viewing the Audit Trail 1 Select Display Audit Trail from the File menu 2 When you have finished viewing the information click OK GC Control Printing the Audit Trail TurboMass displays a print options dialog when you select Print from the Method Editor File menu This dialog includes an option to print the Audit Trail for the current file Creating Instrument Notes The Notes command in the Instrument menu lets you create original text or use the preset template to record information about the instrument section of the method The information you enter has no effect on data analysis You can view these notes when you select Print Preview from the Method Editor File menu You can print these notes when you print the full method Creating or editing header information for the GC method 1 Select Notes from the Instrument menu to open the Instrument Notes dialog Header text i e Template None v OK Cancel Reset Display the conditions template for the selected instrument type 2 Enter the header text that you want to appear in the printed reports for this method To start a new line press CTRL M To erase the contents of the text field click Reset OR 177 TurboMass Software User s Guide Select the CAP GC template from the Template drop down list 3 Ifyou are working with the CAP GC template edit the information as necessary 4 Click OK to save your changes Printing GC M
139. the Quantify Display dialog Quantify Quantify ol x File Edit Display Process Window Help BS aida BSS FELRE Graphs METH1 _ jo x Compound 2 name Compound B 458 5 Coefficient of Determination 0 974154 Calibration curve 0 012594 x 0 005516 Response type Internal Std Ref 1 Area IS Conc IS Area Curve type Linear Origin Exclude Weighting 1 x Axis trans None 1 26 Response x x SoC OC The current calibration curve file holds a calibration curve for each of the compounds being analyzed The toolbar within the Graphs window allows you to easily select other calibration curves by clicking or The calibration curve graph displays concentration against response value The vertical axis is labeled as a percentage of the maximum response The horizontal axis is labeled with the concentration units specified in the method The displayed calibration curve shows the response value expected for particular concentrations Crosses mark the calibration points used to form the curve The residual plot displays concentration against delta concentration at the calibration points This shows the difference between the concentration predicted by the calibration curve and the actual concentration at the calibration points Selecting another calibration curve To select another calibration curve from within the current file use the following to
140. the Tolerance will be set to the default value Pasting a spectrum will have the following effect when the current setting of Peak Selection is Multiple Ion Ratio to Quantify Trace or Multiple Ion Ratio to Base Peak e The largest four peaks excluding the Quantify Trace will be entered as the qualifier ions The Target Ratio values will be set according to the ratio of each ion to the ion indicated by the Peak Selection setting i e to the Quantify Trace or to the Base Peak The Tolerances will be set to the default value m z Mass of the qualifier ion displayed to two decimal places Target Ratio The expected intensity of the qualifier ion to the quant ion as a displayed to one decimal place Tolerance The variance permitted in the actual intensity ratio from the set Target Ratio displayed to one decimal place Use of this value is different depending on the tolerance type set in the Tolerance drop down list Quantify Trace Controls for defining the Target Ratio and Tolerance for the Quantify Trace where applicable Tolerance Control to set type of tolerance test applied to qualifier ions Coelution Window sec Control to set allowed time window for qualifier ions to maximize Quantify Setting Quantify Method Peak Integration Parameters The Peak Integration parameters are used when automated chromatogram peak detection is being performed You can set integration parameter
141. the Tune page You can ask for readbacks to be displayed continuously never or only when they differ from their associated set points by more than 10 Note that a number of the readbacks are for diagnostic purposes only and thus do not need to be very precise Their function is to indicate if the voltage is present or not The acceptable variation between the set value and the readback value will vary depending on the particular tune parameter If you are concerned about the values contact your local service office for advice Changing Readback Style 1 Select Readbacks from the Tune Options menu Display options C Always Off Always On Cancel C Dn out of range 2 Select the readback style required Selecting Always On will always display readbacks Selecting Out of Range will display readbacks when they differ from their associated set points by more than 10 3 Click OK 109 TurboMass Software User s Guide Starting an Acquisition from the Tune Page The easiest way to acquire data for a sample is to acquire it directly from the Tune page You cannot use inlet programs for example GC methods from the Tune page acquire analog data or acquire multiple sample sequences but you can start and stop acquisitions and control most of the scanning parameters 1 Select Acquire from the Tune Window menu OR Click Acquire at the bottom of the Tune page Start Acquisition Ea Data File Name SU
142. the Select Forms dialog the Report Generation Window Form 5 Tab appears E Report Generation DER Sample List Forms Options Help Sample List Fom 1 Form1 TIC Fom2 Fom3 Fom4 Fom 5 Status SamplelD Sample Type File Name Matrix Level Vial Quantify Method Submitter Task Analysis Qualitative M Tune Eval BFB TuneEval B10040501 Water Mediu 8260b_Tutorial VOA_Tutori VOA_Tutori VOA TiCsearch10 VOA STD 5ng Init Calib B10040504 Water Medu 8260b_Tutorial VOA_Tutori VOA_Tutori VOA TiCsearchi0 VOA STD 20ng Init Calib B10040505 Water Medu 6260b_Tutorial VOA_Tutori VOA_Tutori VOA TiCsearchi0 VOA STD 50ng Init Calo B10040506 Water Medu 8260b_Tutorial VOA_Tutori VOA_Tutori VOA TiCsearchl VOA STD 100n Init Calib B10040507 Water Mediu 8260b_Tutorial VOA_Tutori VOA_Tutori VOA TiCsearch10 VOA STD 200n Init Calib B10040509 Water Mediu 8260b_Tutorial VOA_Tutori VOA_Tutori VOA TiCsearchi0 MethodBlankt Meth Blank B10040510 Water Medu B260b_Tutorial VOA_Tutori VOA_Tutori VOA TiCsearchi0 SpikeDupt Spike B10040511 Water Medu 8260b_Tutorial VOA_Tutori VOA_Tutori VOA TiCsearchi0 SpikeDup2 Spike Dup B10040512 Water Mediu 260b_Tutorial VOA_Tutori VOA_Tutori VOA TiCsearch10 MethodBlank2 Meth Blank B10040513 Water Mediu 8260b_Tutorial VOA_Tutori VOA_Tutori VOA TiCsearch10 00123 Analyte B10040514 Water Mediu 8260b_Tutorial VOA_Tutori VOA_Tutori VOA TiCsear
143. the account has not been disabled The username determines the user s level of access allowed within TurboMass or the Security Manager If the user does not have full administrative privileges the following message may be displayed TurboMass Security Manager x You do not have the permissions required to access this feature Please contact your Administrator for futher advice Appendix A TurboMass Security 4 Ifauser needs access to a particular area assign the user to a group that has the necessary access privileges See Assigning an access privilege to an individual user on page 676 for more information If the username entered does not belong to a group with administrative privileges the user is limited to viewing their own account information Changing a password without administrative privileges 1 Exit TurboMass if necessary Start the Security application to open the Security Manager dialog and display a list of user accounts TurboMass Security Manager User Policies Tools View Help Ee HAE Fee Usemame Full Name Description Administrator TurboMass Administrator Built in account for administering TurboMass Group Name Description coma embers can fully administer TurboMass Select the account for which you want to change the password and select Properties from the User menu The User Properties dialog is displayed 667 TurboMass Software User s Guide 668 User Name Warren
144. tuning parameters can be sent to the printer by clicking or by selecting Print from the Tune File menu This report contains a copy of the tune peak information displayed on the screen along with a record of each parameter setting You can also automatically print out a Tune report by selecting the Print Report Target Tune option See UltraTune on page 93 87 TurboMass Software User s Guide Experimental Record Tuning parameters are stored with every data file as part of the experimental record The tuning parameters for a particular data file can be viewed or printed from the Data Browser 88 NOTE Instrument Tuning Saving and Restoring Parameters Whole sets of instrument tuning parameters can be saved to disk as a named file and then recalled at a future date A tune parameter file contains the latest settings for the source parameters for all supported ionization modes not just the ionization mode you are currently using Tune parameter files also contain settings for the analyzer and GC inlet line transfer line temperature setpoint Saving a Set of Parameters 1 To save the current tune parameters with the existing file name click OR Select Save from the Tune File menu To save the current tune parameters with a new file name select Save As from the Tune File menu 2 Enter a new file name under which you want the parameters to be saved or alternatively select an existing file from the list displayed
145. used in the calibration acceptance testing Maximum RSD Init Cal An edit box that defines the maximum acceptable RSD percentage relative standard deviation 0 0 to 100 0 or left empty between response factors calculated for each concentration level of the initial calibration Maximum Difference Maximum Drift For compounds using curve fit An edit box that defines the maximum acceptable percentage difference between the RRF calculated for this compound from the continuing calibration and the average RRF from the initial calibration For compounds using curve fit e g linear least squares this becomes the Maximum Drift the acceptable difference between the concentration calculated for the compound in the continuing calibration standard using the calibration equation and the known concentration 281 TurboMass Software User s Guide Surrogate SMC Environmental Parameters Compounds Type Name Int Std Int Std Int Std Surrogate Surrogate Surrogate Target Target Target Target Spike Target Target Target Target Target Spike Spike Target Target Spike Target Target Target Target Target Pentafluorobenzene 1 4 Difluorobenzene 1 4 Dichlorobenzene D4 Dibromofluoromethane Toluene d8 Bromoflurorobenzene Dichlorodifluoromethane Vinyl Chloride Bromomethane Trichlorofluoromethane 1 1 Dichloroethene Methyl Tert butyl Ether Methylene Chloride 1 1 Dichloroethane 2 2 Dich
146. waste vial set that you want to use Wash waste vial set 1 uses vials 1 and 2 Wash waste vial set 2 uses vials 3 and 4 161 TurboMass Software User s Guide 162 8 Select the number of Pre injection solvent washes that you want to have This value determines how many times the syringe is washed with solvent before each injection 9 Select the number of Pre injection sample washes and Post injection solvent washes that you want to have Setting GC Oven Inlets Parameters The Oven Inlets tab of the Instrument Control dialog controls the oven temperature of your gas chromatograph the rate at which the temperature increases the type of coolant that you are using and the zone setpoints for injectors and detectors The Ovens Inlets tab also includes a temperature curve that corresponds to the values that you enter in the table beneath it The table has the following columns Rate Represents the rate at which the oven is heated You can create up to three ramps which are periods during which the temperature increases Ramps are in degrees per minute Temp Gives the temperature to which the oven is being raised during the ramp Hold Represents the period for which the temperature is held before starting the next ramp The initial setting is the temperature of the oven at the start of the run or throughout the run for an isothermal analysis The Initial Rate field is always 0 0 and you cannot edit this field To edit the other
147. will need to select Retry Injection from the top level GC menu to restart the GC For more information on starting and stopping the GC see Stopping and Restarting the GC on page 179 Data Acquisition Automatic Startup TurboMass includes a Startup facility that can be used to startup an instrument to perform an acquisition Startup can be used in any ionization mode The Startup facility will do the following e Switch the instrument into Operate mode e Load the Tune page and the startup Tune parameters e Turn off Operate at the end of the Sample List and shut off the CI gas Running Startup Startup uses the current Tune page settings To change these settings open a new file on the Tune page Startup can be run in any of the following ways e Select Startup from the TurboMass Run menu e Start an acquisition from the Tune page e Start a Sample List run e Inthe Sample List Run menu select Edit Shutdown In the Shutdown dialog select Startup from the Control List menu 359 TurboMass Software User s Guide 360 Automatic Shutdown TurboMass includes a Shutdown facility that can be used to shut down the mass spectrometer at the end of a Sample List Shutdown can be used in any ionization mode The Shutdown process will do the following e Switch the instrument to Standby mode e Open the appropriate Autoshutdown Tune file and apply the shutdown parameters e Wait for a user specified delay time Running
148. 0516 Water Mediu 8260b_Tutorial TiCsearch10 VOA_Tutori VOA_Tutori VOA w 13 50ug L Cont Calib B10040506 Water Mediu 8260b_Tutorial TiCsearch10 VOA_Tutori VOA_Tutori VOA Enrors Wamings General errors must be corrected before Form details can be viewed Row Colors The color in which rows are displayed indicates how they will be used in the generation of the current form Disregard Gray Gray indicates that the row is not involved in the generation of the Form Primary Blue Blue indicates that the row is the primary data set for a Form For example multiple blue rows in the Form 1 tab indicate that a separate Form 1 will 604 Environmental Reporting be generated for each row Most other Forms have just one blue row indicating that just one Form of that type will be generated for the sample list Summary Black Black indicates that the row will form part of a summary table on the form For example see Form 2 or Form 5 Other Colors Form 3 is a unique case in that it involves three or possibly just two files that are interrelated Each of these three rows uses a unique color to indicate its role About this Window 1 You can size this window and the relative sizes of the sample list and message panes may be adjusted using the splitter bar 2 The first column in the list view check box and row number always appears but the other columns are configura
149. 166 control parameters 161 descriptive information 174 detector parameters 171 instrument timed events 173 notes 178 oven inlet parameters 163 printing 179 GC Method Editor 157 GC status box 142 Generic TIC Names 659 group rights 679 groups 677 H Hands On command 189 headers 54 heater parameters 104 help 59 high mass calibration 135 Hits chemical structure 512 hits listing 507 I inlet heater parameters 104 inlet selection 69 instrument data thresholds 70 instrument status GC 183 integrating chromatograms 401 integration parameters 273 Interactive Data Review 304 L lab and user information in data file 78 Lab Infromation 225 library append 519 automated search 504 print search results 512 search filters 500 search parameters 498 search process 491 search results 503 start search 503 Library Compare 515 library hits 507 Library Locator 524 library search automatic 420 Library Subtract 515 LIMS Sample list import worksheet 228 M magnify chromatograms 383 magnifying spectra 434 manual conventions 22 Map file 530 intensity scaling 537 overview 529 range 534 Mapping RT to RRT 269 mass axis Spectrum 434 mass calculator description 547 user elements 548 mass calibration 115 mass chromatograms display 377 mass measure parameters 126 Matrix 218 Modify Active command 190 multiple ion ratios setting 271 multiple samples acqu
150. 19 and 502 for EI UltraTune are suitable for tuning with Heptacosa There is no need to alter the Tune Mass or Peak Width parameters if you are using Heptacosa The Full Width at Half Max parameters set the peak width at half height for the Low and High Masses being monitored Typical values are 0 55 for both but applications requiring higher mass resolution e g the environmental BFB tune or more accurate isotope ratios may need higher resolution e g 0 50 with Custom UltraTune 3 Select your After UltraTune settings Print Report Automatically prints a tune report after a successful UltraTune Save Alternate Tune Files Saves the top three UltraTune result sets as tune files rather than just the top one Prompt for Recalibration Prompts you to perform a mass calibration after a successful UltraTune Evacuate Reference Gas Automatically pumps out the reference gas following UltraTune 4 Set the Final Multiplier Setting 95 TurboMass Software User s Guide 96 User Set V Check this box if following UltraTune you want to set the PMT voltage to the value you enter in the field 5 When you are satisfied with the UltraTune Setup parameters choose OK to exit this dialog 6 Choose Start to start UltraTune and the following occurs If the source is not at the set temperature within normal tolerance then the message Waiting for the source temperature to equilibrate is displayed in the UltraTune St
151. 3 TurboMass Software User s Guide The following message is displayed 15 Click OK The following message is displayed Configuration Editor 16 Click Yes The following message is displayed Configuration Editor Q 17 Click Yes If your Clarus 500 GC has PPC the following message is displayed Configuration Editor Q 724 Appendix B TurboMass Software Installation 18 Click Yes The following message is displayed 19 20 21 Click Yes The following message is displayed Click Yes The following message is displayed Configuration Editor Q Click Yes The following screen is displayed ale m S alal ef insti 725 TurboMass Software User s Guide 22 Select Configure from the nstrument menu The following screen is displayed GC Configuration none 23 Click the Query Inst for Config button 726 Appendix B TurboMass Software Installation The following screen is displayed 24 Click OK The Configuration Editor window is updated and your instrument is now configured and the GC Configuration screen displays 727 TurboMass Software User s Guide GC Configuration xi r Instrument at port COM2 Type Clarus 500 GC with Autosampler Name finst Injector B Pko x Injector A Psst gt Car A Press He 7 Options r Detectors PPCinsta
152. 5 57 fe 170 0 Reference Spectrum 77 72 7 25 Ratio Range Ratio Pass Fail Quantify trace Qualifier ion 85 9 1to 49 1 Qualifier ion2 7 36 5to 76 5 Page 1 Sec 1 2 3 To view data for the next or previous peak click the toolbar button or aj 303 TurboMass Software User s Guide 304 To modify peak data l Double click on the compound name in the Summary window you wish to manually integrate If the Edit Quantify Peak dialog is not displayed select Chromatogram from the Display menu in Quantify and make sure the Show Edit Quantify Peak dialog is selected Then try step 1 again Quantify Chromatogram Display Add to existing chromatograms _Cancel NV Show Edit Quantify Peak dialog Display Range Integration x 3 Perform manual reintegration if necessary See Manual Peak Integration on page 311 4 Click OK to accept the changes made and have the results display updated Saving the Summary window In the Summary window select Save Summary by Compound or Save Summary by Sample from the File menu The Graphs Window The Quantify Graphs window contains a graphical display of the current calibration curve and or its residuals plot Statistical information on the calibration curve is displayed above the graphs A user configurable header can be displayed at the top of the window The Graphs window is available if you selected Curve and or Residuals in
153. 509 Water dediu 8260b a TiCsearchtC OA_Tuton VOA_Tutori MethodBlank1 B10040510 Water dediu 8260b_Tutorial TlCsearch10 VOA_Tutori VOA_Tutori VO SpikeDupt B10040511 Water ji 8260b_Tutorial TICsearch10 VOA_Tutori_ VOA_Tutori SpikeDup2 Spike Dup B10040512 Water 8260b_Tutorial TiCsearch10 VOA_Tutori VOA_Tutori Meth Blank MethodBlank2 Meth Blank B10040513 Water ji 8260b_Tutorial TiCsearchi0 VOA_Tutori_ VOA_Tutori 00123 Analyte B10040514 Water 8260b_Tutorial TiCsearch10 VOA_Tutori_ VOA_Tutori 00124 Analyte B10040516 Water ji 8260b_Tutorial TiCsearchi0 VOA_Tutori_ VOA_Tutori 5Oug B10040506 Water jedi 8260b_Tutorial TiCsearchi0 DA_Tutori VOA_Tutori VO lt Comment Errors Warnings for Form 4 Method Blank Summary Section of the Window Sample List view Comment Message pane 620 Description This is a read only display The view cannot be sorted and no data item in any cell can be directly edited Column widths can be changed in the standard way by dragging the header divider You may enter up to 120 characters which will be printed on the report This is a read only display window Shows general warnings and all form specific errors warnings Environmental Reporting Row Colors Form 4 uses the primary data file data color see Row Colors for the method blank
154. 8 66 62 63 43 oS So ioo i50 200 250 300 Selecting a Data File to Process 350 400 Changing the current input file 450500 550 600 gt The Input section of the Strip Datafile dialog identifies the data file and function number that will be processed gt Select Input from the Strip File menu to open a Datafile Browser dialog from which a new file function and directory can be selected By default TurboMass will process the entire selected function NOTE Strip and Combine Functions Selecting a new input file automatically defaults the name of the output file Selecting a Data File and Subrange to Process CODA does not allow subrange selection This is because all functions in the dataset are processed Processing a mass or retention time subrange of the input file has the advantages of reducing both processing time and the size of the resulting output file Selecting a different file and function 1 Select File to open the Strip Data Browser dialog 2 Selecting a new file automatically defaults mass and retention time to full range 3 Enter values for the Mass Range and Retention Time range that you wish to process These ranges can be set from Spectrum and Chromatogram respectively by right clicking and selecting the desired range 4 To set the Mass Range parameters right click at one end of the Spectrum region of interest and drag the mouse horizontally to the other end TurboMass indic
155. 8 98877 3 24 180 98877 1 31 218 98560 38 07 263 98705 8 38 313 98386 0 32 375 98067 0 38 413 97748 1 64 463 97429 1 02 501 97110 1 90 537 97112 0 13 575 96796 0 32 613 96471 0 64 133 TurboMass Software User s Guide 134 You can create or edit calibration reference files using any Windows text editor To read the currently selected reference file into the Notepad text editor select Reference File from the Calibration Edit menu After editing the reference file can either be saved under the current name by selecting Save from the Notepad File menu or saved as a new reference file by selecting Save as from the Notepad File menu and giving the file a new name Textual information or comments can be stored in the reference file Lines which are textual information or comments must start with a semi colon character Mass Calibration High Mass Calibration Heptacosa s highest mass peak for calibration is m z 614 Calibrating to higher mass requires a different compound that has ions at higher m z One compound useful for this purpose is Tris perfluoroheptyl s triazine found in the mass calibration file Triazine ref This compound has calibration ions up to m z 1185 It is soluble in methanol and hexane has a low boiling point and may be chromatographed easily Performing a High Mass Calibration 1 Calibrate as usual to Heptacosa 2 Change the reference file from helpta to Triazine 3 Inject 0 2 nL of th
156. 89 Function List Editor seesoesoessesoossessorsessoesoesoesossoesoossessorseesossossoesossoesoosee 191 ntroduc tiOn rrenan or AR AA E A A E a Ri 193 Function List Editor eroice eerie a 196 Adding a New FUunction ccceccesccesscessceseceeeceeeeeeeeeeseesseeeseeesaeenaeenaees 196 Modifying an Existing FUNCTION ccccccesseceteceteceteceeeeeeeeeeeeseeessees 196 Removing a FUNCTION 00 0 cecceecceesseesceceteceeceseceseceeeceeeeeeneeeseeeseeeseeesaees 196 Changing a Function s Start and End Times eceecceseeseeeeeeneeneees 196 Setting a Solvent Delay Sariren cecinere e ee 197 Saving and Restoring an MS Method ccecceesceseceteceeeeeeeeeseeeeeeeees 198 Setting Up an MS Scan Function ccccccecsseesseeseceeeeeeeeeeeeeeeeeeeeennes 199 Setting Up an SIR Function cc cccccccccscesseceteceseceeeceeeseeeseeeseeeeeeeeeaes 202 Sample Lii8tsi ccsseesndsavasestsssesssecsuccessvisssesessnvesuessessasosensseesssossnsosseseseeasesues 205 Top Level Memes vscs si se fel serds catia Sestsate dines ue dasta aan side A ENA ORES 207 The TurboMass Menu Toolbar ceecceccsseesceseceseeeeeeceeeeeeeeeceaeeaeeereeaeenee 208 Creating and Editing Sample Lists cccccccsseeseesseeeteeeeceeeeeeeeeseeeeneennes 211 Adding Sample to the Sample List cc eccccscecseeseeetseeteeeseeeneeesees 219 Sample Injection Information cccccceeseceteceteceseceseceseeeseeeeeeenseenaes 220 Sample Prep Information cccccccssee
157. 89 Saving a Set of Parameters ccccccsccsssceseceseceeeceeeeeeeeseeeseecsseenseenseens 89 Restoring a Saved Set of Parameters cccccssccsseceteceseceseeeeeeeeeeeseeeses 90 Modifying the Peak Display ccccccccssecssecstecseceeceneeeeeeeeeeeseeeseeeseeesaeesaees 91 Selecting PEAKS 3263 cdesesssurdsgs a sovedesadevianes oy vedeus a a e 91 Zooming or Unzooming a Peak ccccescesseceseceneceseceneeeeeeseeeeeeeesneeeaes 92 To Change the Tune Mass Span or Galti cccecccceescceeceseceeeeeeeeeeneeeees 92 Contents NMA UT CR E ER E E AA E EET 93 Running Standard UltraTune DFTPP BFB seesesesesesesreeeesseserse 93 Running UltraTune Custom AutoTune cccecccesccesseeeeeseeeeeeeeeneeeaes 98 Running UltraTume Custom ccc ccccccccsseesteceseceneceeceeeseecseeeseeeenneenaes 98 Setting Scope Parameters cccccssecsseeseceseceseceeeceeeeeeeeeeneeeseeeseeeeeenaeesaees 103 Changing the Scope Setup ceccecccsssssseeeseeeseeeseecssecssecneeneenseenseenes 103 Changing Inlet Heaters 00 0 0 cccecccecssessseesceessecseecaecnseensecnseesseeeeeeseeeenseeaes 104 Setting Gas Control sits vvcccasncatieteea nevis E Mian AE 105 Turning a Gas On or Off cccccccccccsecsteceteceeeeeeeeeeeseeeeeneeeseeeseeeaeeeaaees 105 Vacuna n a bods cdn a leaiaren dozen A oh leet sent ts 106 Pumping Down the Vacuum System ccccecccesseseseeesseeteeeseeseeaees 106 Venting the Vacuum System ccccesccssecesecesecee
158. 9 3 0 12345 67890 1 25 1 0 1 0 1 0 2 0 3 0 Spare1 Spare2 Spare3 Spare4 Spare5 QuantMethod QuantCalfile QualMe thod ReportMethod Data2 Filename filetext2 MSFile2 MsTuneFile2 InletFile2 InletPreRun2 INletPostRun2 InletSwitch2 AutoFile2 Process2 ProcessParam2 ProcessOptions2 SampleLocation2 Job2 Task2 User2 Submitter2 Conditions2 Analyte ID2 22 10 2 10 3 10 4 10 5 10 6 10 7 10 8 10 9 20 0 20 1 20 2 20 3 20 4 20 5 20 6 20 7 20 8 20 9 30 0 222 5 55 2 25 2 5 1 0 2 0 22 5E 2 32 12E 3 Spare12 Spare22 Spare32 Spare42 Spare52 QuantMethod2 QuantCalfile2 QualMethod2 R eportMethod2 Appendix F Environmental Reporting Calculations NOTE Appendix F Environmental Reporting Calculations About the Calculations The calculation of compound concentration to be employed for a given sample will be determined by the analysis type VOA or SV taken from the Analysis field in the sample list matrix type water soil taken from the Matrix field in the sample list and concentration level low medium taken from the Level field in the sample list This value calculated from the equations below will be included in the data source as the item under the TargetCompounds collection i e it will not replace the standard TurboMass Concentration value found in the Quantify view results The equations below are shown in two forms Firstly the form defined in the EPA methods and or SOW The TurboMass software will not p
159. 91 gg 10511211 3494 140 142 Figure 1 A TurboMass multiple window layout Function Keys The function keys can be configured by selecting Options from the Sample List Tools menu On the Processes tab use the Add Edit and Remove buttons to change function key assignments By default the F1 key provides a link between the Getting Started TurboMass spectrum environment and the optional NIST library search program Refer to the NIST manuals for instructions on using the NIST library search program Other function keys can be assigned to other commands exe files Changing Colors and Fonts The fonts and colors used to display information in TurboMass windows can be altered using the Color and Font Editor To change TurboMass fonts or colors 1 Select Colors and Fonts from the TurboMass Tools menu The Color and Font Editor dialog is displayed Color and Font Editor Ea e Curent Settings abels cale ist Tent ser Tex s ata ata 2 Select a font Type from the list Header Text User Text List Text cae The Font or Color button will become active as appropriate Select the appropriate button to enter the Font or Color editor OR Double click a Type from the list to open the relevant editor OR Double click a portion of the Current Settings spectrum to open the relevant editor Make any changes required to the fonts or colors of any part of the display Your changes will be reflected i
160. 96 L Delte Clear All 3543 ll eng favs End 9795 x Edd Hoa Area 15631 072 2 Do one of the following to select the peak whose baseline you want to edit e Right click and select the peak in the Chromatogram display e Select the peak from the Peak Tops list in the Edit Integrated Peaks dialog 3 Modify a baseline range by doing one of the following e Edit the Start or End values e Right click and select a range and click Modify e Left click on one of the end markers boxes and drag it to the required position 4 The values in Peak Information will be updated to reflect the edited baseline Adding a new peak 1 Select Integrated Peaks from the Chromatogram Edit menu to open the Edit Integrated Peaks dialog 2 Enter the Start and End points of the baseline for the new peak or right click and select a range 3 Click Add to update the values in Peak Information to reflect the new peak 407 TurboMass Software User s Guide Deleting a single peak 1 Select Integrated Peaks from the Chromatogram Edit menu to open the Edit Integrated Peaks dialog 2 Do one of the following to select the peak you want to delete e Right click and select the peak in the Chromatogram display e Select the peak from the Peak Tops list in the Edit Integrated Peaks dialog 3 Click Delete Deleting all the peaks 1 Select Integrated Peaks from the Chromatogram Edit menu 2 Click Clear All in the Edit
161. CA mode It is recommended that the calibration uses the same data type as the sample data you will be acquiring GC MS uses the Centroid type almost exclusively 3 To acquire data for static calibration the portion of the mass scale immediately around each reference peak is scanned Static Span Specifies the distance to be scanned either side of the reference peak Typically set to 4 122 6 Mass Calibration Static Dwell Specifies the time taken to scan the static span range Typically set to 0 1 To acquire data for scanning calibration the mass scale is scanned over the selected range in a time specified by the Slow Scan Time parameter This should be as long or longer than the slowest rate you will use Typically set to 2 To acquire data for the Scan Speed compensation calibration the mass scale is also scanned over the selected range in a time specified by the Fast Scan Time parameter This should be as fast or faster than the fastest scan rate you will use Typically set to 0 1 Inter Scan Delay specifies the time between one scan ending and the next scan starting If this is too short typically less than 0 05 sec the recorded spectra may be incomplete depending upon mass range Typically set to 0 1 Very fast scanning over wide mass ranges may require verifying that all data are properly written to the data file The mass calibration should also be carefully checked To reset all parameters to their default valu
162. Carbon disulfide 2 475 2 439 2 481 2 488 1 1 2 Trichloro 1 2 2 trifluor 0 231 0 218 0 222 0 230 lodomethane CofD 0 999 Allyl Chloride 0 488 0 484 0 494 0 481 Methyl Tert butyl Ether P 0 9995 Propionitrile I 1 015 0 964 0 993 0 998 Methylene Chloride CofD 0 999 Form 6 header sample File name B10040514 z Errors Wamings for Form 6 Initial Calibration Data 624 Section of the Window Calibration Sample Table Compound Data Table Environmental Reporting Description The table lists all the initial calibration data files identified in the calibration file The table includes columns for e Row number e Sample ID e File Name the raw file name e Time and date of injection of the standard sample The data for this table is taken from the first Calibration file referenced by the selected lines of the Sample List When a row is selected the arrow keys can be used to change the selected row and cause the list to scroll Column widths can be changed in the standard way by dragging the header divider The data for this table are also taken from the Calibration file The table lists all compounds identified in the calibration file and displays the RRF value calculated for each concentration level plus the average RRF and the percentage relative standard deviation for the RRF values For compounds using a linear or higher order curve fit calibration in place of Average RRF the goodness of fit value r correl
163. Compound Name Water Limit Soil Limit CLP Like Pentafluorobenzene Default VOA_Tutovial VOA_Tutorial VOA_Tuterial_ 9060048 1 4 Difluorobenzene 1 4 Dichlorobenzene D4 Dibromofk Toluene jaramethane List of Compounds showing status and reporting limit value Bromoflurorobenzene Dichlorodifluoramethane Vinyl Chloride Bromomethane Trichlorafluoramethane T 1 Dichloroethene Methyl Tert butyl Ether Methylene Chloride T 1 Dichloroethane 2 2 Dichloropropane Chloroform Benzene Trichloroethene Dibromomethane TWESISIS S S S 5 5 S S ETARA 1 Bromo 2 chloroethane Toluene Previous Next Set reporting limits for all compounds Reporting limits Water Set All Soil oOo Set All fE 5 TurboMass Gh 09936691c TurboMas TG Report_Method_Usa The basic requirements for Custom Compound Lists are that an environmental laboratory should be able to define subsets of the compounds in a quantify method to be reported for a particular project Task in TurboMass terms of a particular client Submitter in TurboMass terms and also to set the concentration reporting level of each of these compounds uniquely for each client s Submitter s projects Environmental Reporting The mapping of Forms to Re
164. DATASOURCE 0 MS 1 GC CHANI 2 GC CHAN2 INVALIDCNC TRUE if there was something wrong with the internal standard data EPA_CONC Adjusted Concentration SPIKERECOV RPD Matrix Spike Matrix Spike Duplicate Recovery Relative Percent Difference MATRIXTYPE 0 Soil 1 Water EPAQUALTXT EPA_MCONC N 29 9 EPA Qualifier Ions Moisture Adjusted Concentration 5 2 747 TurboMass Software Guide 748 Field Name Format Description Version Added GOODEPACAL Bit Fields 1 if valid operation performed 0 if not Valid Adjusted Concentration 0x00000001 Valid Moisture Adjusted Concentration 0x00000002 Valid Matrix Spike Recovery 0x00000004 Valid Matrix Spike RPD 0x00000008 EPA FLAG Manually Changed 0x00000010 Appendix E LIMS Import File Example Appendix E LIMS Import File Example Example of a Sample List Import File System Description Description EXAMPLE SIF FILE MaxNoOfSamples 250 Constant Parameters BatchID InitialCalibration Sample List Filename From the list below build a cross reference map relating the intems in the Data section to Sample list entries Build a new INTERNAL Sample record and append it to the newly created sample list file Variable Parameter List NumberOfParameters 56 Parameter1 FILE_NAME Parameter2 FILE_TEXT Parameter3 MS_FILE Parameter4 MS_TUNE_FILE Parameter5 INLET_FILE Parameter6 INLET_PRER
165. Determines whether the minimum match value will be used lt text box gt Only compounds with a match value above the entered value will be included in the hits list The value is only enabled when Minimum match drop down list is set to On Molecular weight constraints Between Lower limit for library compound molecular weight and Upper limit for library compound molecular weight Reporting Reporting Maximum hits The maximum number of hits for which text information Text will be provided for reporting Maximum hits The maximum number of hits for which plots will be Plots available for reporting 335 TurboMass Software User s Guide Qualitative Method Editor Library Settings Tab You may have several mass spectral libraries on your computer Some are from NIST mainlib the main library and replib a smaller library of replicate spectra same compounds different spectra which can improve the chances of finding the right compound There can also be other commercial libraries e g the Pfleger Mauer Weber drug library or user created libraries This tab allows you to select which libraries to search and in what order Restricting the number of libraries spectra searched increases speed in a linear fashion Searching libraries which have only the target compounds with few unlikely matches also increases the chance of a correct match For example someone doing drug analyses might search a drug library
166. Determining the Header Information in a TurboMass Window 54 Printing Data in a a A A E E E 57 Printing a Specific TurboMass Window using the Menu 00 57 TurboMass Software User s Guide Window Commands ccceescsscssseeseesecceeseeeeceaecaesecceaecaeeeeeeaeenaeeaeeeeeeaeeaeees 58 Grettin gg Helper aan takwestab stevia tases aa neste etait 59 The About Boka hee Ssteesiecks sae elope vacsh E A ala das toads EA 59 TurboMass Overview sesessesserseesesoessecoorseesoesessoesocsoeeoesseeoorseesocsessoesossoeeoesee 61 Starting TurboM assis sss sscelacei chessinacclacesaandapeassacavsaaszecsanealagsaasasezaan caiiest 63 Configuring the Inlet System eceecceesceeseeeeceeeeeeseeeseeeeeeteeeseeenaees 63 Preparing the Mass Spectrometer for USC ccccecsseeeteeeeceeeeeseeeeeeeenes 63 Tuning the Mass Spectrometer ccccccsccsseceteceseceseceeeeeeeeseeeeeeeeeneeeaes 63 Calibrating the Mass Scale cccccssccssecsseceseceseceseceseeeeeeseeeeeeeeseeesaeenaees 64 Setting up your GC i rarere i Aa aTa E E RAT 64 Developing your Mass Spectrometer Method c ccccescseseeeteeeteeeees 64 Setting up your Sample List and acquiring Initial Data 0 64 Developing your Quantification Method ccceceesceeseeeteetesteeeseeees 64 Developing your Qualitative Method 0 0 ccccccccssesteceteceeeeeeeeeeeeeneeeees 64 Acquiring Data based on your Method ccccccecsseesseesteesteesteenteeeaeees 65
167. Environmental Reporting 591 equilibration GC 180 error messages GC 188 F files open multiple 45 filtering template list 559 fonts change 32 Form 1 Tab Organics Analysis Data Sheet 607 Form 1 TIC Tab Tentatively Identified Compounds 610 Form 2 Tab SMC Surrogate Compound Recovery 617 Form 3 Tab Matrix Spike Matrix Duplicate Recovery 619 Form 4 Tab Method Blank Summary 621 Form 5 Tab Instrument Performance Check 624 Form 6 Tab Initial Calibration Data 626 Form 7 Tab Continuing Calibration Check 629 Form 8 Tab Internal Standard Area and RT Summary 631 Form Specific Checks 636 Forms Dialog 593 Forms Error Messages 633 Forms Row Colors 606 function add 198 Combine 483 list 200 modify 198 MS Scan 201 remove 198 SIR 204 solvent delay 199 start end 198 Strip 465 G gas controls 105 GC acquisition port 151 acquisition status 183 data channels 159 equilibration 180 error messages 188 instrument status 183 keypad control 181 method development 157 modify active method 190 oven temperature 163 reconfiguration 150 run data storage 160 Run Log 160 run status 182 start and stop 180 status messages 186 temperature ramp 164 GC configuration printing 156 user options 152 with TurboMass control 145 without TurboMass control 152 GC Configuration Editor 144 GC menu 141 GC method audit trail 176 carrier parameters
168. Filters from the Locate dialog to set the match locate criteria and click OK to confirm the criteria A message notifies you which filters are to be used for the Locate process TurboMass searches the library and displays the first entry that satisfies the locate criteria Click Fwd gt gt or lt lt Rev to find the next entry matching the locate criteria Both operations start at the current entry and search in ascending Fwd or descending Rev entry number order A message appears indicating the progress of the location When the next suitable entry is found TurboMass updates the display Repeat step 2 as required To stop the Locate process before it is finished click Cancel When you have finished your search click Close to return to the Library Hits window 523 TurboMass Software User s Guide 524 Map 17 Map Overview The Map application provides a three dimensional representation of an entire data file C Map GAS2 Scan El of x File Edit Display Process Help 5 ajaj s XIE nleaded gasoline 100 Scan El 120 00 D Scan El 9 699 100 110 120 130 140 150 160 170 180 9 70 120 0 Figure 10 Map display of gasoline data file The vertical axis displays mass charge units m z and the horizontal axis displays retention time in minutes The third dimension is the intensity of a particular mass at a particular retention time which is represented by a user selected color sche
169. For more information about setting the default Chromatogram display range see Controlling the Appearance of the Display on page 385 Excluding erroneous calibration points If once the calibration curves have been formed a calibration point is seen to be erroneous it can be removed from the calibration as follows 1 Select Calibration Curve from the Quantify Edit menu to open the Calibration Curve Edit dialog 313 TurboMass Software User s Guide 314 Calibration Curve Edit Meth1 x Compound 1 Compound amp 430 5 OK Calibration Points Cancel STANGROL 1 000 14 8 Thc ude e 6 4 Include 716 9 Include 6 4 Include The Calibration Curve Editor will display a list of the calibration points used to form the calibration curve Each point is displayed with Peak List name standard concentration residual error and a label to indicate whether the point has been included or excluded from the current calibration curve 2 To exclude a point that is currently being used to form the calibration curve select the calibration point in the list and click Exclude The label for the point will change from Include to Exclude 3 To include a point that is not currently being used to form the calibration curve select the calibration point in the list and click Include The label for the point will change from Exclude to Include 4 When you have finished making changes click OK to save the changes You wil
170. Injector pH Date extracted Dilution factor Soil aliquot vol Cone extracted vol Cleanup Heated purge Vol surrogate added Adding Sample to the Sample List Sample List Sample Rows as amp LE List File Save Save As Fle Uk The Sample List window is a listing of the Row numbers and Sample IDs for the samples in the current sample list As long at least one sample exists in the list a sample is always selected The currently selected sample is indicated with a highlight You can change the selected row using the up and down arrow keys or with the mouse If the Ctrl key is held down the up arrow will move the currently selected sample row up one position in the list Similarly with the Ctrl key held down the down arrow will move the currently selected sample row down one position in the list gt Enter the Sample Injection Information This window contains many fields required for environmental and QA QC data Not all fields need to be entered since they are not used for calculations but only displayed on the reports They can be ignored or added later on a LIMS system 219 TurboMass Software User s Guide 220 Sample Injection Information File name Enter the raw data file name File text Enter additional comments about the sample Sample Type Select the type of sample from a drop down box The following Sample Types are displayed in the order in which they ar
171. Integrated Peaks dialog 3 When you are satisfied with your changes click OK Clicking Cancel aborts the edit and discards your changes Peak Purity The Peak Purity process works on TIC chromatograms that have already been integrated Note that it is important not to have Enable Smoothing selected in the Integrate chromatogram dialog this is because smoothing tends to increase the peak width and hence when the Purity process selects scans from the edges of the smoothed peak the scans that are chosen are actually in the noise portion of the raw data Since it is the raw data that is used for the purity calculation this will have the effect of artificially depressing the purity value for each peak Select Peak Purity from the Chromatogram Process menu to open the Peak Purity dialog 408 Chromatogram Peak Purity x r Method Simple method Bayesian method r Bayesian Parameters Max no of masses fiz Max no of moments fi There are two separate methods for calculating Peak Purity The first called the Simple method requires no parameters It selects five spectra from across the peak and correlates each spectrum with the other spectra The mean correlation value is displayed scaled to a percentage 0 100 with 100 representing total purity and 0 total impurity A purity value of 60 does not mean that the peak has two components in the ratio 60 40 The second method
172. List Forms Options Help Eales Sample List Form1 Form1TIC Form2 Form3 Form 4 Form5 Form6 Form Status Sample ID Sample Type File Name Matrix Level Vial tify Method Qualitative Method Submitter Anah 1 BFB Tune Eval B10040501 ater Medi 8 _Tutorial TiCsearch10 DA_T JA 2 B10040504 e Medi JA 3 B10040505 Water Medi JA 4 B10040506 ter Medi J 5 7 i Medi 14 6 ter Medi JA rd Water Medi JA 9 B10040512 a Medi JA 1 el B1004051 Water Medi JA T1 00123 nalt B10040514 ater Medi DA_Tuten VOA_Tutori VOA 12 1012 Analyte B10040516 ater Medi IC ht DA_Tutori DA_Tutori JA 13 Cont Calib 50ug L Cont Calib B10040506 Water Mediu ICsearch10 VOA_Tutori VOA_Tutori YOA eA gt Enors Wamings for Form 7 Continuing Calibration Check Section of the Window Description Sample List view This is a read only display The view cannot be sorted and no data item in any cell can be directly edited Column widths can be changed in the standard way by dragging the header divider Message pane This is a read only display window Shows general warnings and all form specific errors warnings NOTE Ifyou change the Min RRF value in the Quantify method you must reprocess recalibrate the sample list for this new value to display in the report 627 TurboMass Software User s Guide 628 Row Colors Form 7 uses a single data file in
173. Meth Blank sample Any Tune Eval Cont Calib Init Calib or additional Meth Blank rows will be shown in the disregard color since they are not included in Form 4 All remaining rows will be shown in the summary color indicating they will be included in the summary section of the printed report Status Column The Status column indicates which row is currently flagged as the method blank This may be used to distinguish between several Meth Blank rows in the sample list only one can be treated as the primary data set for Form 4 or to flag a row of another Sample Type as being the method blank Reassign Sample Type The software allows the Method Blank assignments to be altered without going back to the Sample List The basic procedure is the same for all forms where appropriate 1 Select the tab associated with the Form for which a primary data set will be changed 2 Select the sample list row which is to become the new primary data set 3 Right click on that row and select the required assignment Context Menu This pop up menu appears when you right click on a row in the Form 4 sample list view pane Assign Method Blank Assigns the selected row as the Method Blank sample for Form 4 Displays Meth Blank in the Status column for that row and displays the row in the primary data color 621 TurboMass Software User s Guide Form 5 Tab Instrument Performance Check When you select Form 5 Instrument Performance Check from
174. OA_Tutori VOA_Tutori TICsearch10 MethodBlank1 Meth Blank SpikeDupl Spike B10040511 8260b_Tutorial VOA_Tutori VOA_Tutori TICsearch10 SpikeDup2 Spike Dup B10040512 8260b_Tutorial VOA_Tutori VOA_Tutori TiCsearch10 MethodBlank2 Meth Blank B10040513 8260b_Tutorial VOA_Tutori VOA_Tutori TICsearch10 Header 00123 Analte B10040514 8260b_Tutorial VOA_Tutori VOA_Tutori TICsearch10 00124 Analyte B10040516 8260b_Tutorial VOA_Tutori VOA_Tutori TiCsearch10 S0ug L B10040506 Mediu 8260b_Tutorial JA_Tutori VOA_Tutori TiCsearch10 Sample List view Message pane Section of the Window Enrors Wamings for Form 2 SMC Surogate Compound Recovery Description This is a read only display The view cannot be sorted and no data item in any cell can be directly edited Column widths can be changed in the standard way by dragging the header divider The selected columns can be changed using the Options Customize Display This is a read only display window Shows general warnings and all form specific errors warnings Environmental Reporting Context Menu A pop up menu appears when you right click on a row any cell of the table containing the following item Assign Header Sample If the row is an active one it assigns the selected row as the source of report header information for Form 2 It displays Header in the Statu
175. OR Use the TurboMass Data Browser 2 Inthe Spectrum window click OR Select Real Time Update from the Display menu 356 Data Acquisition Spectrum Real Time Update x I Enable Real Time update l Cancel Update Latest scan Average all scans Average latest fs scans To turn on Real Time Update select Enable Real Time update to turn it off deselect Enable Real Time update When Real Time Update is turned on the display will continually be updated with spectra from the current acquisition The actual information displayed is determined by selecting one of the options Real Time Update can also be turned on and off by clicking the Real Time spectrum toolbar button Latest scan Displays the last acquired scan This is the default option Average all Updates the display with spectra formed by averaging scans all the spectra that have so far been acquired Average latest Updates the display with spectra formed by averaging scans the last n scans acquired where n is specified in the associated field 357 TurboMass Software User s Guide 358 Stopping an Acquisition To stop an acquisition do one of the following e From the Tune page click aj e From the TurboMass top level window select Stop from the Run menu OR Click Data acquired up to this point will be saved TurboMass will ask whether you want to stop the GC as well Respond appropriately If you stop the GC you
176. Quantify windows Printing Quantify windows using the Quantify toolbar A Prints the current Quantify window display in portrait format A Prints the current Quantify window display in landscape format Writing Quantify Summary to the Clipboard Quantify allows the equivalent of the Quantify Summary Report to be written to the Clipboard From there the information can be pasted into other applications such as a spreadsheet Quantify uses the currently selected Sample List Method and Peak List files The Quantify Summary Report can either be ordered by compound or by sample To write the Quantify summary information to the clipboard select Copy Summary By Compound or Copy Summary By Sample from the Quantify Edit menu Files Used During Quantify Four types of files are used by the Quantify program Sample List Method Peak List and Calibration Curve The current file of each type can be selected from the Quantify File menu It is recommended that you use the Projects option when doing quantification as this allows you to organize and access your data more easily For more information see Projects on page 47 319 TurboMass Software User s Guide 320 The Sample List SPL File Three items in the Sample List are required for quantification File Name Specifies the sample data file name which will be the same name as the corresponding Peak List file Type Specifies the type of sample This should be set to Standa
177. RD4 Sm SG 2x7 SIR of 2 Channels ES 1359 TIC 100 8 06e4 10 50 11 00 11 50 Integrating Chromatograms The integration process locates the peaks in a chromatogram draws baselines and calculates peak heights and areas for quantification You can integrate a chromatogram using the current parameters by clicking 24 You can use the Integrate chromatogram dialog to change the parameters The integration process operates only on the currently displayed range and not on the whole chromatogram Integrate chromatogram Ea r Noise OK Peak to peak amplitude 2000 EA Smooth I Enable smoothing Copy Beak detect Fse Threshold Copy Allows you to copy the current integration parameters to the Clipboard These parameters can then be pasted into another application such as the Quantify Method Editor Paste Allows you to paste a set of integration parameters from the 399 TurboMass Software User s Guide Clipboard Noise The Integrate chromatogram dialog requires that you enter the Peak to peak Peak to peak Noise amplitude This value is used by the amplitude integration software to pre filter the chromatogram A suitable value can be measured directly from the chromatogram by right clicking and dragging the mouse across a section of noise in the chromatogram The sensitivity of the integration algorithm can be fine tuned by manually adjusting this value Note that the optimum value is
178. Reference standard will have their RTs modified according to the equation RT RTA RTi RTa Where RTa is the new retention time of the analyte compound RTi is the new retention time of the internal reference standard RTi is the old retention time of the internal reference standard RTa is the old retention time of the analyte compound When the updating is complete a dialog will be displayed indicating the number of compounds that were updated This will act as a confirmation to the user that the action took place This same sequence of events will occur if you do not click the Modify button but respond Yes to the Entry has been modified Keep changes dialog displayed NOTE Quantify after you have edited the Internal Reference RT and then select another compound or command Setting Multiple lon Ratios To set multiple ion ratios 1 Select one of the Multiple Ion Ratio options in the Peak Selection drop down list e Multiple Ion Ratio to Quantify Trace e Multiple Ion Ratio to Base Peak 2 Enter an appropriate REV Fit Threshold or leave the current value 3 Enter m z Target Ratio and Tolerance for each of up to four qualifier ions in the grid OR Paste in a spectrum previously copied from another environment This action will automatically add m z and target ratio values based on the data for the four highest intensity ions excluding the Quant ion Default values for Toleran
179. Report then click Save This Report Method is now available for the Report Method column of the Sample List Add the Report Method to the Sample List 1 Double click in the Report Method field and select Qualitative Method from the drop down list TurboMass TUTORIALQUANT TutorialQuant SPL loj x Fie Edit Samples Run View Quantify Configure GC Tools Help Gc O m f j ee Temp General Status EPA 525 Starflard EPA 525 Stand GC Status ESS er a Operate Ed Pressures Filament No Instrument 0 0 Shutdown Enabled Ready 2 Close the Report Method Editor by clicking the Close box in the upper right hand corner of the screen 585 TurboMass Software User s Guide 586 Environmental Reporting 21 Environmental Reporting About Environmental Reporting TurboMass Environmental Reporting software generates reports based on lists of PerkinElmer TurboMass and Clarus GC MS samples Sample List These reports while based on U S Environmental Protection Agency US EPA requirements are designed to be flexible and customizable to support worldwide environmental and QA QC reporting requirements governed by NELAC and ISO 17025 You can add samples to the list or create new lists using either the Sample List or Sample List Wizard While the Sample List is typically created prior to data acquisition it can be created and edited any time prio
180. Reset to replace the original paths Printing Configuration Information The Print command in the File menu lets you print a copy of the LINK and GC configuration information Configuration information includes font choices quick paths and GC and interface data 155 TurboMass Software User s Guide GC Method Editor You use the Method Editor for all GC method operations When opening the Method Editor from the GC menu the Method Summary Window is displayed E Method Editor untitled Method Summary Z File Instrument Equilbrate View Help BEE Disia S R e 2 A Ready LECIO Ld The Method Summary Window contains the data acquisition and GC control information including the run time information and control options such as injector temperatures carrier gas settings and oven program Developing a GC Method To develop a new GC method set data channels and set your GC control options You can also create a new method by editing an existing method file and renaming it with the Save As Command Creating a new GC method 1 Select Method Editor from the GC menu in the TurboMass top level window OR 2 Click in the GC panel 3 Select Create new method in the Startup dialog and click OK to open the Method Editor 156 GC Control imi Method Editor c peneze turbomass Ver4 1 U examples birub mth Method Summary Fle Instrument Equiibrats View Help S 20 Aha te a Fead e
181. S a a eai 664 Audit Log Management ccccccccccsceessesneceeeeeeeeeeseeeeeeeseeeseeeeeenaeentees 664 Security Manager sce EE EE 665 Security Manager Toolbar ceccceccsecssesseceseceeceecneeseeeeeeeeeeeeeneennes 668 Setting up an Account Policy cccccccsesseceneceteceseceseeeeeeeeeeeseeenseenaes 669 Creating a User Account cccccesccessceseceseceeeceeeeeeeeeseeeeseeeseeeaeeneenaeeees 670 Creating a Groups ics ccsstizsseet aE aaa a aaea eaa a aE 672 Managing the Audit Logo ecceccceesseesecsecseenseceseceseeeseeseeseeeseeeens 676 Appendix B TurboMass Software Installation scssscssscsssseseeees 681 TurboMass Software Installation cccesccescessceeeceeeeeeseesseessecnseenseenseenes 683 Installation Summary ccccccccccecsseesseeseeesceescecseecstecssecesecnseeneeseeeseeeseneeses 684 Uninstalling the TurboMass Software and all of its Components 684 Installing the TurboMass software cccccsccescessceeeceseeeeeeeeentecnsecnseeeseenes 692 Installing Clarus 500 MS NIST EPA NIH Library 2002 esceesceee 707 Installing the NIST Library 0 c cc ccccccccsceseceseceeeeseeeeeseeeseeeeeeeeeasees 707 Configuring TurboMass for GC Control ccccecceseceseceseceeeeeeeeeseeeeeeeeees 718 Configuring the GC for the First Time eeeececeeseeeeceeeneeeeceeeeaeees 718 Appendix C TurboMass Quantify Calculations sccsscssscsssosseones 729 TurboMass Quantify Calc
182. Select Audit from the Policies menu The Audit Policy dialog is displayed 676 Appendix A TurboMass Security M Enable audit trails i m Auditable events Cancel Logon and Logoff I Policy changes I Object access I Other event r Event log settings Maximum List Entries 1000 I Overwrite events as needed 2 Select the auditable events that you want to monitor in the audit log and specify the event log settings Enable audit trails When selected audit information is written to the audit log Deselecting this checkbox disables the audit log and the audit log is not updated when an auditable event occurs Auditable events The auditable events checkboxes determine which event types are written to the audit log file Maximum List Use this field to specify the maximum number of Entries entries allowed in the audit log After the specified number of entries is reached the Overwrite events as needed setting automatically takes effect Overwrite events as If selected and the number of list entries exceeds needed the Maximum List Entries specified then Security replaces older entries with newer ones as necessary If not selected new entries are not added after the Maximum List Entries value is reached Monitoring audit log 1 From the Security Manager window select Audit Log Viewer from the Tools menu 677 TurboMass Software User s Guide The Audit Log Viewer dialog is displayed
183. Select an entry from the list or enter in a new value Enter in a new value Deleting rows and columns gt To delete a row click to delete the selected rows If the entire table is selected the cells are cleared not deleted gt To delete a column select the column and click fa 239 TurboMass Software User s Guide Starting the Analysis gt Before starting an analysis save any changes made to the Sample List by selecting Save from the Sample List File menu NOTE The GC status must be either No Method or Run Done to successfully set up Otherwise GC communication lockups may occur Acquiring data 1 Select Start from the TurboMass top level Run menu OR Click gt to open the Start Sample List Run dialog Start Sample List Run xj Project C TurboMass DEFAULT PRO AS IV Acquire Sample Data zh T Auto Process Samples Bre d alp T Qualitative Calculations L IV Generate Communiqu Reports I Preview Reports Run J Erom Sample f1 IoSample 4 r Quantify Qualify and Generate Reports J After Each Run At End of Sample List r Process I Pre Run I Post Run Cancel Project The name of the current project appears in this field To acquire data to a different project click OK or Cancel to exit 240 Acquire Sample Data Auto Process Samples Auto Quantify Samples Qualitative Calculations Generate Communiqu Reports Preview R
184. Selecting this option will acquire data for the specified samples in the list Auto Process Samples Selecting this option will process the acquired data as specified in the Process column of the Sample List Auto Quantify Samples Selecting this option will automatically enable sample quantification Qualitative Method Qualitative Calculations Selecting this option will enable Qualitative Method processing Generate Communiqu Reports Selecting this option will enable Communiqu Report generation Preview Reports Check this box to specify that the Communiqu reports generated during processing will be displayed in a preview window prior to printing or saving to a file or database NOTE The five options above allow you to acquire and immediately process and quantify data as desired Or you may choose to process or quantify data at a later time Run From Sample n To Sample m Sets the range of samples in the sample list which will be acquired and or analyzed If you highlight a range of rows before starting the analysis the first and last rows of the highlighted region will be displayed here Quantify Qualify and Generate Reports After Each Run Indicates specified processing will occur after each row in the Sample List At End of Sample List Indicates specified processing will occur only after the sample list is complete Process Pre Run Specify the name of the process that will be run before the acquisi
185. Software User s Guide 384 2 To delete all magnification ranges select Magnify from the Chromatogram Display Range menu Click Default to delete all magnification ranges 3 Click OK to exit Restoring the display gt Click EJ to toggle the display between the previous display range and the default range OR Selecting Default from the Chromatogram Display Range menu toggles the display between the previous display range and the default range These operations do not remove magnification ranges Setting the Display Range Defaults The display range default settings specify both the effects of choosing and adding a new chromatogram to the display Changing the default display 1 Select Range Default from the Chromatogram Display menu r Default graph aro Ka Current ie i Cancel I Automatic range default 2 Make any changes Default graph If there is more than one chromatogram in the same window this option specifies whether the default time scan range for that window is made large enough to include the time scan ranges of All the chromatograms or large enough for the Current chromatogram only Chromatogram Automatic range default If this option is selected the display range will return to the specified default see Default graph when a new chromatogram is added to a chromatogram window If this option is not selected the display range will remain unchanged when a new chromatogram is adde
186. Standard DFTPP BFB Warnings Custom AutoTune Scope Parameters Operate Reinitialize Pump vacuum Monitor Instrument Threshold Settings Communications Status Instrument Name y Diagnostics Page Instrument Tuning NOTE The instrument must be in Operate mode and the reference gas must be on before you can run UltraTune Custom AutoTune TS AUTOTUNE STATUS READY TO START AUTOTUNE Ramping 2 Click Setup to set the AutoTune setup parameters The default setup parameters FWHM 0 6 and masses 69 and 502 for EI UltraTune are suitable for tuning with Heptacosa There is no need to alter the Tune Mass or Peak Width parameters if you are using Heptacosa The Level of AutoTune performed can be selected as Maintenance or Full A Full AutoTune starts from a default set of tuning parameters but uses your current settings for the Inlet Line Temperature and Source Temperature In a Maintenance AutoTune the software uses your current settings for Inlet Line Temperature Source Temperature Electron Energy and Source Emission A Maintenance AutoTune can be quicker than a Full AutoTune but should only be performed if the instrument is reasonably well tuned already If the current tuning is too poor AutoTune will give an error and ask you to perform a Full AutoTune The Tune Masses parameters set a Low Mass and High Mass that will be used to tune on The Peak Width at Half Height parameters set the
187. Strip and Combine functions Reporting your Data You can use supplied templates or create your own templates using the Communiqu template designer to generate custom reports 65 TurboMass Software User s Guide 66 Instrument Data 4 Thresholds Instrument Data Thresholds Selecting the Inlet System Before you acquire data you must first configure the software to support the inlet system selected You do this from the Select Interface dialog which displays the available inlet systems 1 Select Select Inlet Interface from the Sample List Configure menu The Select Interface dialog is displayed Select Interface x AutoSystem XL GC Interface to AutoSystem XL GC Cancel 2 Select your interface The list of inlet options that appears in the Select Interface dialog reflects the inlet system selected when TurboMass was installed If at a later date you add a new inlet system or change one of your existing inlets you may need to reinstall TurboMass to gain access to the control software for the new inlet system 3 Select your choice for an inlet to use and click OK to reconfigure the software to reflect the new inlet system Once you have selected the inlet system TurboMass will give you access to the parts of the acquisition system that are appropriate to the inlet selected and the Tune application 69 TurboMass Software User s Guide 70 Setting Instrument Data Thresholds TurboMass has Instr
188. The calibration base can be either Area or Height the examples below are shown for Area External Peak Response Area Where Area is the area of a peak calculated by peak detection Internal Peak Response Area Amounty Areay Where Area is the area of a peak calculated by peak detection Amounty is the given amount of the Internal Standard in the sample Areay is the area of the internal standard peak calculated by peak detection 731 TurboMass Software User s Guide 732 Calibration Curve Calculations TurboMass can fit several types of calibration curves which are described below Weighted Calibration Curves Calibration points used when fitting curves can be given a weighted importance the larger the weighting the more significant a point is treated when the curve is fitted Weighting wi of ith calibration point is calculated using one of the following all w are set to 1 for no weighting De Wipe n 2 WF gr 3 Wj xj 4 Wj xj Where yj is Y value response of ith calibration point Xj is X value concentration of ith calibration point Include Origin If Include Origin is selected as a calibration curve type an extra point with zero concentration and response is used in the regression The extra point has a weighting of 1 Appendix C TurboMass Quantify Calculations Average RF The calibration curve formed is linear passing through the origin with a gradient equal to the aver
189. Time units for setting the From and To values in the grid Scan Selects Scan numbers for setting the From and To values in the grid Enter the number of largest peaks you want to report Set a coelution window parameter to ensure reliable identification of target compounds within the qualitative chromatograms Peaks identified in the quantitative results can be missed in the qualitative report if their retentions do not exactly match those found by the qualitative report method This can occur because two specific masses in a peak may maximize one or two scans away from each other of the TIC due to noise and scan rate induced spectral skewing Click on the Search Parameters tab 5 x File Help O 2 ele S m l General Search Parameters Library Settings Spectrum treatment Limits T None Window size scans T Apply limits Set Defaults AutoRefine j Minimum abundance Off Noise threshold Minimum m z Off F 000 Spectrum search type Magimum m z Off Identity Similarity Normal z Minimum match Spectrum search options Molecular weight constraint J Reverse search Between fi and J Penalize rare compounds Reporting Presearch Maximum hits Text Defaut C Off Maximum hits Plots Qualitative Method 15 Select the Spectrum Treatment to be applied to the spectrum before initiating the search For example Background Subtracted 16 S
190. TurboMass Software User s Guide TurboMass Software User s Guide Release History Part Number Publication Date For Software Version 09936691 March 2006 5 2 Any comments about the documentation for this product should be addressed to User Assistance PerkinElmer Inc 710 Bridgeport Avenue Shelton Connecticut 06484 4794 U S A Or emailed to info perkinelmer com Notices The information contained in this document is subject to change without notice Except as specifically set forth in its terms and conditions of sale PerkinElmer makes no warranty of any kind with regard to this document including but not limited to the implied warranties of merchantability and fitness for a particular purpose PerkinElmer shall not be liable for errors contained herein for incidental consequential damages in connection with furnishing performance or use of this material Copyright Information This document contains proprietary information that is protected by copyright All rights are reserved No part of this publication may be reproduced in any form whatsoever or translated into any language without the prior written permission of PerkinElmer Inc Copyright 2006 PerkinElmer Inc Produced in the U S A Trademarks Registered names trademarks etc used in this document even when not specifically marked as such are protected by law PerkinElmer is a registered trademark of PerkinElmer Inc TurboMass Clarus 500
191. UN Parameter7 INLET_POSTRUN Parameter8 INLET_SWITCH Parameter9 AUTO_FILE Parameter10 PROCESS Parameter11 PROCESS_PARAMS Parameter12 PROCESS_OPTIONS Parameter13 SAMPLE_LOCATION Parameter14 JOB Parameter15 TASK Parameter16 USER Parameter17 SUBMITTER Parameter18 CONDITIONS Parameter19 TYPE Parameter20 ID Parameter21 CONC_A Parameter22 CONC_B Parameter23 CONC_C Parameter24 CONC_D Parameter25 CONC_E Parameter26 CONC_F Parameter27 CONC_G Parameter28 CONC_H Parameter29 CONC_ Parameter30 CONC_J 751 TurboMass Software User s Guide 752 Parameter31 CONC_K Parameter32 CONC_L Parameter33 CONC_M Parameter34 CONC_N Parameter35 CONC_O Parameter36 CONC_P Parameter37 CONC_Q Parameter38 CONC_R Parameter39 CONC_S Parameter40 CONC_T Parameter41 FRACTION_MASS Parameter42 INJ_VOL Parameter43 STOCK_DIL Parameter44 USER_DIVISOR_1 Parameter45 USER_FACTOR_1 Parameter46 USER_FACTOR_2 Parameter47 USER_FACTOR_3 Parameter48 SPARE_1 Parameter49 SPARE_2 Parameter50 SPARE_3 Parameter51 SPARE_4 Parameter52 SPARE_5 Parameter53 QUANT_METHOD Parameter54 QUANT_CALFILE Parameter55 QUAL_METHOD Parameters6 REPORT_METHOD Variable Parameter Data NumberOfDataValues 2 Data1 Filena me file text MSFile Ms TuneFile InletFile InletPreRun INletPostRun InletSwitch AutoFile Process ProcessParam ProcessOptions SampleLocation Job Task User Submitter C onditions Standard ID 12 1 2 1 3 1 4 1 5 1 6 1 7 1 8 1 9 2 0 2 1 2 2 2 3 2 4 2 5 2 6 2 7 2 8 2
192. V and it is located in the primary TurboMass path C TurboMass The goal of Standard UltraTune is to give a satisfactory library searchable spectrum not to achieve maximum sensitivity Running Standard UltraTune DFTPP BFB If you cancel UltraTune during the data acquisition phase the instrument will be restored to the state it was in prior to the start of UltraTune i e previous tune parameters reference gas off etc 1 Click 5 OR 93 TurboMass Software User s Guide Select UltraTune followed by Standard DFTPP BFB from the Tune page Options menu File IonMode Calibration Gas Kesimga Help a Readbacks SIC ICAL Standard OFTPPIBFS Warnings Custom AutoTune Scope Parameters Operate Reinitialize Pump vacuum Monitor Instrument Threshold Settings Communications Status Instrument Name v Diagnostics Page You will hear a click when the reference gas solenoid valve opens and UltraTune begins The first page of UltraTune is displayed UltraTune Progress TS ULTRATUNE STATUS 2 Click Setup to display the UltraTune Setup dialog 94 Instrument Tuning UltraTune Setup x m After UltraT une I Print Report Saye Altemate Tune Files I Prompt for Recalibration Evacuate Reference Gas m Final Multiplier Setting T User Set Cancel The default setup parameters Full Width Half Max FWHM 0 55 for masses 69 131 2
193. _Defaut Appending new fields to the Summary window 1 Select the field you want to append from the Available Fields list 2 Click Append 3 Repeat steps 1 and 2 as required 4 Click OK to save the changes and update the Summary window Inserting new fields in the Summary window 1 Select the field you want to insert from the Available Fields list 2 Select the field before which you want to insert the new field in the Report Format list and click Insert 3 Repeat steps through 2 as required 4 Click OK to save the changes and update the Summary window 301 TurboMass Software User s Guide 302 Removing a field from the Summary window 3 4 Select the field you want to remove in the Report Format list Click Remove To remove all the fields in the Summary window click Remove All Repeat steps 1 and 2 as required Click OK to save the changes and update the Summary window Formatting the display of a field in the Summary window Select the field whose display settings you want to change in either the Available Fields or Displayed Fields list Change the Header field to display the heading you want to display above this column Change the Justification setting to Left Right or Center as required Change the Field Width and Decimal Places as required Change the Not Found parameter as required Not Found determines what will be printed in the Quantify report for this field if the peak i
194. a file without having to display a chromatogram or spectrum The Data Browser also holds the history information that gives you access to any processed data that have been derived from the original data easing the management of processed data m mies c turbomass quantify pro data T Cancel E TurboMass QUANTIFY PRO te E Data Experiment Delete Drives c x Network m Information Chromatogram Sample Description Spectrum Acquired Function History Figure 2 Data Browser Getting Started Selecting a new raw data file In the File Name field enter or select the name of the raw data file you require and click OK If you do not see the name of the raw data file you want to work with select a new drive or directory or double click an item in the File Name list Main Data Browser The main Data Browser appears when you select Open Data File from the TurboMass top level File menu It has the following two options that do not appear on the Spectrum or Chromatogram Data Browsers Chromatogram Automatically opens the Chromatogram window displaying the chromatogram of the new data file Spectrum Automatically opens the Spectrum window displaying the spectrum of the new data file Spectrum and Chromatogram Data Browsers The Spectrum and Chromatogram Data Browsers appear when you select File Open from Spectrum or Chromatogram They have the following three parameters
195. abetical order Included libraries Libraries being searched The order in which items appear in the Included libraries list is the order in which they were moved over i e new items are appended to the list Search selected libraries Do not search selected libraries gt gt Search all libraries lt lt Remove all libraries from search list 337 TurboMass Software User s Guide 338 Compound must appear in database A list of other databases that the compound must be in The list is processed as a logical OR that is if 5 of the databases are checked the compound is found if it is either of the five databases All of these are only enabled when Compound must appear in database is checked These states are remembered from the last setting EINECS European Index of Commercial Chemical Substances EPA US EPA Environmental Monitoring Methods Index Fine Commercially Available Fine Chemical Index HODOC CRC Handbook of Data of Organic Compounds IR NIST EPA Gas Phase IR Database NIH NIH NCI Inventory File RTECS Registry of Toxic Effects of Chemical Substances TSCA Toxic Substances Control Act Inventory USP U S Pharmacopoeia U S A N A Step by Step Qualitative Method Summary e Create a Sample List e Create a Qualitative Method e Put the Qualitative Method in the Sample List e Start the Analysis 1 Create a Sample List The first thing that you must do is to create a list of samples that you want to use to
196. age response values of the calibration points Average RF Swy Sw Where Swy 2 yi Wi Xj Sw 2 wi yj 1s Y value response of ith calibration point Xj is X value concentration of ith calibration point wj is weighting of ith calibration point all set to 1 for no weighting Linear The calibration curve is formed by fitting a line using linear regression to a set of calibration points Gradient Swxy Swxx Intercept Yw mean Gradient xw mean Where Yw mean T 2 yj wi ZWwj Xw mean E xj wi ZWj 733 TurboMass Software User s Guide 734 Xj Xw mean Yi Yw mean Swxy Swxx x x Xw mean 2 yj is Y value response of ith calibration point x is X value concentration of ith calibration point w is weighting of ith calibration point all set to 1 for no weighting i gnung p If Force Origin is selected a line with zero intercept is fitted Gradient xj yi wi OE yy X42 wi Quadratic and Higher Order Curves TurboMass uses a general Least Squares Fit algorithm to regress a polynomial of any order against the calibration points The method used is outlined below Polynomial regression can be described as the fitting of m independent variables Xj j 0 to m 1 to a single dependent variable y i e y Xbte where y is the n x 1 vector containing the n y values y X is the n x m matrix of x values xi b is the m x 1 vector of regression coeffici
197. ainsearch is often much larger than the Viables value Sig Determines how many spectral peaks are compared during the Peaks Mainsearch Exclude Masses Masses Allow you to exclude up to four specific masses in the search 1 4 spectrum from the Mainsearch These excluded peaks are not compared to library entries This can be useful for example to exclude a contaminating ion that cannot be removed from the spectrum by any physical or chemical means All below Allows you to exclude all masses below a certain value Ranking These parameters determine whether hits are listed in order of Forward or Reverse Fit Forward Indicates how likely it is that the search spectrum is a pure sample of the library entry Any peaks present in the search spectrum but not present in the Library spectrum decrease the Forward Fit value Likewise any peaks present in the library spectrum but not 497 TurboMass Software User s Guide present in the search spectrum decrease the Forward Fit value Reverse Indicates how likely it is that the search spectrum contains the library entry in this case the search spectrum may be a mixture of compounds Any peaks present in the library spectrum but not present in the search spectrum decrease the Reverse Fit value However peaks that are present in the search spectrum but not present in the library spectrum have no effect on the Reverse Fit value Setting Library Search Filters Library search filters
198. aks matched to reference peaks are highlighted in a different color Calibrate olx Print Edit Display Cancel Default Data file SOLSEI10 Uncalibrated 12 matches of 12 tested references 100 168 80 n 230 97 5 180 76 218 81 230 97 963 79 313 48 325 37 Reference file HEPTACOS 100 218 99 263 99 168 99 180 99 225 99 313 98 358 Mass difference Raw Ref mass 0 02 xXx x amu 0 64 Residuals Mean residual 8 575929e 9 0 076559 x Mass Calibration Altering the Displayed Range You can alter the range of the spectrum on display by left clicking at one end of the range of interest and dragging the mouse to the other end of the range of interest TurboMass indicates the selected range Clicking Default restores the default display range Manually Matching Peaks e You can match a calibration peak to the closest reference peak by positioning the mouse over the calibration peak in the top window and right clicking If the closest reference peak is already matched to another calibration peak the previous match will be removed e You can also right click to undo a peak match Position the mouse over the matched calibration peak and right click For small peaks this must be done very close to the baseline 129 TurboMass Software User s Guide Other Calibration Facilities Deleting the Instrument Calibration 1 Select Delete Calibration from the Calibration Calibrate menu This res
199. al Parameters command in the Edit menu The specific form of the Environmental Parameters dialog depends on the type of the currently selected compound If the Type is Internal Standard a dialog appears with the Type CAS number and Abbreviation parameters Environmental Parameters Compounds Type Type Int Std Int Std Surrogate Surrogate Surrogate Target Target Target Target Spike Target Target Target Target Target Spike Spike Target Target Spike Target Target Target Target Target Target Target Target Target Target 363 72 4 Abbreviation PFB Pentafluorobenzene CAS number 1 4 Difluorobenzene 1 4 Dichlorobenzene D4 Dibromofluoromethane Toluene d8 Bromoflurorobenzene Dichlorodifluoromethane Vinyl Chloride Bromomethane Trichlorofluoromethane 1 1 Dichloroethene Methyl Tert butyl Ether Methylene Chloride 1 1 Dichloroethane 2 2 Dichloropropane Chloroform Benzene Trichloroethene Dibromomethane 1 Bromo 2 chloroethane Toluene trans 1 3 Dichloropropene 1 1 2 Trichloroethane Ethylbenzene p m Xylene o Xylene Isopropylbenzene Bromobenzene n Propylbenzene 1 3 5 trimethylbenzene sec Butylbenzene If the Type is Target the following dialog appears 278 Environmental Parameters Compounds Type Name Int Std Pentafluorobenzene Int Std 1 4 Difluorobenzene Int Std 1 4 Dichlorobenzene D4 Surrogate Dibromofluoromethane Surrogate Toluene d8 S
200. all saved processes with the original raw data at the top of the tree Processed data that have been derived from previously processed data are indented to show the relationship to those data Each process is labeled with a unique identification number and the time and date when it was created This aids differentiation of similar processes Displays sample description text obtained from the header of the currently selected data file Displays a description of the currently selected function Displays full history of the currently selected process The history starts with raw data at the top of the list and describes each processing step made to reach the current process Exits the History Selector using the current selection Exits the History Selector defaulting to the original selection Deletes the currently selected process from the process history tree Deletes all processes belonging to the current data file function 43 TurboMass Software User s Guide 44 Displaying processed data 1 Select the relevant raw data file in the Data Browser dialog and click History The History Selector dialog is displayed Select the required processed data in the Process History list and click OK 3 Click OK in the Data Browser dialog Processed Data Labels Each of the processed data labels is followed by a series of letters and numbers that describe the parameters used during the process Refine Rf nl n2 Rf Refined spec
201. all users O Only for me PerkinElmer Instruments Select the option Anyone who uses this computer all users 16 Enter the requested information and click Next to continue the installation The Setup Type dialog appears 700 Appendix B TurboMass Software Installation iz Communique 2 3 Customer Edition InstallShield Wizard Setup Type Choose the setup type that best suits your needs 17 Select Complete and click Next The Ready to Install the Program dialog appears ie Communique 2 3 Customer Edition InstallShield Wizard Ready to Install the Program The wizard is ready to begin installation 701 TurboMass Software User s Guide 18 Click Install to continue the installation Communique installation begins Installing Communique 2 3 Customer Edition The program features you selected are being installed Please wait while the InstallShield Wizard installs Communique 2 3 Customer Edition This may take several minutes Status Writing system registry values InstallShield The install process continues until the Install Wizard Complete screen is displayed ie Communique 2 3 Customer Edition InstallShield Wizard InstallShield Wizard Completed The InstallShield Wizard has successfully installed Communique 2 3 Customer Edition Click Finish to exit the wizard 702 Appendix B TurboMass Software Installation 19 When complete click Finish and start the MATLAB insta
202. alysis start 242 294 audit log Security Manager 681 Auto Refine 515 AutoBuild 288 automatic shutdown 362 startup 361 automatic library searching 420 504 AutoTune 98 AutoUltraTune 93 B background data files 474 background subtract chromatogram 395 Spectrum 452 BPI chromatograms 379 Browser Report template 555 558 C calibration automatic 121 curve 306 from data files 131 high mass 135 parameters 120 process 116 process overview 118 saving 137 Index types 117 chemical structure library hit 512 chromatograms align 381 background subtract 395 BPI 379 delete displayed 392 display 52 376 integration 401 magnification ranges 383 peak annotation 390 printing 439 processing 395 real time data 358 real time display 393 smoothing 399 text labels 393 TIC 379 clustered data files 471 Collections 563 combine spectra 450 Combine data files 483 functions 483 output selection 485 spectra 415 Communiqu 21 563 Concentration Level 219 configuration GC options 148 initial GC 145 LINK 147 Custom Compounds 655 D data printing 57 Data Browser 38 data channels GC 159 data file structure 50 765 Index 766 data files background 474 clustered 471 CODA 472 Combine 483 delete 46 enhanced 469 output 475 processing 472 raw 41 subtracted 466 Data object Indexing 580 detection flags peak 315 E enhanced data files 469
203. ample List window Clicking this button displays the Help window for this dialog Building a Sample List You can build a sample list manually or use the Sample List Wizard This procedure describes how to use the Sample List Wizard to build your sample list In this example we will show how to use the Sample List Wizard to build a sample list Select Sample List Wizard from the File menu to display the Sample List dialog 217 TurboMass Software User s Guide Sample List Wizard SampleList Existing sample list C New sample list Analysis e Matrix Cc Concentration level Cc Cancel Help You can modify an existing sample list or create a new sample list This example shows how to build a new sample list 2 Click the New sample list button 3 Select the type of Analysis Volatiles Semi Volatiles or QA QC 4 Select the Matrix Soil or Water 5 Select a Concentration level Low or Medium 6 Click OK The next dialog appears for you to enter the Sample Information and Lab Information for each of the Samples 218 amp Sample List Wizard Sample List Row Sample ID HE Lab Information 1 Sample Injection Information Sample type Vial No GC Column Moisture Sample Prep Information v Date received Sample wt Soil extract vol Extraction type GPC Cleanup Decanted Surrogate lot ID ISTD lot ID File name Eile text Sample ID Injection vol
204. analysis Qualitative Method A drop down list enabling you to select the Qualitative Method typically the TIC library search to be used for the analysis After editing a Sample List the Environmental Reports generated do not reflect the Sample List until Quantify is first run on the new list The Sample List is saved with the RAW data file when data is acquired If you change the Sample ID field in the Sample List and try to print Environmental Reports the Sample ID reverts back to the original setting when the files were acquired You may Sample List want to change the Sample ID field if you modify the Sample List to acquire new samples Saving a Sample List 1 Click OR Select Save or Save As from the File menu If this is a new Sample List or the Save As option has been selected the Save Sample List dialog is displayed Save As 21x Save in fa Sampledb X Sl c E a Default spl Save as type Sample Lists SPL BA Cancel 2 Enter a name into the File Name field and click Save The following characters cannot be used in the filename amp lt gt Editing a Sample List by importing a worksheet from LIMS The TurboMass software supports text file import for creating a Sample List from a LIMS worklist and text file export for passing results on to LIMS The import file format is compatible with one generated by PerkinElmer LABWORKS but it can be generated by most LIMS systems
205. and 600 Series LINK Interface are trademarks of PerkinElmer Inc Microsoft is a registered trademark of the Microsoft Corporation Windows is a trademark of the Microsoft Corporation Contents Table of Contents Table of Contents sn onene Seles asa een alana 3 INtrOductiOn scsscscsssssscssccssscsssscsscssscnsssnssensssnessesssessssssscsssssescsssoeses 17 Compatability rrari renani ian a a Eae aaO E RESA 19 Using this Guid essre iien ar ie EE EE E 19 Conventions used in this Guide cccccccsecsssceseceseceeeceeeeeeeeeeneeeseeeseeeeeensees 22 Getting Started cccccrcccsscsccscsccsssssssesccccscccssscessssssssccssescesssssesesescesoeees 23 Getting Started assess csvete n aena bev cocdosna Sa A al eave A dees 25 Starting TurboMass cccccssecsseessecseceecesecesecseeseeeseeeeeseeeseeeseeesaeensees 25 Quitting TurboMass cccceseceseceseceseceseceseeeeeeseeeeeeeseeeeeseeeseeeseeeaeesaees 25 General Guidelines for TurboMass Operation c ccesccesccereeeteeeteetseeneees 26 The TurboMass Top Level Window cccccsccescessceeseeeeeeeseeseeeeeeeeeneeesees 27 The TurboMass Tool bat ccccccccssecsseeseeseeceeeeeceeeeeeseesseesseeeseeeeeesaes 28 Accessing Menu Commands cccesccssscesseeeeeeneeeeeeseeeaeesaeenseenseenseens 28 The TurboMass Desktop ccccccsccsseceteceteeeeceseeeeseesseecseeeseecaaecseesaecnaeenaeens 30 PUnictlOn KCYS 223 aeccceakevas cei heared ee desis
206. andard concentrations of target compounds A QC sample is used as a quality control measure to compare the calibration curve of the acquired data against a known concentration The QC field in the Sample List has no effect on any calculations performed When sample quantification is performed the deviation of the analyte concentration is calculated against the QC concentration and this is shown as a percentage in the Quantify window under the heading Dev To select this heading select Conc Deviation from the Sample Format menu The value determined for a Blank sample is subtracted from future analyte runs From the Quantify Process menu select Calculate and then select Blank Subtract Compounds The quantification procedure checks through the Sample List and subtracts the concentration of each compound in a Blank from the corresponding concentration in an analyte If several blanks are specified in a Sample List then the preceding Blank is used for each analyte If no Blanks are specified or there is no preceding Blank for the analyte of interest then no Blank Subtraction is carried out Blank Subtraction can only be done from the Quantify window It cannot be done from the Sample List 231 TurboMass Software User s Guide 232 In addition the following Sample Types are added for Environmental Reporting An Analyte Duplicate Analyte Dup is used when an Analyte is reprepared and reanalyzed Typically the Sample ID remains th
207. ania n a iara aaa aE en 501 Automatic Library Search cccccccsceseceseeseceeeeeseeeeeeeeseeeeeeneeeeeenaees 502 Manipulating the Library Display cccccesscessceeeeeeteeeeeeeeeeeeseens 503 Printing the Results of a Library Search eceeeeeeeereeteeeeceeeeeeeeees 510 Copying To and From the Windows Clipboard ccsceeseeeseeeteeees 511 Refining the Search Spectrum cccccccescceseeseceeeeeeeeeeeeeeseeeeeeteeetees 512 AUTO ROPING iazesnssattyt E a E eaten ean ash Ess 513 Using the Library Compare Process cccccsccsseesteesteesteesteenteenteeeaeens 513 Using the Library Subtract Process ccccesccessceeseeeeeeeeeteeeseeeteeetees 513 Creating User Libraries c ccccecccessceeseeeseeeeeeeeeeecaecnsecesecnseeneeeeeeesnneeses 515 Creating a User Library eneinio aie 515 Adding Text Data to the Library Entries 00 0 cccecesseeceseeeeeereeteenee 517 Indexing a User Library insae e alia aa n 519 Deleting Library Entries ssseeesessesseesesseosssserssosseseessesorssessesseososseesee 520 Using the Library Locator 0 ccccccecccecsceeseeseeseeeecesecesecsaeeneeseeeseneeeeeeaes 522 TurboMass Software User s Guide OVETVICW es EAE AEE AE tient Sateahs Stout ben EET EE 527 How to create a data file Map eee ecccsseesseceteceteceseceseeeseeeeeeteeensees 528 About the Map Display ninenin caei akr E i r E 530 The Map Toolbar masce aaae aa e NT R aiaa siani 531 Selecting a Range to Map from the
208. arance of Peak Labels Each chromatogram window has its own set of Peak Annotation parameters which determine the appearance of peak labels You can inspect and alter the parameters for the current window from the Chromatogram Peak Annotation dialog Changing the peak annotation parameters 1 Select Peak Annotation from the Chromatogram Display menu to display the Chromatogram Peak Annotation dialog Annotation Type pm Annotation Threshold M Peak Top Time Full Scale foo J Peak Top Scan C Intensity p M Peak Purit r Decimal Places fo 7 oi Sas Medium se I Scan Base Peak Mass Decimal Places 0 ba lV Peak Response Area Decimal Places 1 J Peak Response Height Cancel 2 Make any changes 3 Click OK Annotation Type Parameters These parameters control which types of peak annotation will appear on the chromatogram The types of peak annotation available are Peak Top Time Peak Top Scan Peak Purity Scan Base Peak Mass Peak Response Area and Peak Response Height To display a particular peak annotation select its checkbox NOTE Chromatogram For Scan Base Peak Mass you can set the number of decimal places to a value from 0 to 4 For Peak Response Area and Peak Purity you can set the number of decimal places to a value from 0 to 3 The illustration above shows typical defaults for GC MS If Display Peak Name is selected the peak name if available will be displayed above the p
209. are all saved together under a common name You may find it useful to calibrate the instrument for each of the different types of experiments that you do and save these calibrations to disk This means that when you switch between experiments you can restore a suitable calibration from disk rather than having to recalibrate from scratch Saving a Named Calibration 1 Click Save As from the Calibration File menu and enter a new file name Save As 1 1x Save as type Calibration File cal z Cancel 2 Click Save If the selected file exists you will be asked to confirm that you want to overwrite the existing information Click OK to continue or Cancel to enter a different file name Restoring a Saved Calibration 1 Select Open from the Tune File menu 2 Select the calibration file required either by entering its name or by selecting it from the displayed list 137 TurboMass Software User s Guide 3 Click Open to display the Load Instrument Calibration dialog Open File name Files of type Calibration File cal x Cancel 4 Select the desired calibration file 5 Click OK 138 GC Control F GC Control Overview of TurboMass GC Control This section contains the software procedures required for GC control when the PerkinElmer Clarus 500 GC or AutoSystem XL GC is used as the inlet for the mass spectrometry system You need to configure the mass spectrometer for GC co
210. ary Both PKI4_SV Volatile Organic Instrument Performance Check BFB Both PKI5_VOA Semi volatile Organic Instrument Performance Check DFTPP Both PKI5_SV Volatile Organics Initial Calibration Data Both PKIGE_VOA Semi volatile Organics Initial Calibration Data Both PKI6_SV Volatile Continuing Calibration Check Both PKI7_VOA Semi volatile Continuing Calibration Check Both PKI7_SV Volatile Internal Standard Area and RT Summary Both PKIG_VOA Semi volatile Internal Standard Area and RT Summary Bath Quantify Method 8260b_Tutorial mdb Environmental Reporting In the Report Method form the only column that contains information that you can change is the Report Method column The columns can be sized in the standard way by dragging the header divider Form Description VOA SV Matrix Report Method The EPA Form number and subcategory letter from OLM04 2 The full description of the Form The analysis type the Form is used for volatiles or semivolatiles The matrix type the Form is used for water samples soil samples or both The Communiqu Report Method used to generate this Form Positioning your cursor in the Report Method column displays a button Clicking this button displays a file selector for the MethDB directory of the current Project To define the report methods To define the report methods
211. as formed For more information on examining modifying and creating peak lists see Chromatogram on page 365 The peak list files are normally stored in the PEAKDB directory Calibration Curves CRV File Stores the Quantify Calibration Curves that are produced for each of the compounds within the method The Calibration Curve file has the same name as the method used to create it The Calibration files are normally stored in the CURVEDB directory 321 TurboMass Software User s Guide 322 Qualitative Method 11 Qualitative Method Introduction to Qualitative Processing You can determine the identity of your sample through the qualitative processing of sample data To do this you create a Qualitative Method of the data that you can specify in each row of the Sample List This defines the parameters required for generating reports that do not make use of quantitative results The parameters fall into two main categories 1 Definition of input data for generating a peak data set 2 Library search parameters Qualitative processing can have one or two stages 1 Integration of one of more defined chromatograms to generate a peak list 2 Automatic library searching of the peak spectra and reporting of potential hits The first step will always be carried out if a qualitative method is specified in the Sample List The output of this process will be a collection of peak data which can be made available to Communiqu a
212. ask list Click E to display the Open file browser and select the required Tune file e To add a Task select a Task from the drop down list enter a Pre Delay or Post Delay time and click e To delete a single Task left click on the Task in the timetable and click e To delete all entries click gt a e To modify a Task select the required entry in the timetable The values will then be displayed in the edit fields and can be altered as appropriate Once changed click to modify the values in the timetable Data Acquisition Running the Auto Control tasks gt Select Run List from the Control List menu OR Click gt Stopping the Auto Control tasks gt Select Stop List from the Control List menu OR Click m Saving and Restoring Auto Control Task Lists gt To save the settings select Save or Save As from the File menu OR Click and enter a file name in the dialog displayed gt To restore settings select Open from the File menu OR Click and select the required file 363 TurboMass Software User s Guide 364 Chromatogram 1 3 Chromatogram Getting Started Chromatograms are displayed in the TurboMass Chromatogram window Displaying the Total lon Current TIC chromatogram gt Select Chromatogram from the TurboMass View menu OR Click aa Displaying a summed mass chromatogram around a peak in a spectrum gt Select a peak in a spectrum to display the summed
213. ass Window using the Menu 1 To print a specific TurboMass window using the menu commands select the window you want to print and then select Print from the window s File menu 2 Select All Windows to print all document windows on display OR Select Current Window to print only the currently selected document window Trace Width allows you to specify the thickness of the line used to print chromatogram traces or spectral peaks Trace Width can be set to values between 1 and 5 a higher value will give a thicker line Print All Colors Black will map all the colors in the TurboMass display except white to black This option is useful when using black and white printers 57 TurboMass Software User s Guide 58 Window Commands Most of the TurboMass program windows have a top level menu command called Window that contains the standard Windows commands Those specific to TurboMass are described here Window list Window list gives a list of available windows The currently active window has a check mark next to its name Selecting another window will make that the currently active window In the case of Spectrum and Chromatogram this becomes a list of the traces displayed in each window Window Choosing this option causes each New Trace subsequent trace to replace the currently selected trace Replace Trace Window Choosing this option causes each New Trace subsequent trace to be displayed in a new window New Window
214. assLynx Group Name e WEMBELS CAN fully administer Mas ON nnn When you copy an existing group the Group Properties dialog contains some of the information from the copied group and the new group inherits all the members and group rights from the copied group 2 Enter the new group information Group Name The name assigned to a group of users Description A brief description of the group for example department or tasks performed Members The list of users who belong to a group The Members list is empty when you are creating a new group If you create a new group by copying an existing group then Security copies the list of members from the original group to the new group Currently The list of rights granted to the current group When Assigned creating a new group or copying an existing group Rights the list is empty and unavailable 3 For each member you want to add click Assign to open the Group Membership dialog select the user you want to add from the Non Members list and click Add to move the new member to the Members list 673 TurboMass Software User s Guide Group Membership x Group Members 4 For each user you want to remove select the user you want to remove from the Members list and click Remove to move the selected user from the Members to the Non Members list 5 Click OK to return to the Group Properties dialog 6 Click OK to return to the Security Manager window The
215. ate your original template sample list so that all the per sample information is correctly filled in When you run later sets of samples which follow a similar sequence you may then read in the original template sample list rename it and make your per sample changes in the Wizard or sample list window spreadsheet environment which ever you find most convenient for your current task More specifically the Sample List Wizard provides e The ability to read an existing sample list template e Only the parameters required for the current analysis VOA SV or QA QC and current matrix water soil are displayed e Grouping of controls for efficient entry of sample specific data e The ability to propagate changes made in one row to subsequent rows e A command to update vial numbers e A command to update sample IDs with automatic incrementing of numeric values Setting Up the Sample List Wizard The Sample List Wizard dialog started from the Samples Sample List Wizard dialog provides you with the ability to select and specify an existing sample list or create a new sample list The display of editable sample parameters will depend on your choice of Analysis Matrix and Concentration Level 213 TurboMass Software User s Guide 214 NOTE Sample List Wizard SampleList Existing sample list New sample list X Browse Analysis o Matrix of Concentration level Cc f gt OK Cancel
216. ates the range you have selected The Input Datafile dialog will be updated to show the new mass range 5 To set the Retention Time parameters right click at one end of the Chromatogram region of interest and drag the mouse horizontally to the other end TurboMass indicates the range you have selected The Input Datafile dialog will be updated to show the new retention time range 6 Click Default to set both mass and retention time to the full range of the current file 471 TurboMass Software User s Guide 472 Selecting a Background Data File The Background section of the Strip Datafile dialog identifies the data file function and scan number to be used as background when performing the Subtract process Previously processed spectra can be used as background The background file is not used for Enhance processing Subtracting a background file 1 Click Background in the Strip Datafile dialog to open the Subtract Background File dialog Subtract Background File x p Background O Eai Background scan fi a I Use all background file j Eile File 588 Function 1 Process 0 2 To select a different file and function click File to open the Strip Data Browser 3 A previously processed spectrum can be selected by clicking Browser History Selecting a new file automatically defaults to the first scan in the data file 4 Ifa single background scan is to be subtracted enter the s
217. ates when convergence is less than tolerance Select the appropriate parameters in the Spectrum Display dialog to choose whether to view the zero level and negative data in the spectrum When Flatten edges is selected TurboMass verifies that the polynomial applied is flat or horizontal at the beginning and end of the trace Smooth Smoothing reduces the high frequency noise present in a spectrum thus aiding interpretation We strongly recommend that you smooth data before attempting mass measurement with the Center process otherwise peaks may result from the noise spikes Three types of smoothing are available in TurboMass Mean Median and Savitzky Golay The most generally useful technique is Mean Using Savitzky Golay smoothing will allow you to use a heavier smooth without broadening the peak as much Median is used for removing noise spikes that are much narrower than actual real peaks for example single ions electronic spikes 451 TurboMass Software User s Guide 452 Spectrum Smooth x Peak width Da jars Number of smooths B Cancel j fA Smoothing Ooo a C Median C Savitzky Golay All three methods slide a window along the data averaging the data in the window to produce a point in the smoothed spectrum The width of the smoothing window in data points is determined by the data system using the equation Full peak width at 50 intensity 36m Halfwidth of smoothing window Where 6m is t
218. ation Click Finish in the LINK Configuration dialog to save the configuration TurboMass creates a configuration file CFG for the GC and downloads the appropriate IPM The IPMs available to you are installed during TurboMass installation When you first configure the GC the Config message appears GC Control Config gt Check communication for Instrument Autosystem 1 at Port windfall COM 2 LINK Port A 2 Note it must be connected to the LINK box and turned on If you do not connect to the GC and check the firmware revision the Modify Active Method In Run feature will be disabled If the GC is connected and turned on click Yes TurboMass will attempt to check the physical connection with the GC by taking and then releasing control of the GC The Confirm Configuration message appears To compare the configuration options you selected with those that are being reported by the GC click Yes A series of confirmation messages appear Respond to each message When TurboMass is finished the Configuration Editor appears Yes appears in the Configured column if your LINK and GC are adequately configured If No appears you need to complete the configuration before you can acquire data Reconfiguring the GC If you make hardware or other configuration changes to your GC after you have configured TurboMass for GC control you can reconfigure the GC settings without changing the LINK configuration However
219. ation 223 Sample Tracking 225 scope parameters 103 Search parameters 344 Security Manager account policies 674 audit log 681 group rights 679 groups 677 logon 670 password change 672 tasks 670 Security Model 669 serial port GC 151 signal to noise ratio calculation 412 SIR function 204 smoothing spectra 453 smoothing chromatograms 399 spectra display 51 433 processing 448 real time display 446 refine 449 smoothing 453 Spectra combine 450 spectrum delete displayed 445 display parameters 440 list 438 peak annotation 443 real time data 359 status messages GC 186 Strip functions 465 Submitter Task Data window 647 subtracted data files 466 T Take Control command 181 Template Report Browser 555 558 text labels Spectrum 446 thresholds instrument data 70 TIC chromatograms 379 transputer thresholds 70 Tune Custom AutoTune 98 peak display 91 Standard DFTPP BFB 93 zero level 108 Tune Page 83 TurboMass Desktop 30 directory structure 48 menu commands 28 quit 25 system global parameters 34 window colors and fonts 31 window commands 58 TurboMass ini file 37 U user accounts creating 675 deleting 679 user elements 548 user libraries append 519 create 517 delete entry 522 index 521 Vv vacuum controls 106 Z zero level Tune 108 769 Index 770
220. ation coefficient for first order coefficient of determination CofD for higher orders RRF values flagged as below the minimum required value for that compound as defined in the Quantify method will be displayed in red Similarly if the average RRF value is below the minimum required value or the RSD value for a compound is greater than the specified maximum value for that compound they will be displayed in red 625 TurboMass Software User s Guide 626 Section of the Window Form 6 Header sample Message pane Description This drop down list enables you to indicate the source of the information that will appear in the Form 6 header Note that this information is not related to the calibration standard samples but rather the samples analyzed utilizing the calibration This means that in general the source of the header information will be one of the Analyte samples from the Sample List tab The drop down list contains the file names of all the checked samples from the Sample List tab The initial selection will be the first checked Analyte or Analyte Dup row from the Sample List tab This displays errors and warnings associated with Form 6 in a similar manner to that for all other Forms Environmental Reporting Form 7 Tab Continuing Calibration Check When you select Form 7 Continuing Calibration Check from the Select Forms dialog the Report Generation Window Form 7 Tab appears Sample
221. atogram Integrated Peak Height of Baseline ION3_EN_HT N 12 End 5 0 ION3RATIO N 19 9 Qualifier Ion 1 Ratio 5 0 ION3LOWLIM N 19 9 Qualifier Ion 1 Ratio Low Limit 5 0 ION3HIGLIM N 19 9 Qualifier Ion 1 Ratio High Limit 5 0 ION3PERTOL N 19 9 Qualifier Ion 1 Percent Tolerance 5 0 ION3PASS L TRUE if within the limits 5 0 Appendix D Sample and Compound Table Output Fields Version Field Name Format Description Added ION4MASS N 10 2 Qualifier Ion 1 Mass 5 0 ION4RT N 8 3 Qualifier Ion 1 Mass Chromatogram Peak Top Retention Time 5 0 ION4AREA N 16 3 Qualifier Ion 1 Mass chromatogram Integrated Peak Area 5 0 ION4HEIGHT N 12 2 Qualifier Ion 1 Mass chromatogram Integrated Peak Height 5 0 ION4 ST_ RT N 8 3 Qualifier Ion 1 Mass chromatogram Integrated Peak RT of Baseline Start 5 0 ION4 EN RT Qualifier Ion 1 Mass chromatogram Integrated Peak RT of Baseline End ION4 ST HT ION4 EN_HT Qualifier Ion 1 Mass chromatogram Integrated Peak Height of Baseline Start Qualifier Ion 1 Mass chromatogram Integrated Peak Height of Baseline End ION4RATIO Qualifier Ion 1 Ratio ION4LOWLIM Qualifier Ion 1 Ratio Low Limit ION4HIGLIM Qualifier Ion 1 Ratio High Limit ION4PERTOL Qualifier Ion 1 Percent Tolerance ION4PASS TRUE if within the limits CLSTMULTRT TRUE if this is the closest Peak to the Retention time that does not pass the ratio tests
222. atten edges I Make graph of fitted polynomial 2 Set the Polynomial order parameter to 0 for a flat baseline 1 for a sloping straight baseline or 5 for a curved baseline 3 Ifdesired the Below curve parameter can be changed from its default value of 40 The effect of increasing this parameter is to raise the zero level in the spectrum Half the noise lies above the zero line and half below Therefore half of 80 or 40 of the total number of data points should lie below the background zero level Spectrum If desired you can change the Tolerance parameter from its default value of 0 01 Increasing this parameter causes the algorithm to terminate sooner but the result may not be as good If you want to see what the effect of this Background Subtraction would be on the data before actually performing the run select Make a graph of fitted polynomial and click OK TurboMass displays a graph of the polynomial function that would be subtracted from the spectrum above the resulting subtracted spectrum If you select Link Vertical Axes and Overlay Graphs from the Spectrum Display dialog the new baseline will be superimposed on the existing data When you are satisfied with the parameters deselect Make a graph of fitted polynomial Click OK The Background Subtract dialog indicates the progress of the subtract algorithm After every iteration the convergence value in the dialog is updated The algorithm termin
223. atus dialog Once the source reaches the set temperature if Operate is Off Reference Gas is Off or Pump Out Reference Gas in On the message Waiting for Reference Gas pressure to stabilize will be displayed If Pump Out Reference Gas is On it will be turned off followed by a delay of 50 seconds If Reference Gas is Off it will be turned on followed by a delay of 100 seconds The Waiting for Reference Gas pressure to stabilize message will then be removed If Operate is Off it will be turned on followed by a delay of 5 seconds A check is then made to determine if the Electron Energy and Trap Emission current are at the set values within 7 and 10 respectively If either or both readbacks are out of tolerance the error message is displayed is Electron energy not at the set value And or Trap emission current not at the set value and the UltraTune procedure stopped The UltraTune status dialog is displayed The status dialog displays the part of the tuning process that is currently occurring The UltraTune status bar is updated to show the progress of UltraTune Instrument Tuning UltraTune Progress TS ULTRATUNE STATUS 7 When UltraTune has finished the UltraTune completed message is displayed Click OK The tuning parameters determined by U traTune will be saved to the current tune parameter file If the Prompt for Recalibration box was checked in the UltraTune Setup dialog you
224. ave to database save to file send via email The printer if printed and or the file name if saved 4 The email address es and message text if emailed 5 Sections of the report template to be printed or suppressed Only a single report method can be loaded in the Editor at a time and only a single instance of the Report Method Editor can be run If you edit a Report Method while the Editor is already open e g by choosing the Open command from the context menu when the Report Method cell is selected in the sample table then the new report method will replace the existing one provided it is not in a modified state If the current method is in a modified state the Do you want to save the changes to lt report method name gt warning dialog will be displayed 549 TurboMass Software User s Guide 550 A Report Method Editor New Report Method loj xj File Help U386 6 Reports T emplate Template Browse Frequency Generate report for every run Output J Print hardcopy Report name prefix F Send vie email Setup Sections Sections On Sections Dff Delete GlearList For Help press the Help toolbar button You open the Report Method Editor in one of two ways 1 By choosing Open from the context menu when the Report Method cell is selected in the Sample List If no method name is specified in the cell or if there is currently no report method of t
225. b Control samples only Lab Control samples only Lab Control samples only Lab Control samples only a valid calibration file must be specified on the sample list row a valid calibration file must be specified on the sample list row Cont Calib samples only Cont Calib samples only report method must appear only on the last row and the first row must be a Cont Calib report method must appear only on the last row and the first row must be a Cont Calib intended for Analyte samples will give incomplete results for calibration samples In addition to the above Report Methods and associated templates there are three other included templates of use if CSV comma separated variable reports are required All must be produced within the environmental report generation window Examples are in the same directories as the PDF files Forml CSV reports both Form 1 and Form 1 TIC Form5 CSV Form6_CSV 641 TurboMass Software User s Guide 642 Submitter Task Data Window The Submitter Task Data Window combines several related functions e Maintenance of Submitter Task hierarchy e Maintenance of Custom Compound Lists e Mapping of Forms to Report Methods These functions are combined in one Submitter Task Data window since both Custom Compound Lists and mapping of Forms to Report Methods are specific to a Task EE Submitter Task Data File Edit Help Assign a report method to each form Submitter Task Default
226. be reported and optionally exclude Quantify target compounds where applicable e Set a coelution window parameter to ensure reliable identification of target compounds within the qualitative chromatograms when the Quantify Trace and qualitative peak do not maximize at the identical retention time default 1 second 329 TurboMass Software User s Guide The General Tab Fields Qualitative Method Editor Untitled la x EOC General Search Parameters Library Settings Peak integration parameters Peak to peak Noise amplitude 2000 00 X Axis units Time mins Scan Reporting parameters Beport largest 10 peaks J7 Exclude target compounds Coelution window sec 1 00 Full chromatogram Integrate the full chromatogram to create a peak list Window 1 Use the first data segment in creating a peak list Window 2 Use the second data segment in creating a peak list Window 3 Use the third data segment in creating a peak list Window 4 Use the fourth data segment in creating a peak list grid Defines time segments and integration thresholds The first two cells in the first edit row alongside Full Chromatogram are always disabled and cannot be selected Peak to peak noise Sets the maximum noise expected on the signal amplitude X Axis units Time Selects Time units for setting the From and To values in the grid 330 Qualitative Method Scan Selects Scan numbers for sett
227. be rescaled if required without distorting the original image as long as the original aspect ratio is maintained When you use the TurboMass Edit Copy Picture command both a metafile and a bitmap are copied to the Windows Clipboard Copying a spectrum as a picture to the Clipboard 1 Produce the required display in a Spectrum window 2 Click OR Select Copy Picture from the Spectrum Edit menu to copy the contents of the window to the Clipboard as both a metafile and a bitmap 3 To read the image into another application as a metafile select Paste from the other application s Edit menu If you select Paste Special from the other application s Edit menu you will be given the option of pasting either the metafile or the bitmap Copying a spectrum as a text list to the Clipboard 1 Display the required mass range in a Spectrum window Spectrum 2 Click OR Select Copy Spectrum List from the Spectrum Edit menu The section of the spectrum on display will be transferred to the Clipboard as mass intensity pairs 3 To read the information into another application select Paste from the other application s Edit menu Pasting information into a spectrum window from the Windows Clipboard 1 Click OR Select Paste from the Spectrum Edit menu to paste the default Clipboard object to Spectrum 2 Select Paste Special to choose which object to paste into Spectrum These objects would typically be metafiles bitmaps or text
228. bers separated by a colon as above and if there are two ranges they should be separated by a comma for example 606 612 631 637 If you use the mouse right click and drag the mouse across the first background scan range then optionally repeat for a second range 5 Optionally enter a background factor in the X field 6 Optionally enter a Peak separation value 7 Click OK 449 TurboMass Software User s Guide 450 Subtract Background Subtract adjusts the zero level in a continuum spectrum to lessen the effect of chemical noise caused for example by column bleed A low order polynomial is fitted to the data to remove a constant sloping or curved background from a spectrum The algorithm fits a polynomial of specified order zero is a flat baseline one is a straight sloping line two is a quadratic shape etc to a spectrum such that a specified percentage usually 30 50 of the data points in the spectrum lie below the polynomial This operation is performed to an arithmetical tolerance that you specify The Background Subtract process also gives you the option to display a graph of the baseline which will be fitted to the data before doing the Background Subtraction Subtracting the background from a continuum spectrum 1 Select Subtract from the Spectrum Process menu to open the Background Subtract dialog Background Subtract Polynomial order 1 Below curve 40 00 Cancel Tolerance 0 010 T Fl
229. ble by the user in the same way as for the main TurboMass Sample List window 3 Any rows in the sample list that do not contain a raw data file name will be ignored and not added to the view This would remove the comments added to the Tutorial Reports sample list included with the example data 4 The row number associated with each row in the sample list remains unchanged on all tabs That is if rows are unchecked on the Sample List tab then there will be gaps in the numbering on the Form tabs which only display data files that have been selected for reporting 605 TurboMass Software User s Guide Form 1 Tab Organics Analysis Data Sheet When you select Form 1 Organics Analysis Data Sheet from the Select Forms dialog the Report Generation Window Form 1 Tab appears H Report Generatio 5 Sample List Forms Options Help eamele Sample List Fom 1 Status ample ID Matix Level Vial Quantify Method Submitter Task Analysis Qualitative M 1 er Me 60b_Tutorial VOA_Tutari VOA_Tutori VOA TiCsearch10 2 7 r 3 a Init Caib 7 4 a Init Caib r 5 O0n Irit Caib r 6 On Init Caib B10040503 ater Medu 8260b_Tutorial VOA_Tutori VOA_Tuton VOA TCsearch10 7 MethodBlankt Meth Blank B10040510 Wat Mediu 8260b_Tutorial VOA_Tuton VOA_Tuton VOA TlCsearcht0 8 SpikeDupt Spike B10040511 Water Mediu 8260b_Tutorial VOA_Tut
230. but would not want to search a flavors and fragrances one Compounds in mainlib the primary NIST library have flags indicating which databases they originally came from or in which industry standard lists of compounds they occur If the unknown compound is expected to be in one of these databases or lists the speed and accuracy of the search can be improved by restricting results to members of those databases or lists About NIST Results e The names in the Qualitative Results may come from the Library Search results or the Quantify results if they exist e Ifa peak has both Qualitative and Quantify results the Quantify name is used e NIST Library Search results are in upper case Quantify can have upper or lower e NIST results should use the fonts NIST Serif or NIST Sans Serif to permit display of Greek letters NOTE To prevent library searching during Qualitative Calculations make sure the Included libraries field is empty 336 Qualitative Method The Library Settings Tab Qualitative Method Editor Tutorial Qualitative File Help O 2 8 6 fi l General Search Parameters Library Settings Unused libraries Included libraries i mainlib J Compound must appear in database F EINECS F NH F EPA RTECS I Fine I ISCA F HODOC F use FR Unused Included libraries Unused libraries Libraries not being searched The order in which items appear in the Unused libraries list is alph
231. by a factor of 2 The span specifies a small mass window applied centrally about the highlighted mass When specifying a mass that is close to either the low mass limit 1 or high mass limit 1205 you must first enter a span that does not force the mass outside of the mass limits For example to specify a mass of 2 you must first enter a span of 2 or less NOTE NOTE Instrument Tuning UltraTune TurboMass can automatically tune the mass spectrometer by using UltraTune with an EI ion source UltraTune ramps the settings for the tuning parameters until they are optimized to give good intensity resolution and peak shape Reference Gas and Filament Control Since reference gas is always required for the UltraTune process the TurboMass software will assume control for switching the flow on and off Tune History A tune history file is maintained that records the tune parameters following a successful UltraTune It is saved in an ASCII comma separated format with one tune record per line The file is located in the main TurboMass directory Each new successful UltraTune will append a new line to the end of the file If the tune history file does not exist when a record comes to be written to it it will be created The first line of the file will contain names for each field in the record which may be used as column headings when the data are imported into Excel The tune history file is named UltraTuneHistory CS
232. by selecting the ON or OFF button as appropriate 5 Click Set Valves to implement the settings and click Close You must clickt Set Temp Set Valves or Autozero before clicking Close in order to change settings Modifying the Active Method The Modify Active command in the GC menu lets you change method parameters in a method that has been downloaded by selecting Start from the TurboMass top level window Run menu When a method has been downloaded it is by definition the active method the one that is being used in the current run and the Method Editor opens when you select the Modify Active command The commands and options available in the Method Editor depend on whether or not a run is in progress When you modify the active method the term Modify Active is displayed in the title bar of the Method Editor When you modify the active method with a run in progress the instrument parameters that you can modify are limited to those that can be downloaded during a run That is you can modify the oven inlet and detector parameters When you modify the active method and there is no run in progress you can modify all method parameters in the active method When you finish editing the method TurboMass downloads the modified method to the LINK and uses it for the next run If you select a method that is not the active method you can modify all parameters within that method during or outside of a run 189 Modifying the
233. can number in the Background scan field The scan number can also be set from Spectrum and Chromatogram by right clicking and selecting the desired scan If Background scan is deselected deselect Use all background file 5 To subtract the entire background file select Use all background file In this case the background scan with the closest retention time to each input scan will be subtracted Selecting an Output Data File Strip and Combine Functions The Output section of the Strip Datafile dialog identifies the data file that will be created by Strip when processing When an Input File is selected the Output File defaults to the same directory and a name based upon the Input name with an extra letter appended For example if the input file was turbomass data v50 raw the default output file might be turbomass data v50a raw When defaulting the output name TurboMass attempts to choose a name that does not already exist Changing the default output file and directory 1 Click Output in the Strip Datafile dialog to display the Output File dialog 2 Enter a name for the output file To change the directory of the file enter the full path name of the file Setting Subtract Datafile options 1 Select Subtract Datafile Options from the Strip Options menu to display the Subtract Datafile Options dialog and enter the appropriate values Peak Width amu centroid ony I Background multiplication factor fi oo0 Cancel Defau
234. ccordingly If the cross hairs cursor is displayed you can change the current cursor position by left clicking anywhere on the cross hairs and dragging them to the new position OR Select Select Mass or Select Time from the Map Display menu enter the new value and click OK Editing the Header Information The Map Window has a customizable header Various pieces of information such as raw data file name can be displayed here as well as any user text For more detailed information about the Header Editor see The Header Editor on page 54 Changing the displayed header gt Select Header from the Map Display menu make the required changes and click OK Map Printing from Map To print the Map window 1 Select Print from the Map File menu 2 Make any changes required to the print parameters 3 Click OK 541 TurboMass Software User s Guide 542 Copying to the Windows Clipboard The Windows Clipboard provides temporary storage for information that is being transferred between application programs for example word processors spreadsheets TurboMass You can copy a bitmap of the Map window to the Clipboard and then for example paste the bitmap into a report written with a Windows compatible word processor Copying the Map display to the Clipboard 1 Produce the required display in the Map window 2 Click OR Select Copy Bitmap from the Map Edit menu to copy the contents of the window to the Clipboar
235. ce will also be entered automatically You may then edit any of these values if desired If the Multiple Ion Ratio to Base Peak is selected then Target Ratio and Tolerance values must be entered below the grid for the Quantify Trace 4 Accept the default Tolerance type or select the desired alternative from the drop down list 5 Accept the default Coelution Window value or enter the desired value Qualifier lons Type into the grid to define or modify the qualifier ions but the grid can also be filled in automatically using AutoBuild or by pasting a spectrum from the clipboard 269 TurboMass Software User s Guide 270 When the AutoBuild process is used Chromatogram Library Search Peaks etc the Paste Chromatogram command will have the following effect when the current setting of Peak Selection is Multiple Ion Ratio to Quantify Trace or Multiple Ion Ratio to Base Peak e The largest peak from the spectrum will be entered as the Quantify Trace as occurs currently in TurboMass e The next four largest peaks will be entered as the qualifier ions The Target Ratio values will be set according to the ratio of each ion to the quantify ion from the spectrum The Tolerances will be set to the default value When the current setting of Peak Selection is Multiple Ion Ratio to Base Peak the Quantify Trace Target Ratio will be set to its relative intensity in the pasted spectrum and
236. ceeceeceneceeeeeeeeeeseeeseeeseeeeeeaaees 375 TIC and BPI Chromatograms cccccccsccesscessceeeeeseeeeeeeeeeeeeeneeeasees 377 GC Detector Trace cecc ciiaieecodetisiivdes Gangtl enini ae ave Babee 378 Aligning GC Detector Traces ccccccesccsssceseesseesseeeseeeeeeaeeeeeeaeestees 379 Manipulating the Display cccccesccessceesceesceeeceeseeeseeeseeeseecnsecnseenseenaeenes 380 Altering the Horizontal AXIS cccccecscessceseceneceeeeeseeeseeeseeenseeeeeaaees 380 Altering the Range of the Intensity AXIS 2 0 ceeeeeeceeseeeeceeeneeereeseeaee 381 Altering the Range of Both Axes 000 ccccccecccecseeeseeeeeeeeeeeenseeseeetees 381 Setting Magnified Ranges 00 cccccecssecssecsseesseeseeessecsteceseeeeeeseeeeeeeenes 381 Setting the Display Range Defaults cccccccesccesseeeeeeeeeeeeeeeneennes 384 Controlling the Appearance of the Display ececceecceseeeeeeeeeeeeeeees 385 Controlling the Appearance of Peak Labels cceeceeeeceeseeteeeeeeeees 388 Removing Chromatograms from the Display cceseseeeeeeeeeees 390 Real time Display of Chromatograms ccceesceseeeceereeeeceeeeeeeeeenees 391 Changing the Order of Displayed Chromatograms e ecceseseees 391 Adding Text to the Chromatogram Display cccccssesseeeteetteeneees 391 Processing Chromatograms ccscccsccesscesseeseceeeeeeseeeseeeseecsaecaecnseeneesaeenes 393 Processing Multiple Chromatograms c cccsc
237. cessing are of sample type other than Tune Eval Init Calib or Cont Calib then an error message will be displayed Form 1 TIC Error Sample list contains no sample types reported on Form 1 TIC Either of these errors will prevent the TIC assignment process being performed Warnings If any rows selected for processing other than Tune Eval Init Calib or Cont Calib rows still have the Pending status then an error message will be displayed Form TIC Warning Samples with incomplete TIC selection will not be reported Rows a b x z Form 2 The sample list is checked for the existence of sample types reported on Form The first Analyte or Analyte Dup row found in the selected rows will be marked as the source of the header information for Form 2 You can change this assignment if necessary Errors If no rows selected for processing are of sample type other than Tune Eval Initi Calib or Cont Calib then an error message will be displayed Form 2 Error Sample list contains no sample types reported on Form 2 Warnings No warnings specific to Form 2 have been identified Form 3 Generation of Form 3 requires three and only three files An Analyte sample a Matrix Spike sample prepared by spiking the analyte and a Matrix Spike a second spiked sample The default rows are identified as follows Matrix Spike Duplicate e Look for the last Spike Dup sample in the list If no Spike Dup can be located a warning condition exists see below
238. chi0 00124 Analyte B10040516 Water Mediu B260b_Tutorial VOA_Tutori VOA_Tutori VOA TiCsearchi0 S0ug L Cont Caib B10040506 Water Mediu 260b_Tutorial VOA_Tutori VOA_Tuton VOA TiCsearchi0 Errors Wamings for Form 5 Instrument Performance Check Section of the Window Description Sample List view This is a read only display The view cannot be sorted and no data item in any cell can be directly edited Column widths can be changed in the standard way by dragging the header divider Message pane This is a read only display window that shows general warnings and all form specific errors warnings 622 Environmental Reporting Row Colors Form 5 uses the primary data color see Row Colors represent the tune evaluation Tune Eval sample BFB DFTPP Any additional Tune Eval rows will be shown in the disregard color All other sample type rows will be shown in the summary color and printed on the report Status Column The Status column indicates which row is currently flagged as the tune evaluation sample This may be used to distinguish between several Tune Eval rows in the sample list only one can be treated as the primary data set for Form 5 or to flag a row of another Sample Type e g the Continuing Calibration as being the tune evaluation sample Reassign Sample Type The software allows the Tune Eval assignments to be al
239. continue NOTE Files sent to the recycle bin are not deleted from the system they will stay in the recycle bin until you delete or retrieve them from there 46 Getting Started Projects TurboMass comes with predefined projects Default pro TutorialQuant pro TutorialReports pro Tutorial VOA PRO and Tutorial SVOA PRO All data are stored in the Default pro project until a new project has been selected or created All TurboMass data storage is organized into projects When you create a TurboMass project TurboMass creates a new directory called ProjectName pro and the following sub directories AcquDB Acquisition settings files CurvedDB Quantify calibration curves Data Raw data files MethDB Quantify methods PeakDB Peak lists QualDB Environmental Library Search results SampleDB Sample lists Creating a new project 1 Select Project Wizard from the TurboMass File menu The Create project dialog is displayed 2 Enter a Project name and Description in the appropriate fields A default location for saving the project to appears in the location field 3 To save the file to a different location enter a new file name into the field OR Click Browse and select a file from the dialog displayed 4 Click Next to display the next page 47 TurboMass Software User s Guide 48 By Select one of the following as appropriate Create New Project Create Using Current Project As Template or Create Using Existing Proj
240. cssccesseeeseeeeeeeseeseeenees 393 SAT LOLI Kele EEE tt sssets ceanth causes EE sirote suman tatesteten tert ectencs 393 Smoothing Chromatograms and or Reducing Noise ceseseeeeeee 397 Integrating Chromatograms cccccsccssecesecessceseceeeceseeeeseesseeeeeeseeeaaees 399 Editing Detected Peaks ccccccecccecsseesecseeseceeceeceseeneeeeseeeseeesseeaaees 406 Peak Purity sci eera ea e e E deseo baviedat TEE 408 Signal to Nols E reniei eea i e a E E A E e 410 Combine Spectra ioei atir a a a ai t 413 Pak EEE E ote caceaaytas ceasdezantes eaves 415 Creating and Editing a Peak List cccceccceesceeseeeneeeeeeseeeseeeseeeneeees 415 Reading a Peak List into a Chromatogram eceseeceeseeteeeeeeeeeeees 416 TurboMass Software User s Guide Automatic Library Searching cccccceeccesscesseeeeeeeeeeeseeeseeeseeeseeesaeesaeeneenes 418 Copying to and from the Windows Clipboard cccccsccesseesseeeeeeeeeeeeees 420 Spectr UMs sisissscesdvsstecccsssconseaccsssedscsssesvevessecceecevssvendssdessteedasvsvessbecsscedsassoss 423 Getting Started iaeei i Eo A E EE AEA E a CATET 425 About the Displays icssanessiecas casa varcsiavesseiadeansecaeccacesaaesnoed stiaacteabas atic 425 The Spectrum TOI Dar inenen cash ves oj encepats te shespucevitd de ceesatvens 427 Customizing the Spectrum Toolbar cccceccccssecsceestecsteeeteceteeeeees 428 Displaying Specta eserinin A A E E EAEE T EA 431 Adding or Replacing Spectra
241. ctrum by spectrum match factor calculation Off Search the entire database using only the detailed match algorithm Limits Apply limits Constrain the possible matches with the selected limits State of check box does not affect accessibility to other controls in the group Set Defaults Set all limits to Default values Clicking this button restores the settings in the Limits group to default values Minimum abundance Determines whether the minimum abundance limit lt drop down list gt will be used lt text box gt Smallest peak that will be used in comparison Used to force small peaks in the target spectrum to be ignored The value is only enabled when Minimum abundance drop down list is set to On Minimum m z lt drop Determines whether or how the minimum m z down list gt limit will be used Qualitative Method lt text box gt Used to determine the lowest m z used for match factor calculation Without this specification the matching algorithm starts comparison at the HIGHER of the minimum m z values in the target or the library spectra The value is enabled when Minimum m z drop down list is not set to Off Maximum m z Determines whether the maximum m z limit will be used lt text box gt Peaks above the specified mass are ignored Use to exclude spurious high mass peaks in the search spectrum The value is only enabled when Maximum m z drop down list is set to On Minimum match
242. ctrum with intensity less than the specified Intensity threshold will not be used to form the calibration curve The threshold is specified as a percentage of the most intense peak in the acquired spectrum Normal operating range for the Intensity threshold parameter is 0 to 5 Mass Calibration Polynomial When each peak in the reference spectrum has been order matched with a corresponding peak in the acquired spectrum the mass difference acquired mass reference mass is calculated for each pair of peaks These mass differences are plotted as points on a graph Each data point has the mass of the acquired peak as its x coordinate and the above mass difference as its y coordinate A smooth curve is drawn through the points The Polynomial order parameter controls the type of curve that is drawn and can be set to any value between 1 and 5 If Polynomial order 1 a straight line is drawn through the points If Polynomial order 2 a quadratic curve is drawn through the points If Polynomial order 3 a cubic curve is used For a typical EI calibration where the mass range calibrated starts below 100 amu and extends up to 650 amu the recommended setting for the Polynomial order parameter is 4 Intensity If selected the curve fit is weighted toward the points weighting representing the more intense acquired peaks The weight of each point is proportional to the square root of the intensity of the acquired peak Calibrate If selec
243. cular window by seeing if is selected or by making that window current then choosing the Spectrum Display menu If real time update is enabled for the current window Real Time Update has a check mark next to it Changing the Order of Displayed Spectra When a window contains multiple traces you can change the order in which spectra are displayed The first spectrum in the list is displayed at the bottom of the window The first spectrum is displayed on top of the others if traces are overlaid Select Move To First from the Spectrum Display menu to display the currently selected spectrum at the bottom of the display Select Move To Last from the Spectrum Display menu to display the currently selected spectrum at the top of the display Adding Text to the Spectrum Display To add text labels to the spectrum display click A When selected the Text toolbar button changes color to show that it is active Move the mouse to where you want to position text and left click to open the Edit Text String dialog Spectrum Edit Text String x Justification M Border i ed I Vettical det Cancel Center C Right IV Autosize IV Attach to axis Enter the text in the Text field select desired options and click OK You can change the position of the user text by dragging it to a new position Use the handles at the sides or corners of the text box to size the text If you want to edit the text double click it to redi
244. culator Report Method Editor Calibrating the mass axis Configuring the GC developing a GC method and equilibrating the GC Managing MS methods Developing sample lists for data acquisition Entering quantitative parameters into a mass spectrometry quantification method Creating a Qualitative Method to determine the identity of your sample through the qualitative processing of sample data Initiating and monitoring data acquisition Working with mass chromatographic data Working with mass spectral data Optimizing data analysis by removing background noise and combining spectral data Performing library searches Using the 3 D data display Map process Using the Molecular mass calculator Enables you to specify a collection of report definitions Communiqu report templates and related parameters that are printed sequentially Chapter 20 Chapter 21 Appendix A Appendix B Appendix C Appendix D Appendix E Appendix F Communiqu Reporting Environmental Reporting TurboMass Security TurboMass Software Installation TurboMass Quantify Calculations Sample and Compound Table Output Fields LIMS Import File Example Environmental Reporting Calculations Introduction Using the Report Method Editor and Communiqu to modify an existing report template and create a new report template Using the Environmental Reporting features to generate reports based on samples collec
245. d 3 Click OK Controlling the Appearance of the Display Each chromatogram window has its own set of display parameters that determines the appearance of the chromatogram display You can inspect and alter the parameters for the current chromatogram window from the Chromatogram Display View dialog Changing the display parameters 1 Select View from the Chromatogram Display menu to open the Chromatogram Display View dialog Chromatogram Display View x r Normalize Data To q r Style Largest Peak T Overlay Graphs Intensity fo F Fill Trace Baseline atZero T Fill Detected Peaks C Baseline p M Graph Header I Process Description C Lowest Point T Link Vertical Axes Spit Axis fi Z Dverlay Step Ts Axis Label vora STP l 0 Grid Off Horizontal Axis Time Cancel Header 2 Make any changes Normalize Data To These parameters specify the scale on the intensity axis Largest If selected the vertical axis is scaled such that the largest 385 TurboMass Software User s Guide 386 Peak Intensity Baseline at Zero Baseline Lowest Point Link Vertical Axes Axis Label Style Overlay Graphs Fill Trace Fill Detected peak on the display is at 100 If you select Intensity and specify a normalizing intensity in the text field the vertical axis is scaled such that your specified intensity is at 100 If selected the vertical ax
246. d 3 To read the image into another application select Paste from the other application s Edit menu Molecular Mass 4 8 Calculator NOTE Molecular Mass Calculator Calculating the Molecular Mass The mass calculator can calculate two different molecular masses for a given chemical formula e Monoisotopic mass Calculates the mass using the atomic weight of the most abundant isotope of each element e Average mass Calculates the mass using the average atomic weight of each element taking into account the relative abundance of its isotopes Calculating the molecular mass for a given chemical formula 1 Select MW Calculator from the TurboMass Tools menu or click a to open the Molecular Mass Calculator dialog 2 Enter the chemical formula using standard International Union of Pure and Applied Chemistry IUPAC notation 3 To specify user defined elements or isotopes follow the procedure Defining User Elements on page 546 4 Select either Monoisotopic or Average Mass Monoisotopic mass is the usual choice for GC MS 5 To display the calculated mass in the Mass field click Calculate 6 To edit the current formula and recalculate the mass click Calculate 7 To clear the current formula click Reset 8 To copy selected formulas or calculated masses to the Windows clipboard click Copy The Copy function is convenient for pasting ion masses into the SIR scan function 545 TurboMass Software User s Guide
247. d 1 Produce the required display in a chromatogram window 2 Click OR Select Copy Picture from the Chromatogram Edit menu to copy the contents of the window to the Clipboard as both a metafile and a bitmap 3 To read the image into another application as a metafile select Paste from the other application s Edit menu If you select Paste Special from the other application s Edit menu you will be given the option of pasting either the metafile or the bitmap Copying a chromatogram as a text list to the Clipboard 1 Display the required time range in a chromatogram window Chromatogram 2 Click OR Select Copy Chromatogram List from the Chromatogram Edit menu The section of the chromatogram on display will be transferred to the Clipboard as time intensity pairs or scan intensity pairs depending on the horizontal axis setting 3 To read the information into another application select Paste from the other application s Edit menu Copying integrated chromatogram peaks as a text list to the Clipboard 1 Display the required time range in a chromatogram window 2 Click or select Copy Detected Peaks from the Chromatogram Edit menu The chromatogram peaks on display will be transferred to the Clipboard The information transferred for each peak is the peak top height area start end start height and end height 3 To read the information into another application select Paste from the other application s Edit men
248. d Data are stored for every scan As data is being acquired and continuously stored to disk even when there are no peaks being acquired continuum data acquisition places some extra burden on the acquisition system as compared to centroided acquisition Data file sizes will tend to be significantly larger than centroided one sided and the absolute scanning speed Da sec will be slower You can set a threshold below which the data will not be stored to disk which can reduce these effects depending on the nature of the data being acquired You can set the threshold so that data considered to be noise can be discarded thereby improving data acquisition speed and reducing data file sizes For more information about setting instrument data thresholds see Setting Instrument Data Thresholds on page 70 Multi Channel Analysis MCA MCA data can be thought of as summed continuum with only one intensity accumulated scan being stored to disk for a given experiment As each scan is acquired its intensity data is added to the accumulated summed data of previous scans An advantage of MCA is that random noise will not accumulate as rapidly as real data and therefore will effectively average out over a number of scans This will emphasize the real data and improve the signal to noise ratio A further advantage of MCA is that as data is written to disk only at the end of an experiment scanning speeds can be increased and significantly
249. d You can control how many candidates are passed to the Mainsearch by changing the Match By parameter in the Library Search Parameters dialog The Mainsearch For the Mainsearch the unknown spectrum is again reduced this time to a number of peaks determined by the Sig Peaks parameter in the Library Search dialog The Search spectrum is compared to each of the possible candidates from the library and the results of this comparison are displayed in the Hits Hit List Delta and Structure windows The hits are ranked in order of best fit to the search spectrum You can apply various filters to the Mainsearch process to make it more specific These filters contain requirements that must be met in order for the library entry to be included in the Hits list These filters can contain information about the compound elemental formula and molecular weight 489 TurboMass Software User s Guide TurboMass computes two types of fit values for each hit Forward and Reverse Fit The maximum obtainable fit value is 1 000 which represents a perfect match between the search spectrum and the library entry The Forward Fit value shows how likely it is that the search spectrum is a pure sample of the library entry Any peaks that are present in the search spectrum but not present in the library spectrum decrease the Forward Fit value Likewise any peaks that are present in the library spectrum but not present in the search spectrum decrease the Fo
250. d values to limit the integrated peaks to only those you wish to library search 2 Integrate the chromatogram of interest 3 To append specific peaks select Peak List Write from the Chromatogram Edit menu select the desired peaks and click Append Repeat for each peak required OR To append all peaks click Append All 4 To automatically remove calculated background spectra select Auto Refine from the Library Hits Process menu 5 Select Search Peak List from the Library Hits Process menu The Library search process performs a search for the first peak in the list and displays the Print dialog 6 To print results for all currently displayed Library windows select All Windows OR To print results for the currently selected window select Current Window and click OK All other spectra matches will also be printed out in this format Manipulating the Library Display The appearance of the display can be changed from the Library Display menu 1 Select View from the Library Display menu to open the Library Display View dialog 503 TurboMass Software User s Guide 504 Library Display View r Peak Label Threshold xEul Scale p i I Visible I Visible Fi U Header 4 ha C Intensity p E Window Structure Window r Hits Window Decimal Places mE T Visible No Hits 5 list Window 7 Visible Header Header Header
251. d List with a particular Task but not directly with a Submitter Context Menu for the Submitter Task List Right clicking on a node of the Submitter Task tree view displays the Context menu Note that it will not appear if you click on empty space within the list Command Description New Submitter Displays the New Submitter dialog to create a new Submitter name New Task Displays the New Task dialog to create a new task for the Submitter Collapse All Closes all expanded nodes so that only the top level nodes are displayed Expand All Displays all nodes Rename Enables you to change the name of the selected node Delete Deletes the Task node and its associated data compound list and or report methods Info Environmental Reporting Displays a Task Info dialog showing the comments entered by the user when the Task was created The Submitter Task Data window has the following Menu item commands Menu File Edit Command Save Export Import Exit New Submitter New Task Description Saves the Submitter Task data Displays the to export Submitter Task data from TurboMass to archive or another computer Displays a File Open dialog allowing you to select a previously exported Submitter Task Data file When a file has been chosen the Import dialog will be displayed Closes the Submitter Task Data window If unsaved changes exist then a dialog will be displayed with the message Save cha
252. d in the printed report If no peak was detected the chromatogram that should have contained the peak can be displayed by using the mouse to select the appropriate Summary window entry To add a baseline right click at one end of the chromatogram region of interest and drag the mouse horizontally to the other end As you drag the mouse TurboMass indicates the selected range When you release the mouse a baseline will be drawn To delete the current peak click Delete and then OK in the Edit Quantify Peak dialog Quantify The peak list and associated windows will be updated If the peak is a calibration standard you will be asked if you want to recalculate the calibration curve If a new curve is calculated all compounds will be requantified The Summary window can be formatted to include the Detection Flags for each peak The Detection Flags give information about the start and end points of the peak and can have the following values b v t X Peak baseline starts or ends on the chromatographic curves Peak starts or ends as a valley dropline between two peaks Peak baseline starts or ends as a shoulder dropline between two peaks Peak start or end point has been manually assigned Peak end was not detected within the retention time window Calibration point has been excluded from the calibration curve The default Chromatogram display range can be controlled by selecting Chromatogram from the Quantify Display menu
253. d to all compounds in the method Propagating integration parameters to all compounds gt To use the same integration parameters for all compounds in the method select Propagate Integration Parameters from the Quantify Method Editor Edit menu A check mark will appear next to this option and the integration parameters will be copied to all compounds in the method Adding a new compound 1 Enter the required information for a new compound 2 Click Append to add the new compound to the end of the compound list Inserting a new compound 1 Select the entry in the compound list before which the new compound is to be inserted 2 Enter the required information for the new compound and click Insert Modifying information for an existing compound 1 Select the entry in the compound list that is to be modified 2 Enter the updated information and click Modify Deleting a compound 1 Select the entry in the compound list that is to be deleted 2 Click Delete or press DELETE to remove the selected compound from the list Deleting all compounds in the method 289 TurboMass Software User s Guide 1 Select Delete All Compounds from the Method Editor Edit menu 2 Click OK to delete all compounds in the method Printing a Quant Method Report You can print out Method data in two compressed formats 1 Select Print Table from the Quantify File menu 2 Select the desired options in the Print Method Report dialog Sort
254. der 2 Make any changes to the following parameters and click OK Normalize Data To This set of parameters specifies the scale on the intensity axis Largest Peak If selected then 100 on the intensity axis represents 438 on Display Base Peak in Spectrum Mass Intensity Baseline at Zero Baseline Link Vertical Axes Data Threshold Spectrum the intensity of the most intense peak currently on the display If selected then 100 on the intensity axis represents the intensity of the most intense peak in the spectrum If selected then 100 on the intensity axis represents the height of the peak at the specified mass If selected then 100 on the intensity axis represents the specified intensity If selected the vertical axis is scaled from 0 If you select Baseline and specify an intensity offset the vertical axis is scaled from your specified intensity This option can be useful for displaying spectra that have a raised baseline When comparing two spectra by overlaying them on the same mass scale it may be useful to plot both spectra on the same intensity scale also Link Vertical Axes allows you to do this if you select this option all axes in the current window will be given a common vertical scale When processing centroid type data it can be useful to specify an intensity threshold Peaks whose intensity is less than the threshold will not be displayed There are two methods
255. dialog to open the Output File dialog Output File x Directory C TurboMass DEFAULT PRO Data 2 Enter a name for the output file To change the directory of the file enter the full path name of the file Stopping a Process When you stop a process before completion the output data file will contain all the information written up to the point at which the process was stopped gt Click Stop in the Combine Datafile Functions dialog Confirmation of the action will be requested 484 Library 1 6 NOTE Library The Library application is used to identify unknown spectra by comparing the unknown spectrum to a library of known spectra The result of a library search is a list of library compounds or hits The spectra in these compounds give the best match with the unknown spectrum This chapter describes how to search the libraries supplied create your own mass spectral libraries and how to use the Library Locator The terms scan and spectrum are used interchangeably in this chapter and in the TurboMass software 487 TurboMass Software User s Guide 488 TurboMass Library Windows The Library window presents the search results in several formats Hit List Gives a text listing of the best hits You can format the Hit List window to display a variety of information about each hit including compound name fit values formula and molecular weight Hits Window Shows the unknown spectrum
256. displayed Each process performed on a chromatogram adds a summary of its parameters to the chromatogram s header The Process Description parameter allows you to turn off just the process information and leave the remainder of the header on the chromatogram NOTE The Graph Header parameter overrides the Process Description parameter That is if Graph Header is turned off Process Description will be turned off as well Split Axis Overlay Step Grid The Split Axis value is enabled when Overlay Graphs is selected It allows you to change the aspect ratio of the chromatogram by dividing the horizontal axis into segments then arranging the segments vertically For example if a chromatogram 30 min in duration is on display and you set Split Axis to 3 the display will show three axes one from 0 to 10 min one from 10 to 20 min and one from 20 to 30 min The Overlay Step parameter is turned on when Overlay Graphs is selected It allows you to offset each subsequent chromatogram trace by a percentage of the intensity axis This can make it easier to examine overlaid traces Allows you to fit a grid to the chromatogram display The pattern of the lines that make up the grid can be chosen as Dot Dash or Solid 3 Click Header to display the Header Editor where you can edit the header information displayed at the top of the window 387 TurboMass Software User s Guide 388 4 Click OK Controlling the Appe
257. during the solvent delay to prevent it from being damaged The lt Enter gt or arrow key must be pressed after changing the solvent delay Multiple Solvent Delays There are instances where a chromatogram has several peaks large enough that you would want to turn off the filament while they are eluting to protect the filament from burn out and then turn it back on afterwards and continue the analysis The multiple solvent delay functionality is designed to accommodate this along with the conventional solvent delay at the beginning of the chromatographic run The MS Method editor has a Solvent Delay button When selected it brings up a dialog allowing up to four solvent delays to be specified Scan Functions c turbomass tutorialreports pro acqudb stdmix4 exp File Edit Options Toolbars Functions Multiple Solvent Delays Ci tea x v E wsscen SR Total Run Time 12 00 Kad Information S ge MS Scan T Solvent delays are displayed in the method bar as bright green bars at the top of the Function display and numbered from 1 to 4 Double clicking on a solvent delay bar or clicking the edit button with a solvent delay selected brings up the solvent delay dialog Pressing the X delete button or pressing the delete key with a solvent delay 197 TurboMass Software User s Guide 198 selected will remove a solvent delay If it is between other delays then the delays are shuffled up Solven
258. e Before this software can be installed the terms of this EULA must be accepted accept decline 12 Click I accept to start installing the INET Framework Microsoft NET Framework 1 1 Setup Cc F Extracting netfx msi PITT TT When complete the following appears Microsoft NET Framework 1 1 Service Pack 1 KB867460 Microsoft NET Framework 1 1 Service Pack 1 KB867460 was successfully installed on Microsoft NET Framework 1 1 13 Click OK If any Communique Reporting templates had been stored from a previous version of TurboMass software the following dialog appears verifying they have been saved 697 TurboMass Software User s Guide Information J Your existing reporting information from C TurboMass Communique2Templates mdb has been saved into C TurboMass Communique2Templates_2 8 2006_125755 mdb C TurboMass Communique2Reports mdb has been saved into C TurboMass Communique2Reports_2 8 2006_125755 mdb C TurboMass Communique24udit mdb has been saved into C TurboMass Communique2Audit_2 8 2006_125755 mdb 14 Click OK and the Welcome to the Install Shield Wizard for Communiqu appears ie Communique 2 3 Customer Edition InstallShield Wizard Welcome to the InstallShield Wizard for Communique 2 3 Customer Edition The InstallShield R Wizard will install Communique 2 3 Customer Edition on your computer To continue click Next WARNING This program is protected by copyrig
259. e External Std Area Curve type RF 1 7984 Response 0 0 0 Controlling the appearance of the Quantify display 1 Select View from the Quantify Display menu to display the Quantify Display dialog r Graphs M Eud Edt Header T Residuals r Summary I Show Summary Window Format flis by Compound z m Peak List I Show Window _Edit Header cen 2 Specify the Quantify windows you want to display by selecting the appropriate checkboxes You can choose to display any combination of the following the Graphs window showing calibration curves the Graphs window showing residuals the Summary window and the Peak List window 3 Choose whether you want to display the Summary window listed by compound or by sample by selecting the relevant setting from the Summary Format drop down list 296 Quantify A user configurable header can be displayed at the top of the Graphs or the Peak List windows In the default display the header is not displayed To open the Header Editor dialog click Edit Header from the View dialog OR Open the Header Editor from outside the View dialog by selecting an existing header See The Header Editor on page 54 for more information about using the Header Editor Header Editor QuanGraphsHeader x m Header areas 7 P rr ee ss eS l Cancel eee ee eee E EES Sea r Cell Line 1 Left Group SystemList v
260. e Therefore to view data from the current line of the Sample List use Samples Last To report the most recent line in the Sample List we need to change the Indexing of the Peak Number Right click on Peak Number DATA and select Indexing from the menu The Data Object Indexing dialog appears Project S amples Current QualPeaks Current PeakNumber Collection Samples QualitativePeaks ms Double click on Current in the Samples Index cell The following Index dropdown menu appears Project Samples Current QualPeaks Current PeakNumber Collection Samples Curren z Next Last Current ms 578 10 1 12 Communiqu Reporting Select Last then click OK Jnder RT put Retention Time from the Project Samples Qualitative eaks path in the Data Objects toolbox Set to Samples Last nan Under Name put Name from the Project Samples Qualitative Peaks path in the Data Objects toolbox Set to Samples Last Under Match Factor put Match Factor from the Project Samples Qualitative Peaks Text Hits path in the Data Objects toolbox Set to Samples Last Under Area put Area from the Project Samples Qualitative Peaks path in the Data Objects toolbox Set to Samples Last Check your Date Time Data Object Properties for the correct Time Format x Object Fort Alignment Horizontal Yortical
261. e TurboMass indicates the range you have selected When you release the mouse the Quantify Method Editor window will be updated to show the new Time Window and the Retention Time or Relative Retention Time will be set to the middle point of the Time Window The Quantify Trace parameter will be set to the same type as the chromatogram selected with the mouse TIC BPI or mass chromatogram The Retention Time or Relative Retention Time parameters can also be selected by right clicking the chromatogram on the peak apex The spectrum may be inserted by copying it from the Spectrum window with Edit Copy Spectrum List and then selecting the Edit Paste Spectrum menu bar item in the Quantify Method Editor If there is a significant degree of chromatographic or spectral background the best approach to purify the spectrum is as follows 1 Perform a background subtraction in the Chromatogram window using the Process Combine Spectra operations described in Strip and Combine Functions on page 461 261 TurboMass Software User s Guide 2 Edit Copy Spectrum List in the Spectrum window 3 Edit Paste Spectrum in the Quantify window To remove specific contamination peaks from the spectrum paste the spectrum into a text editor or spreadsheet and edit it before pasting it into the Quantify window Using the keyboard a If Retention Time is selected set it to the time in decimal minutes at which the compound is expected to elute and
262. e mass range and ionization mode To select a new function click the arrow at the end of the Function field and left click one of the Functions from the list Contains the history of any processing that has been applied to the current data When raw data are processed for example Refine or Combine the processed data can be saved using the Save Spectrum command from Spectrum File menu Selecting History in the History Selector dialog allows you to select one of the processed data files Getting Started Experimental Record The Experimental Record window displays information about the selected raw data file including e Raw data file header information such as sample description acquisition date and time e Tune parameters including the settings on the Tune page and instrument thresholds e Function description showing the functions set up in the Scan Functions window e GC information including the GC inlet position vial number run log and GC method information Controlling the Experimental Record display 1 From the Chromatogram Data Brower click Experiment to open the Experimental Record window Experimental Record ioj x File Options Acquisition Experiment Report File c tmintro pro data gas2 GAS2 26 Aug 1997 16 59 58 Administrator Lab Inst 5 45 186 16 Split 56 1 ajp Unleaded gasoline Instrument Calibration Parameters 41 TurboMass Software User s Guide 42 2 From the Optio
263. e same The Tune Evaluation Sample Tune Eval is an injection of BFB 4 Bromofluorobenzene or DFTPP Decafluorotripheny phosphine used to verify that the mass calibration mass resolution and relative intensity of the mass spectrometer meets EPA defined standard conditions It might only contain the tune evaluation compound or it might be part of the Continuing Calibration sample It is typically analyzed every 12 hours The Initial Calibration Init Calib is a multi level calibration used to establish the quantitative calibration curves In most environmental methods it is created when the mass spectrometer is new or cleaned Thereafter on a 12 hour basis the Continuing Calibration is analyzed to verify that the Initial Calibration is still valid The Continuing Calibration Cont Calib verifies that the Initial Calibration is still valid It is typically a mid level calibration sample It is typically analyzed every 12 hours A Method Blank Meth Blank sample is a blank used to verify the complete analytical procedure including sample preparation It is typically analyzed every 12 hours for VOA and every extraction batch of 20 samples for SV The Laboratory Control Sample Lab Control is often similar to the Matrix Spike Sample but spiked into a blank matrix clean sand for soils or deionized water for waters instead of a field sample matrix It is typically analyzed every 12 hours A Matrix Spike Spike sample is used to v
264. e BPI chromatogram Alternatively the BPI chromatogram may separate some components that coelute in the TIC Displaying a TIC chromatogram using the toolbar gt Click to update the Chromatogram display to show a single TIC chromatogram for the currently selected trace TIC Chromatogram x File v50 Function Cancel File C Add trace I BPI Chromatogram Replace trace C New window Displaying a TIC or BPI chromatogram using the menu 1 Select TIC from the Chromatogram Display menu 2 Ifyou require a BPI chromatogram select BPI Chromatogram 377 TurboMass Software User s Guide 378 3 Ifyou want to add the new chromatogram to the current chromatogram window select Add trace If you want the new chromatogram to replace the current trace select Replace trace If you want the chromatogram to have its own window select New window 4 Click OK to save changes GC Detector Trace This dialog enables you to display the GC chromatograms previously acquired from GC detectors such as an FID run in parallel to the MS within the Chromatogram window You may also specify the GC detector chromatogram as the Quantify Trace for a compound within the TurboMass Quantify Method 1 Select GC Detector Trace from the Chromatogram Display menu to open the GC Detector Chromatogram dialog GC Detector Chromatogram a x File fast Comot o Offset min Cancel File C Add trace Replace trace
265. e GC and execute all other GC related procedures 3 From the GC menu select Configure The Configuration Editor summary window is displayed This displays the GC information that will be defined during configuration pl Configuration Editor File Instrument User View Help SIRI si l 2e A Instrument Configuration Instrument Type Autosampler Type LINK Box interface information Instrument Configuration information After configuring the GC the area below the Configuration Editor summary list displays key GC information The box on the left contains information about the LINK interface which includes the type model number EPROM version number memory size available in the interface in bytes and serial number The box on the right contains a summary of the GC configuration 719 TurboMass Software User s Guide 720 NOTE Summary of information displayed on the Configuration Editor window Field Description Name The name of the GC Type The GC model or type Acq Port The physical data acquisition port to which the 600 Series LINK Interface is connected LINK Port The physical port in the LINK interface to which the GC is connected Configured Displays YES if you provided all the information needed to configure the GC Otherwise NO is displayed IPM Displays YES if the Instrument Personality Module IPM for the GC has been do
266. e Matrix section is only enabled when you select a Volatiles or Semi volatiles Analysis Other matrices can be analyzed but may require the use of additional scaling factors custom reporting templates or external calculations Water Select this radio button to indicate that the new sample list will be used for the analysis of water samples This together with the Analysis setting determines the calculations Quantify will use to produce concentration results If Water is checked the Concentration level section will be disabled Soil Select this radio button to indicate that the new sample list will be used for the analysis of soil or sediment samples This together with the Analysis and Concentration level settings determines the calculations Quantify will use to produce concentration results 216 Concentration Level Low Medium OK Cancel Help Sample List The Concentration level section is only enabled when you select a Volatiles or Semi volatiles analysis and a Soil matrix Different equations are used for each Select this radio button to indicate that the expected concentration range of soil samples to be analyzed with the sample list Select this radio button to indicate that the expected concentration range of soil samples to be analyzed with the sample list Clicking the OK button displays the Sample List Wizard main window Clicking the Cancel button closes the dialog and returns you to the main S
267. e data will be acquired If you set a value of 20 the threshold would sit well above the noise level so very little noise data will be acquired Conversely a value of 1 would place the threshold just above the noise so almost all of the data will be acquired 73 TurboMass Software User s Guide NOTE When using an lon Counting Threshold you should set the SIR Data SIR Baseline Level and the Profile Data Baseline Level to zero The value of the lon Counting Threshold should be set such that background noise is removed without significantly reducing the intensity of the smallest peaks of interest NOTE When using an lon Counting Threshold you should set the Profile Data Baseline Level and SIR Data SIR Baseline Level to zero 74 NOTE NOTE Profile Data Spike Removal Instrument Data Thresholds Spikes are distinguished from real data by the fact that spikes are very narrow and also very intense when compared to their immediate neighbors Data points that are determined to be spikes are removed by setting the value of each spike data point to the average of its immediate neighbors The use of Spike Removal does involve some additional processing during acquisition which will reduce the maximum achievable acquisition rates by approximately 30 Use Spike Removal Select this checkbox to perform spike removal during an acquisition Spike removal will not be reflected on the Tune page Minimum Spike Inte
268. e end points The default value for the reduce peak tailing parameter is 50 and normal operating range is between 25 and 300 The Raise baseline parameter prevents the baseline end point from moving too high up the peak To prevent the baseline endpoints from moving up the peaks reduce the value of this parameter The default value is 10 and normal operating range is 5 20 This parameter is only relevant when the Reduce peak tailing parameter has a small value less than 50 Determines how well resolved peaks must be before they are separated by a dropline or baselines are drawn up into the valleys depending on the value of the Join valleys parameter If you want poorly resolved peaks to be separated increase the value of this parameter The default value is 90 and normal operating range is 50 100 275 TurboMass Software User s Guide Detect You can optionally attempt to detect completely unresolved peaks or Shoulder shoulders by selecting the Detect Shoulder Peaks checkbox The peaks algorithm will detect a shoulder if the slope of the shoulder top is less than the specified percentage of the steepest slope on the peak Therefore to make shoulder detection more sensitive increase the value of this parameter The default value is 30 and normal operating range is 20 90 Setting Environmental Reporting Parameters The environmental parameters should not have to be changed frequently once establ
269. e name of the user library to be created for File Name Click Open Click OK Spectrum NOTE For this spectrum to be used for library searching it first must be processed by Index Library in the Library Search Process menu 459 TurboMass Software User s Guide 460 Strip and Combine 4 5 Functions NOTE Strip and Combine Functions Strip Functions The Strip application removes unwanted background and noise from a data file Processing a data file using Strip creates a new file that is stored in the same format as a raw data file and can be displayed and processed in the same way as a raw data file The original input file is retained unmodified Opening the Strip application gt Select Strip from the TurboMass top level Tools menu OR Click to open the Strip Datafile dialog m Strip Datafile SBE File Options Help i l al Process Stop Function 1 m Background iG Processes File 588 Enhance Function 1 Process 0 l Subtract Scan 1 Background Cluster l Output l C cova File vs Ot The Strip application cannot be accessed while the Combine Functions application is opened Likewise the Combine Functions application cannot be accessed while the Strip application is opened Strip provides four processing options Subtract Enhance Cluster and CODA Subtract Can subtract either a single background spectrum or a whole data file from the input file
270. e not a valid statistic for any other type of regressed curve For each data point a value of y Yi pred can be predicted from the calibration curve at the position x For each data point a residual between the actual and predicted y value can be calculated as yj Yi pred and the residual sum of squares RSS can be calculated as RSS E yi Yi pred The total variation in the data is reflected in the corrected sum of squares CSS calculated as CSS 2 yj Ymean where Ymean is the mean value of y The model sum of squares MSS is the portion of the total variation accounted for by the regression i e MSS CSS RSS The coefficient of determination r2 is the proportion of the variation accounted for by regression and is given by the ration of the model sum of squares to the corrected sum of squares i e r2 MSS CSS CSS RSS CSS Appendix C TurboMass Quantify Calculations Curve Correlation Coefficient The correlation coefficient is only a valid statistic of fit for regressed unweighted linear curves In this case the square of the correlation coefficient is equivalent to the coefficient of determination described above Internal Peak Response Area Amounty Areay Where Area is the area of a peak calculated by peak detection Amounty is the given amount of the Internal Standard in the sample Areay is the area of the internal standard peak calculated by peak detection 739 Appendix
271. e the name displayed at the top of the column enter a new name in the Field name field 6 To change the alignment of text in the column select Left Right or Center from the Alignment list The text alignment in a cell column or row can also be changed by selecting the area and clicking E E or or selecting Left Center or Right from the Align option in the Field option in the Samples menu 7 To save a customized Sample List format select Save Format from the Samples menu and enter a name in the dialog displayed 8 To retrieve a previously saved format select Load Format from the Samples menu and select the required format from the list Selecting areas You can select with the mouse the keyboard or a combination of both of these methods With the mouse To select Left click A single cell The required cell A block of cells The first cell in the block left click and drag until the required cells are selected A row The row number A column The column heading 235 TurboMass Software User s Guide 236 The entire Sample List The box at the top left corner of the Sample List TO Fenm Ea ID Default ID Default With the keyboard Position the cursor at the top left corner of the area to be selected hold down the shift key and use the arrow keys to select an area Inserting one or more rows gt To insert a single row click El OR Select Insert from the Samples menu OR Press INSERT
272. e to appear in the drop e Lab Control down list e Analyte Analytical sample with unknown concentrations of target compounds e Analyte Dup Reinjection of an Analyte e Blank An analytical blank For environmental and QA QC use Meth Blank instead eQC Quality Control sample e Standard Concentration calibration standard For environmental and QA QC use Init Calib or Cont Calib instead e Tune Eval DFTPP or BFB tuning check e Init Calib Initial calibration standard e g one level of a 5 level calibration e Cont Calib Continuing Calibration standard injected periodically to validate the initial calibration curve e Meth Blank Analytical Method Blank Contains all Internal Standards and Surrogates Laboratory Control Sample LCS typically a Cont Calib prepared from a different stock solution to validate the Init Calib and Cont Calib concentrations e Spike Matrix Spike sample e Spike Dup Matrix Spike Duplicate sample e Dilution Dilution ofan Analyte Sample List Conc values for internal standards and Surrogates will need to be adjusted if they are diluted e Re Extract Re extracted sample Sample List Sample ID Enter this primary sample descriptor for the environmental reporting software This descriptor appears in the Sample List column in this window Vial No The sample position in the autosampler from which the injection will be made Injection vol The amount of sample injected into
273. e triazine compound splitless into a 250 C injector with a 30 mx 0 25 mm x 0 25 nm column at 80 C Program to 300 C at 10 min 4 When the major portion of the peak begins to elute at n6 minutes start the calibration process 5 Open the split valve after calibration is completed 6 Perform a wet needle injection of this compound in splitless mode and acquire a data file over the desired mass calibration range This will drastically overload the GC column and provide several seconds of high intensity ions 7 Use the From File option in the Process menu select Scan Speed Compensation and select your data file with the Browse function 8 Click OK to calibrate 9 Inspect the calibration to verify correctness Make manual identifications if required 135 TurboMass Software User s Guide 136 For SIR start a Static only mass calibration as soon as you see the target peaks in the Tune display For a full scan analysis perform a Scanning and then a Scan Speed Compensation calibration as described above for Static An alternative for full scan calibration is to create a simultaneous two function acquisition method with two different scan times one for the Scanning and one for the Scan Speed Compensation Mass Calibration Saving and Restoring Calibrations The complete instrument calibration can be saved to disk as a named file and then recalled at a future date Static dynamic and lag time calibrations
274. eak The Peak Name may be obtained in several ways While viewing Quantification results double click on one of the report lines In Chromatogram integrate the chromatogram Select Integrated Peaks from the Edit menu Select the desired peak and enter the name Click Modify and then OK In Chromatogram display a selected portion of the desired chromatogram TIC or selection ion Select Lib Search Peaks from the Process menu After the library searching is complete return to Chromatogram Select Integrated Peaks from the Edit menu and click OK This will display the top match library hits for each of the integrated peaks Avoiding Printout of Library Search Results To avoid printing out extensive library search results see the following procedure 1 2 From the Window Start menu select Settings gt Printers In the Printers dialog double click on the name of the printer In the Print Queue dialog select Pause Printing from the Printer menu After library searching is completed purge the files from the print queue by double clicking on the printer icon in the Windows task bar then selecting Purge Print Documents from the Printer menu Before closing the dialog be sure to restart the printer by removing the checkmark from the Pause Printing command in the Printer menu by selecting the command again Pausing the printer pauses it for all users including others who may access it across a network If this is a problem add a
275. eaks from the Process menu Click OK when asked to print 286 NOTE NOTE Quantify To save paper you can pause the printer and later delete the contents of the print queue See Avoiding Printout of Library Search Results on page 389 5 When library searching is complete return to Chromatogram and select Copy Detected Peaks from the Edit menu If Display Peak Name is selected the peak name if available will be displayed above the peak To select Display Peak Name se ect Peak annotation from the Chromatogram Display menu For more information on using names to label the chromatogram see Annotation Type Parameters on page 388 6 Open the Quantification method by selecting Edit Method from the Sample List Quantify menu It may be a new or exisiting method 7 Enter the Time window you wish to use 8 Select Paste Chromatogram from the Edit menu The library search name the largest ion the retention time and the spectrum will be entered into the method 9 You may now enter any compound specific information such as Internal Ref Verify that the Quantify ions are those you wish to use 10 Save the method AutoUpdate Automatically Updating Retention Times in the Quantify Method To automatically update the retention times in the Quantification method 1 Inthe Sample List select View Results from the Quantify menu 2 In Quantify select View from the Display menu 3 Select Show Summary Window and List
276. ear Square Root and Log The log and square root intensity modes will give more weighting to lower intensity masses 3 Set the Color Palette The options available are White On Black Black On White Gray Scale User or one of the Map color schemes The Map color schemes available are Ocean Deep Embers Emerald Forest Hot Metal Cool Metal Morning Frost Polar Dawn and Tropical Lagoon Map 4 Define the User colors The User colors are defined by selecting Fonts and Colors from the TurboMass top level Customize menu and selecting the colors for Data 6 to 10 5 Set the Map Intensity Range values and click OK to create the map Changing user color scheme for Map display 1 Select Fonts and Colors from the Customize menu to open the Color and Font Editor dialog Color and Font Editor x m Current Settings Header Text User Text List Text List Text List Text 2 Select Data 6 to 10 in Type and change the colors as required 3 Click OK to update the Map display with the new colors Controlling the Appearance of the Display The appearance of the Map display is controlled from the Map View dialog 537 TurboMass Software User s Guide Changing the appearance of the Map display 1 Select View from the Map Display menu to open the Map View dialog ie Ex OK IV BPI Chromatogram I Current mass chromatogram T Current Spectrum Cross hairs Inverse Map Grid Dot X Sp
277. eceeeeeeeeeeeeeseeeeees 478 Setting CODA Options ccccccccsseescecssecseceeceeceseeeseeeeeeseeeseeeeeneeenes 479 Stopping a Proces Santa Mica eee e a ea een Shai eet eldest del 480 Combine Functions eiia a E TE ERE 481 Selecting a Data File and Subrange to ProcesS e cesceseeeteereeteeee 482 Selecting an Output Data File cc cccccseeeseceteceteceteceseeeeeeseeeseneeees 483 Stopping a Process areir E EEE deetvidivedeeats E ie 484 MADE ANY E EE E A EA 485 TurboMass Library WindowS cccccsccssecessceteceseeeseeeseeescecseeeaecnseenseesseeaes 488 Searchin ga Library ciren roerien deeds Lede tereb bas docdsvend ones E duteesbag toetsees 489 TRE PLESEAT CN js ecsiyas ss Feheasscedecnogsaseanoah eae A vscestsantspotenterasteibent staas 489 Phe Mains Care i AEE dassue osceaseuSistea etaaas 489 An Overview of Library Searching 0 cccccccsceeseerseeteeeneeesseeneeesees 490 Library Toolbar cece cccecsecsceescecsecseceseceseceseeeeeesseeeeneeeseeeeeeseeesaees 491 Selecting Which Libraries to Search ccccscccsseesceeeteceteeeeeeseeeeeeeenes 492 Selecting a New Search Spectrum cccccsccssecssecstecsteceteeeeeeeeeeeeeenes 494 Setting Library Search Parameters ccccccssccsseceteceteceeeeeeeeeeeeeeeeeees 496 Setting Library Search Filters ccccccecsseesteeeteceteceteceteeeeeeseeeseneeees 498 Starting a Library Search ccc ecccccccesseesseesseceteceseceeceseeeeeeeeeeeeeeeseeeaes 501 Library Search Results oceni
278. ect As Template If Create Using Existing Project As Template is selected the Browse button will be enabled Click Browse to display the Select Existing Project dialog allowing you to select an existing project to use as a template If Create Project Using Current or Existing Project is selected all files in Acqudb Methdb and Sampledb are copied into the new project If an existing project is not chosen as a template all subdirectories will be empty To create the new project click Finish Clicking Back will display the previous page allowing changes to be made Clicking Cancel will discard all information and exit the Project Wizard For TurboMass to create a new project it must close any TurboMass applications that are currently running If you are currently running any of the TurboMass applications such as Spectrum or Chromatogram a message will appear informing you that all applications will be closed Click Yes to close any opened applications and create the new project All new data files sample lists peak lists quantify method files and quantify calibration curves will be saved in this project until you change to a new project NOTE Space on drive C is normally restricted It is often useful to place data on other local drives for example d or e Opening an existing project Select Open Project from the TurboMass File menu Double click one of the projects in the list select one of the projects in the list
279. ect for any errors in the mass scale Setting up your GC gt Set up your GC configuration and develop your GC method Developing your Mass Spectrometer Method gt Develop your mass spectrometer method for scanning the system referred to as a Function in the TurboMass Function List editor Setting up your Sample List and acquiring Initial Data 1 Specify your list of samples to be introduced into the system by manual or autosampler injection Your sample list may contain a single sample or a number of samples 2 Start your run to acquire data to be used for qualitative analysis or quantification method development Developing your Quantification Method If you are performing quantitative analysis develop a peak detection and location method based on the results of your initial data acquisition in the TurboMass Quantify application Developing your Qualitative Method TurboMass Overview This is a dataset you can specify in each row of the sample list to generate reports that do not make use of the quantitative results Acquiring Data based on your Method You can now acquire data and apply your quantification method parameters Monitoring Data Acquisition The progress of the acquisition can be monitored by viewing the data acquired in real time using the Spectrum or Chromatogram displays Manipulating your Data You can manipulate your data in many ways using the TurboMass Chromatogram Spectrum Map Quantify
280. ectrum Grid Ort X Chromatogram Grid Off X I Automatic Link to Spectrum I Automatic Link to Chromatogram 2 Select the appropriate Map View parameters TIC chromatogram If selected the TIC chromatogram of the current data file is displayed at the top of the Map window Deselect this checkbox to remove the TIC chromatogram BPI Chromatogram If selected the BPI chromatogram of the current data file is displayed at the top of the Map window Deselect this checkbox to remove the BPI chromatogram Current mass If selected the mass chromatogram of the currently chromatogram selected mass is displayed at the top of the Map window Deselect this checkbox to remove the mass chromatogram All chromatograms displayed are overlaid on the same axes Current Spectrum If selected the spectrum at the currently selected retention time is displayed at the bottom of the Map window Deselect to remove the spectrum 538 Cross hairs Map Spectrum and Chromatogram Grid Automatic Link to Spectrum Automatic Link to Chromatogram 3 Click OK Map This drop down list controls the color used to display the cross hairs cursor Inverse Black White or Axis color The cross hairs cursor can be moved to change the currently selected mass and retention time Apply a grid to each part of the display The grid pattern can be set to Off Dot Dash or Solid for each part of the display If selected the Spectrum window w
281. ed Processes External processes can be added to the TurboMass Tools menu Select Options from the top level Tools menu and select the Processes tab System Processes Mass Defect F1 NIST C TurboMass OK Cancel Epp Adding a process 1 From the Processes tab click Add to display the Process dialog Menu text Chopos Command CATuboMass Chroproc exe E Arguments OoOo S gt I Prompt for arguments omes 2 Enter the text that will appear on the menu in the Menu text field 3 Enter the process name and path in the Command field Clicking E will open a browser to help locate the required executable program file 4 Ifthe process requires arguments that do not change enter them in the Arguments field TurboMass Software User s Guide 36 NOTE OR For arguments that are variable select Prompt for arguments TurboMass will prompt you to enter the required information 5 Click OK Each process added to the list is assigned an unused function key as a shortcut to the process This shortcut key is displayed in the Key field To run the process either select the process from the top level Tools menu or press the shortcut key Moving a process Left click the Key field of the process to be moved and click e or l Move buttons until the process is in the required position The shortcut keys remain in the same order so some processes may have a new shortcut key Modifying a proc
282. ed if the mass range of interest is less than 1000 amu and includes the range 0 150 amu If selected a message is displayed if an acquisition is started that is outside the range of the current calibration If you are using continuum or MCA acquisition modes to acquire your calibration data you will need to tell the system how it should convert the acquired data into 126 Mass Calibration centroided data needed by the calibration process For more information on Mass Measure parameters see Spectrum on page 423 Setting the Mass Measure Parameters Select Mass Measure Parameters from the Calibration Edit menu to open the Mass Measure dialog 2 Enter the required parameters and click OK Mass Measure M 127 TurboMass Software User s Guide 128 The Calibration Report The peak matching algorithm performed by the calibration may have found wrong peaks or missed some peaks You may need to change the peak match parameters or adjust the peak matching manually You can change the peak match parameters by selecting Peak Match Params from the calibration graph Edit menu If the peak matching algorithm has found the wrong peaks increasing the value of the Peak window parameter will solve the problem You should also try reducing the value of the Intensity threshold parameter if it is not already zero before identifying the peaks in the acquired spectrum by hand The top graph shows the calibration spectrum The pe
283. eeeeeeeeseeeseeeeeeeeenaees 106 Warning Messages in Tune ccsccesccesscesseeeeceseeeeseeeseeeseecseecsaecnseenseenseenes 107 Resetting the Zero Level srian n a i e E 108 Controlling Readbacks 0 cccecccesccessceeeeeseeeseeeseecseeeaeensecesecnseeseeseeeeneeeses 109 Changing Readback Style cccecccecsesscesseeeteeeeeeseeeseecseeneeneenseenes 109 Starting an Acquisition from the Tune Page ceeseeeceseeseeneeeeeeseeaeees 110 Mass Calibration scccsccssssssssssscssscssscsssscsscssscsscsssssssssessnessssssesssosees 113 IO MUCTION ssena aie ctactvavtstel eel ee aa e he ees bade tice eshte A 115 How A Calibration Is Formed 0 cccceceseesceseceseeseeeeeseceeeeaeeeeceaeeaeeereeaeenee 116 Calibration Ey pes aetti E Ta ES E EA a TOTES 117 Overview Of The Calibration Process sseseseseseeesesssesessesessesessesersesseseee 118 Check the Instrument Tuning ec cecccecseeseeeteeeneeseeesecnseeneenseenes 118 Set the Calibration Parameters c ccccccssscetscetsceseceseeeeeeseeeeeeeeeneeenes 118 Start an Automatic Calibration ccccccccssesssceseceseceseceeeeseeeeeeeeseeennes 118 Check the Calibration Report cccccccesssessceseeeeeeeeeseeeseeeseeesaeeeenes 119 Displaying Calibration Parameters cceceesseeeceeeseeeececeeaeeeeceaeeeeeneeaes 120 Setting Parameters that Control Calibration ccccecscessceeseeeseeeteeetseenees 121 Setting Automatic Calibration Parameters
284. een specified and calculated intensity ratios It is specified as a percentage of the intensity ratio s Determines how far apart scans may lie in which peaks forming part of the pair triple are located For instance if time window is 0 5 min with mass difference 5 0 amu then a peak at mass 25 0 Da ina scan at time 2 2 min will match with a peak at mass 30 0 Da in a scan at time 2 7 min 477 TurboMass Software User s Guide 478 Threshold Defines an absolute intensity that a data point must exceed to be regarded as being significant For spectra with a high baseline this parameter will need adjusting so that its value is approximately equal to the intensity at the top of the noise The larger this value the more likely that information will be discarded as being noise 3 Click Default to set the parameters to their default values Setting Cluster Centroid Options The Fast Centroid process is unique to the cluster algorithm It was developed to reduce the time taken to centroid each scan of a run Consequently it will not deal as accurately with multiplets as the standard centroid algorithm but should be perfectly adequate for most applications Setting the Cluster Centroid processing parameters 1 From the Cluster Analysis Options dialog click Centroid to open the Fast Centroid dialog Fast Centroid x m Contermehod Peak width at base amu Baseline threshold Top C Centroid top 2
285. eenaes 552 Report Template Browser ccccccsccesscesscesseeeecseneeeseeeseeeseecsaecsaecnseenseenseeaas 556 Filtering the Template List ccceccccsccessceseceeseeeseeeeeceeeeecnaecsseenseenseenes 557 Report Template Filter Toolbar ccccecccccseesseeceeeneecseeeseecsecseeseenseenes 557 Communiqu Reporting sccccccccscccccscesccsssccecsssscssessssccesssseessessesees 559 About the Report Method Editor c ccccccccsceesseeseeseeseesecnecseenteeseenes 561 Opening a Report Template cccccccecsseesseessecseceseeesecnseeseeseeeseeeeseeenaes 562 Modifying the Template ccccccccescesecesseeeeceeseeeseeeseecseeeaecaecnseenaeenseenes 565 Adding a Data Object to the Template ccceeceeseesseeseeseeteensees 566 Creating a New Report Template 00 0 0 cccccccccseceseceteceteceeceeeeeeeeeeeeeeneeenes 570 Add a Header and Footer c cccesccescesseesceeceeeeeeeseceaeeaeeeeceaeeaeeeneeaeeaee 571 Add Data Objects r vsicccracsasdavansedsvtanssddgeatone iesstoassassacelateeacedapeaeaspeatente 574 Select the Template in the Report Method Editor eee eeeeeeeeeeee 580 Add the Report Method to the Sample List cccsseesseesteetteeneees 585 Environmental Reporting ssessssssessseossoossoessosssoossoossoossoossoosssosssosssssssse 587 About Environmental Reporting ccccccccecssessseesceeseeeseesecnsecneeneeneenes 589 Select Forms Dialog meoc nn n caless eeaehs osc Eaa 591 Report Generation Window
286. efix if it is required by the Output type selected For example if you select Save to file select a Report 583 TurboMass Software User s Guide name prefix of lt Sample Name gt and click the Setup button This drop down list contains the report output file types supported by Communiqu NOTE To ensure that a CSV file puts data items on the same line enclose all items that are required to appear on one line of the CSV file in a Communiqu Section object All items enclosed in the Section should have the Down from Top property set to zero 0 Also all items should have the same Height value set as the Section itself Rich Text Format RTF HTML HTM ASCII Text TXT Comma separated CSV Portable Data Format PDF Web Archive Single File MHT NOTE The Web Archive Single File type embeds the graphics into the same htm as the text portion of the report resulting in a single file with both text and graphics The following dialog appears x Fie Path C TurboMass TUTORIALQUANT PROSData i File Type Rich Text format RTF X OK Cancel 9 Click OK 10 Select Save As from the Report Method Editor File menu 11 The Save Report Method As dialog appears 584 Communiqu Reporting Save in Ga YEW ex Fee File name Qualitative Report rme Save as type Report Method Files rme x Cancel P Za 12 Type a File name for your Report Method for example Qualitative
287. el selections as described above Select this radio button to create a New sample list When selected the lt sample list file name gt drop down list control and Browse button are disabled Select a sample list in the current Project from this field by pressing the down arrow icon or search for another sample list by using the Browse button This field is blank when the New Sample List option is selected Clicking the Browse button displays the standard File Open dialog so that you can search for a stored sample list Typically sample lists are found in the SampleDB directory of your Project directory PRO The Analysis section of the dialog is enabled when the New sample list option is selected There are three radio buttons for this section Volatiles Semi volatiles and QA QC Volatiles and Semi volatiles are environmental sample types If either one is selected the Matrix and Concentration Levels sections remains enabled If QA QC is checked the Matrix and Concentration level sections will be disabled Select this radio button to indicate that the new sample list will be used for volatile organics analysis VOA Select this radio button to indicate the new sample list will be used for semi volatile SV organics analysis Select this radio button to indicate the new sample list will be used for general quality assurance or quality control QA QC 215 TurboMass Software User s Guide analysis purposes Matrix Th
288. elect Acquire amp Calibrate to perform automatic calibration Optionally select Acquire amp Verify Select Print Report if you want a printed calibration report Set the data Acquisition Parameters if your mass range or data acquisition rates are not covered by the defaults Click OK Check the Calibration Report Examine the calibration report and display the calibration graphs if necessary to satisfy yourself that the calibration is satisfactory A good calibration will cover your data acquisition mass range and have a small typically less than 0 3 error for each calibration mass 119 TurboMass Software User s Guide 120 Displaying Calibration Parameters The Calibration dialog displays calibration status information including calibrated mass range and scan speeds and the time and date of the last calibration 1 To open the Calibration dialog select Calibrate Instrument from the Calibration menu on the Tune page a Calibration Default cal Pmj rents AE m Mass Calibration Setting Parameters that Control Calibration Use the following procedures to set calibration parameters Setting Automatic Calibration Parameters 1 Click gt in the Calibration dialog to open the Automatic Calibration dialog Types I Static Calibration Scanning Calibration V Scan Speed Compensation Acquisition Parameters Process F Acquire amp Verity R Print Report
289. elect the thoroughness of the search the Spectrum search type and its options Keep in mind that more thorough searches take longer 17 You can select the Reverse search option to improve the matching capability when there are contaminant peaks in the mass spectrum 18 You can leave the rest of the settings as their default values or optimize as needed 19 Click the Library Settings tab You may have several mass spectral libraries on your computer Some are from NIST mainlib the main library and replib a smaller library of replicate spectra subset of compounds different spectra which can improve the chances of finding the right compound Refer to the NIST2002 Software Manual on the NIST2002 CD There can also be other commercial libraries e g the Pfleger Mauer Weber drug library or user created libraries This tab allows you to select which libraries to search and in what order Restricting the number of libraries spectra searched increases speed in a linear fashion Searching libraries which have only the target compounds with few unlikely matches also increases the chance of a correct match For example someone doing drug analyses might search a drug library but would not want to search a flavors and fragrances one Compounds in mainlib the primary NIST library have flags indicating which databases they originally came from or in which industry standard lists of compounds they occur If the unknown compound is expec
290. entafluorobenzene 1 4 Difluorobenzene 1 4 Dichlorobenzene D4 Dibromofluoromethane Toluene d8 Bromoflurorobenzene Dichlorodifluoromethane Vinyl Chloride Bromomethane Trichlorofluoromethane 1 1 Dichloroethene Methyl Tert butyl Ether Methylene Chloride 1 1 Dichloroethane 2 2 Dichloropropane Chloroform Benzene Trichloroethene Dibromomethane 1 Bromo 2 chloroethane Toluene trans 1 3 Dichloropropene 1 1 2 Trichloroethane Ethylbenzene p m Xylene o Xylene Isopropylbenzene Bromobenzene n Propylbenzene 1 3 5 trimethylbenzene sec Butylbenzene Type CAS number Abbreviation Maximum in blank MDL Water Soil Response Factors Minimum RRF Maximum RSD Init Cal Maximum Difference Matrix Spike Concentration Recovery Limits Water Soil RPD Limit Water This dialog contains all of the above parameters plus the following Quantify RPD Limit for Water An edit box that defines the maximum acceptable RPD relative percent difference value between the matrix spike and matrix spike duplicate recoveries for water samples RPD Limit for Soil An edit box that defines the maximum acceptable RPD relative percent difference value between the matrix spike and matrix spike duplicate recoveries for soil samples To Set QA QC Limits The QA QC limits are a set of values that apply to all compounds global parameters in the method For this reason the QA QC Limits dialog is accessed from the Method Editor Edit menu
291. ents bj and e is the n x 1 vector of residuals from the fit to each yj value Appendix C TurboMass Quantify Calculations The familiar least squares solution for the regression coefficients is given by b X X Lx y where indicates matrix inverse and indicates matrix transpose The above equation can then be solved using Gauss Jordan elimination To implement weighted regression X and y are first multiplied by a diagonal n x n matrix P i e X becomes PX and Y becomes PY before the above equation is solved where each element pij of P is given by Pij wj fori j Pij 0 fori lt gt k w is weighting of ith calibration point all set to 1 for no weighting i gnung p 735 TurboMass Software User s Guide 736 Peak Amount Calculations User Specified Response Factor If a user response factor if selected within the quantitation method calibration curves are not used The following calculation is performed to obtain peak amounts Amount Peak Response Response Factor Where Peak Response is the response value calculated for a peak Response Factor is user entered response factor for that compound Average RF Calibration Curve Amounts are calculated using an Average RF calibration as follows Amount Peak Response Average RF Where Peak Response is the response value calculated for a peak Average RF is average response factor calculated for a set of calibration points Appendix C TurboMass
292. eport Template Browser All Templates PerkinElmer v5 1 1 Chroma 5 1 1 Chroma v5 1 1 Display we 5 1 1 Integra ve 5 1 1 Integr sa 5 1 1 Integra 5 1 1 Integr v5 1 1 Integra v5 1 1 Library v5 1 1 Text re v5 1 1 Display v5 1 1 Option v5 1 1 Table 0 v5 1 1 3 ionr v5 1 1 chroma Select a Template name and click OK for example click Qualitative Report This now appears in the Report Method Editor dialog P Report Method Editor New Report Method z Move Up Move Down Chromatogram Plot 553 TurboMass Software User s Guide 4 Select the Frequency of reporting The options available are Generate report for every run Generate report for every run of specified type Selecting this option enables a second drop down list Here you select the type of run from the available options Generate report only for final row in the sample list 5 Select a desired Output type 6 Click the Append button to add this template to the current method This template appears in the Report Template field This is a display of the reports defined for the current method When the list is empty New Method after Clear List or after all reports have been Deleted the controls on the right will be set to default values In this way the Append butto
293. eports Sample List this dialog open another project and restart data acquisition Selecting this option will acquire data for the specified samples in the list See the Acquisition Help file available in the Help menu for more information on data acquisition Selecting this option will process the acquired data as specified in the Process column of the Sample List Selecting this option will automatically start sample quantification at the end of the Sample List Selecting this option enables Qualitative Method Processing Selecting this option enables Communiqu report generation Check this box to specify that the Communiqu reports generated during processing will be displayed in a preview window prior to printing or saved to a file or database The options above allow you to acquire and immediately process and quantify data as desired Or you may choose to process or quantify data at a later time Run From Sample To Sample Sets the range of samples in the sample list that will be acquired and or analyzed If you highlight a range of rows before starting the analysis the first and last rows of the highlighted region will be displayed here Quantify Qualify and Generate Reports After Each Run At End of Sample List This indicates specified processing will occur after each row in the sample List Indicates specified processing will occur only after the Sample List is complete 241 TurboMass Software
294. er Below Curve Tolerance Flatten Edges Allows you to specify the degrees of freedom allowed to the fitted curve With polynomial order set to 0 a horizontal straight line is fitted With polynomial order set to 1 a sloping straight line is fitted The further the background is from a straight line the higher you must set the Polynomial Order value Too high a value will cause the fitted curve to begin to follow the peak shapes Normal operating range for this parameter is 3rd to 20th order Allows you to move the background curve up and down in the noise The curve fit is constrained to place the specified percentage of data points beneath the fitted background curve The normal operating range for this parameter is 5 30 depending on the abundance and width of peaks in the chromatogram For more or wider peaks increase the value Affects the precision to which the internal arithmetic is performed It should not normally be changed from its default value of 0 01 If selected TurboMass verifies that the polynomial applied is flat or horizontal at the beginning and end of the trace The parameters shown in the figure below produced the background subtracted chromatogram and total ion chromatogram shown in the printed documentation Chromatogram E Fie Edit Display Process Window Help l x S ale wee eaj ea O a nel gt 55 0 17 00 17 50 18 00 18 50 19 00 19 50 20 00 E Fie Edit Display Process W
295. er from the User menu OR Click td to open the User Properties dialog User Properties x User Name Eull Name Description Password Confirm Password Account Policies i User Cannot Change Password T Account Disabled Currently Assigned Rights cee Enter the new user information 670 User Name Full Name Description Password Confirm Password User Cannot Change Password Account Disabled Currently Assigned Rights Appendix A TurboMass Security The name that a user enters to log on to TurboMass The user s full name A brief user description for example position in the company A user s default password which a user can later change unless User Cannot Change Password is selected The user must correctly re enter the default password to confirm it If selected the user is not allowed to change their own password Disables the account When selected the account s user name cannot be used to log on to TurboMass but the account information remains intact The list of rights that is granted to the current user This list depends on the rights that are assigned to the groups to which the user belongs When creating a new user or copying an existing user this list is empty and unavailable NOTE 4 system administrator can change a user s password at any time 3 Click OK Security adds the new user to the list unless the name already ex
296. er to refer to either the Clarus 500 MS or the TurboMass Gold instruments Using this Guide The TurboMass Software Guide is a step by step guide for using TurboMass software It is to be used in conjunction with the Hardware Guide and Tutorial manuals shipped with your instrument when setting up and performing runs on your Gas Chromatograph Mass Spectrometer GC MS System NOTE This guide does not cover the installation and configuration of your computer If you have purchased a complete system from PerkinElmer the computer will already have been configured Chapters in this manual cover the following topics Chapter 1 Introduction Software and hardware requirements Chapter 2 Getting Started Navigating the main desktop and performing some common tasks Chapter 3 TurboMass Overview of the data acquisition process Overview Chapter 4 Instrument Data Preparing the mass spectrometer and setting Thresholds instrument thresholds Chapter 5 Instrument Tuning Tuning the mass spectrometer 19 TurboMass Software User s Guide 20 Chapter 6 Chapter 7 Chapter 8 Chapter 9 Chapter 10 Chapter 11 Chapter 12 Chapter 13 Chapter 14 Chapter 15 Chapter 16 Chapter 17 Chapter 18 Chapter 19 Mass Calibration Clarus 500 GC Control Function List Editor Sample List Quantify Qualitative Method Data Acquisition Chromatogram Spectrum Strip and Combine Functions Library Map Molecular Mass Cal
297. erN ame OperatingS ystem4nd ersion m D e e D D be a B ni Lit DateTimeLocalPC Templates amp Reports 5 Click in the footer then size Date Time Report into the Footer to full width 573 TurboMass Software User s Guide K Communiqu Report Creator lajxi File Edit View Format Actions Tools Help DEAA a9 S AMX an a aa ala ae o all H E E Layout L L L 1 L L L Layout Tools E n New Template 1 Data Objects Ea Header a 3 Global 5 Text 3 Project Sia Footer i S System 4 E Miscellaneous PageXolY Z PageNo 4 NumPages Communiqu SoftwareVersion g OperatingSystemUserName E amp OperatingSystemAndVersion amp ComputerName F 9 4 DateTimeLocalPC 5 Reports EEEo r Custom Objects Position 0 99 0 06 Width 6 73 Height 0 41 6 Click on Page Type 1 in the Layout toolbox on the left of the screen This will display the main body of the template Add Data Objects NOTE The Communiqu user interface supports click and drop rather than drag and drop Simply left click on the object in the Data Objects tree and release the mouse button Next position the mouse pointer in the template click and drag the pointer then release Use this same functionality for placing any object onto a template NOTE To ensure that a CSV file puts data items on the same line enclose all items that are required to appear on one line of the
298. erform these calculations exactly as defined in these equations but will instead derive the environmental concentrations from the concentration value currently calculated and reported The secondary calculations required to generate the required environmental concentration value from the current TurboMass concentration are defined in the equations shown in parenthesis following the EPA version 755 TurboMass Software User s Guide 756 Volatile Organic Compound Analysis Water Samples Concentration ug L 2 ID Xs D1 where Xs is TurboMass concentration Ais RRF Vo Vo where Ax Area of the characteristic ion Extracted lon Current profile EICP for the compound to be measured from integration results Ais Area of the characteristic ion EICP for the specific internal standard from integration results Is Amount of internal standard added in nanograms ng from appropriate Concentration column of the sample list as defined in the Quantify Method and the sample list RRF Average relative response factor from the ambient temperature purge of the calibration standard from calibration file Vo Volume of water purged in milliliters mL Sample Vol from sample list Df Dilution factor The dilution factor for analysis of water samples for volatiles by this method is defined as the ratio of the number of milliliters mL of water purged i e Vo above to the number
299. erify the quantitative extraction recovery of selected compounds surrogates from the sample matrix Sample ID Conc A T Job Task User Submitter Conditions File Text Sample List The Matrix Spike Duplicate Spike Dup is a duplicate of the Matrix Spike sample used to evaluate reproducibility A Dilution Dilution sample is used when a sample s concentration exceeds the calibration range of the method The sample is diluted The surrogates are diluted in a SV sample but not ina VOA A Re Extraction Re Extract is a SV sample where the extraction procedure is suspect and the sample is re extracted An optional user defined tracking number assigned to the sample NOTE This field is filled in prior to acquisition if needed in the final reports It cannot be changed after acquisition occurs The concentration of a designated calibration level of compounds within a sample Used during Quantify Optional Job designation assigned to the sample Recorded in the data file header Optional Task designation assigned to the sample Recorded in the data file header Optional TurboMass User identifier Recorded in the data file header Optional sample Submitter identifier Recorded in the data file header User comment on analysis and or sample preparation conditions Optional Sample text description Recorded in data file header 233 TurboMass Software User s Guide Conditions User Diviso
300. ero All other elements are non integer atomic weight Chlorine for example is 34 9689 Da a mass defect of 0 0311 Da and bromine is 78 9183 Da a mass defect of 0 0817 Da By the time you get to Cy Brio you get 933 1834 Da instead of 12 12 79 10 934 0000 Da The mass defect for this compound is thus 0 8166 Da The mass defect correction is 934 933 1834 934 8 743e 4 Da Da 0 8743 mDa Da By this example a measured mass of 933 1834 Da gives a nominal mass of 933 1834 8 743e 4 933 1834 934 Da TURBOMASS INI The TURBOMASS INI file contains current settings for all TurboMass windows and dialogs When a new user logs on a new Username ini file is created Each time this user uses TurboMass any changes to the current settings are saved to this file 37 TurboMass Software User s Guide 38 Selecting and Viewing Data The Data Browser The Data Browser lets you select a data file to work with The Data Browser can be accessed from the TurboMass window by selecting Open Data File from the File menu or from Spectrum Chromatogram and Library programs by clicking or selecting Open from the programs File menu The data file selected can be in any directory on any disk even a network disk The browser can access the file header information for every data file and uses it to display the sample text information and scanning function information for a selected file This allows you to find out what is in a dat
301. ertical scroll bars if available to move around the Summary window The format of the Summary window listed by sample and listed by compound can be changed independently The fields present in the Summary window are shown in the Displayed Fields list in the Compound Report Table Format dialog Other fields that can be added to the Summary window are displayed in the Available Fields list Any changes made in the Compound Report Table Format dialog will be reflected in the Summary window display and in the Summary Reports The Summary Reports will display up to the maximum number of columns that will fit on one page To include more columns print in landscape mode instead of portrait mode Selecting which fields will be displayed in the Summary window and Summary Reports Select the Summary window column headers Output Compound Format or Output Sample Format from the Quantify Edit menu to display the Compound Report Table Format dialog Quantify m Report Format Available Fields Displayed Fields pai Aovend gt E quired Time ample Name Blank Sub Cone Insert gt Sample ID Calibration Date Sample Type Calibration File Standard Conc Calibration Time lt Remove Found Peak RT Chrom Trace Peak Response Conc Deviation R All Calculated Cone i lemove Detection Flags gt Field Format Header fe Justification RIGHT NotFound Blank x Width Bo Decimal Places fo Cancel
302. es click Default Setting Calibration Parameters Select Calibrate Instrument from the Tune Calibration menu to open the Calibration dialog Select Calibration Parameters from the Calibration Edit menu to open the Calibration Parameters dialog 123 TurboMass Software User s Guide Calibration Parameters Peak Mach OK IV Perform auto peak matching e Peak window Da 1 00 ea Initial error Da 2 00 Intensity threshold 0 01 m Curve Fit Polynomial order T Intensity weighting Display I Calibrate display 3 Specify the Peak Match Curve Fit and Display calibration parameters Perform auto peak matching Peak window Initial error Intensity threshold 124 Select this to turn on auto peak matching When unselected automatic peak matching is turned off Specifies the maximum mass difference between the remaining reference peaks and the expected position of the corresponding peaks in the acquired spectrum Normal operating range for the Peak Window parameter is 0 3 to 1 5 Da It may need to be large for example 4 for very high mass work The first reference peak to be matched is chosen to be close to the center of the calibration mass range The Initial error parameter specifies the maximum mass difference between this reference peak and the corresponding peak in the acquired spectrum Normal operating range for the Initial error parameter is 0 5 to 2 0 Da Any peak in the acquired spe
303. es parameter is only relevant to user libraries No 1and These are numeric values that have been entered in the user 500 Library No 2 library Select the No 1 and No 2 values as required Min and Enter a maximum and minimum value for each User Value in Max the Min and Max fields To specify a particular User Value make the Min and Max values equal 3 Click OK Starting a Library Search You can initiate a library search from either Library or Spectrum gt Click from the Library toolbar OR Select Search from the Library Process menu OR Click from the Spectrum toolbar or select Library Search from the Spectrum Tools menu Library Search Results The result of a library search is a list of library compounds or hits whose spectra give the best match with the unknown spectrum The results are displayed in four windows Hit List Gives a text listing of the best hits The Hit List can be formatted to display a variety of information about each hit including compound name fit values formula and molecular weight Hits Shows the unknown spectrum followed by the spectra of the best hits Structure Shows the chemical structure of the currently selected hit 501 TurboMass Software User s Guide 502 Delta Shows the difference between the unknown spectrum and the spectrum of the current hit The mass spectral library is stored in the Idendb sub directory in the TurboMass installation direct
304. es to include the appropriate fields columns in the Sample List The following fields can be used for GC MS File Name The analog of MS data file name MS Method MS_File The MS method file name 229 TurboMass Software User s Guide GC Method Inlet_File MS Tune File Injector Inlet_Switch Injection Volume The GC method file name The name of the file that contains the MS tuning parameters If left blank the current tune file settings are used Specifies the GC injector site used to introduce the sample A is the front Clarus 500 GC injector and B is the rear Not used for TurboMass control only for quantitative calculations NOTE The injection volume is set in the GC method Inlet Prerun Postrun Parameter File Process_Parms Process Process Options Vial 230 The files that contain the optional GC pre post run program parameters Optional Process parameter file Available to external processes through the MLCURSMP TXT file Optional post run program to be executed after acquiring this sample Optional command line parameters for external Process when it is executed Specifies the Clarus 500 GC autosampler sample or bottle number for injection Sample Type Sample List Sample type used during Quantify Analyte Standard QC or Blank An Analyte is a sample injection with unknown concentrations of target compounds A Standard is a sample injection with known st
305. esceseceseceseceseceeeceeeeeeneeeaeeeseecseeceseesseeeteeesaes 358 Automatic Startup it csctscivcest Aedes wie iestetesecd saver btes aevicdecdebssr nas tanalals 359 RUMI Gs StartUp sess en leaps A elec adyeduats ook eaneegen Foal does ele a ecaaee 359 Automatic Shutdown 0 cececcseescesecsseescesecceeseesecaeeeeeeeceaecaeeeeeesecaeeeeeeaeeaee 360 Running Shutdown ccccccecsseescecscecseeceeceeeeecseeeseeeeeseeeseeeeeeseeeaaees 360 Contents Editing the Shutdown parameters c ccccccesccesscessceeseeeeeeneeeseeeneeensees 360 Running the Auto Control tasks cccccsccesccessceeseeeeeeeeeeeseeeeeeeeensees 363 Stopping the Auto Control tasks ccccccscssecetsceseceeeeeseeeeeeeseeesneennes 363 Saving and Restoring Auto Control Task Lists eceeeeseeseeeeeteees 363 CHrOM ACOSTA siccssscaiccessosecesernscccasesvscsssesiceasecusccssassseaassscesseaseseasossscessuns 365 Getting Started sorsoran eias raita E E EEEE geen ieee E 367 The Chromatogram Display ccccccceccsessseseeeeeeceeseeeseeceeceeentecsseenseenseenes 368 The Chromatogram Toolbar cccecccccscessseeseeeseeessecssecnsecnsecnseeeeeenseeeseenes 369 Customizing the Chromatogram Toolbar cccccccscesseesteeeteceteeeteeees 371 Displaying Chromatograms cccsccesscesseeeseeeeeeeseeeseeeseecseecuecnseenseenseenes 374 Adding or Replacing Chromatogram Traces ccsceeceeseseeeeeereeteenee 374 Mass Chromatograms cccccssccssecssecsse
306. ess 1 Select the key part of the entry you want to modify and click Edit 2 Modify the required text and click OK Deleting a process 1 Select the key part of the entry you want to delete and click Remove 2 Click OK Mass Defect Correction Mass Defect Correction can be used to improve quantification and library searches at higher masses Select Options from the Sample List Tools menu In the Options dialog select the Mass Defect tab Getting Started With the exception of carbon the masses of all elements are non integer Some elements such as chlorine and bromine have larger deviations from integer than others These high mass defects accumulate and can cause mass misidentification which leads to failed quantification and library searches at higher masses You can specify a Mass Defect Correction value to apply a sliding window to correct for this mass defect Mass Defect Correction can be applied post run so you do not need to reacquire your data files The mass defect is the difference between the exact mass of the ion and that calculated from the integer nominal masses The mass defect is used in the mass calculation as nominal mass calibrated mass mass defect calibrated mass where nominal mass 1s what is displayed in Chromatogram or Spectrum calibrated mass is from the FC 43 mass calibration file mass defect n 0 mass defect is in mDa Da Carbon is defined as 12 00000 Da or a mass defect of z
307. et been performed QA QC Calculations The following equations apply to both volatile and semi volatile organics and to all matrix types 284 NOTE Quantify Recoveries The recovery calculation shall be performed for each system monitoring compound surrogate standard in all samples blanks matrix spikes and matrix spike duplicates Recovery Congentalion amount found Concentration amount spiked where Concentration amount found is calculated using the appropriate matrix specific equation Concentration amount spiked is taken from the Quantify Method Matrix Spike Matrix Spike Duplicate Recovery These calculations require that three data files be identified e An analyte sample Analyte or Analyte Dup sample type in the sample list e A spiked sample that was prepared from the original analyte sample Spike sample type in the sample list An optional third sample can also be identified e A second spiked sample prepared independently from the original analyte sample Spike Dup sample type in the sample list Because these calculations require that the user has indicated unambiguously which three data files are involved they will only be performed during the process of environmental report generation The concentration of the matrix spike compounds is calculated using the same equations as used for the target compounds The percentage recovery shall then be calculated as follows SSR SR SA Matri
308. eteeeees 332 The Search Parameter Tab Fields ccccceccseesseesceesceesteeseeeseeneenaeens 333 Qualitative Method Editor Library Settings Tab 0 0 0 ceccesceseereeereeeees 336 The Library Settings Vabi ses scsccesseecdedsasesevs aeni esie naai ane Ea 337 A Step by Step Qualitative Method Summa ry ccccscescsteceteeeteeeteeees 338 1 Create a Sample List ccccccceesceesceesceeeeeseeeeeceeessecneeseeeseeeseneeses 338 2 Create a Qualitative Method ccc ccccccssececsecessceesseeeesseceeseeeeseeees 339 3 Put the Qualitative Method in the Sample List eeeeeeees 344 4 Start the Analysis noorimat enert anoet eT eaei ana E tin edset a aean 345 Data Acquisition ssssssssssssesosssoosessorosossssiososoosrooss ssor osos ost oose sises osso rosses 349 Starting an Acquisition ccccecsscessecstecseceseceseceseceseeeeeeseeeeeseeeseesseeeeeeaaes 351 Single Samplesseensi nsen etsen eia A A RA ar iE RAEES 351 Multiple Sample Snte eel ee e AE KERE EES 351 Automated Analysis of Sample List c ccceccceesseeseetseeneeesseeteeensees 353 Monitoring an ACQUiSItiON ccccsccescceescessceeeeeeeeeeseeeseeeseecseecaecsseenseesseenes 355 GG S taS aa eva sonata pee a a a e Goedel a E 355 INES StAtUs aonne a E A A aT ett 355 Chromatogram Real time Update ccececcecsseesseestecstecsecetecnteenseenes 356 Spectrum Real time Update cccccccsccessecsseceteceeceeceeeeereseeeseeeenes 356 Stopping an ACQUISITION cce
309. eters on the Quantify Method Editor dialog to open the Integrate chromatogram dialog 271 TurboMass Software User s Guide 272 Integrate chromatogram x po 1s l Peak to peak amplitude C ancel Smooth VV Enable smoothing Copy Peak detect Paste Threshold Enter the Noise Peak to peak amplitude value used by the integration software to pre filter the chromatogram by measuring a suitable value directly from a chromatogram Right click and drag the mouse across a section of noise in the chromatogram Then manually adjust this value to fine tune the sensitivity of the integration algorithm OR Enter a value into the Peak to peak amplitude field Click Copy and Paste as necessary to read and write integration parameters to and from the Windows Clipboard This approach can be used to transfer integration parameters between Chromatogram and the Quantify Method which can be useful when experimenting to find the correct integration parameters using Chromatogram Smoothing the chromatogram before integrating Select the Enable smoothing checkbox 2 To examine and edit the smoothing parameters click Smooth on the Integrate chromatogram dialog to open the Smooth chromatogram dialog 3 Quantify E Smooth chromatogram xj m Method Window size scans fE OK Number of smooths 2 Cancel C None C Mean Savitzky Golay Tl Noise Reduction Set the Wi
310. ether or not the TIC names have been reviewed for each sample row When an unreviewed file is selected directly or using the Next Sample button the peak list associated with that file will be displayed in the center list with the first peak selected A single row in the list can be selected which causes the peaks from the associated qualitative file to be displayed in the peak list along with the current TIC name associated with each 611 TurboMass Software User s Guide Peak list This list view displays the peaks from the selected file that require a TIC assignment Del Contains an X if the peak will be deleted from the report RT The peak retention time Assigned Name The currently assigned TIC name for the peak best spectral match originally Est Conc The estimated concentration of the compound based on the ratio of its total ion current area to that of the nearest internal standard Qualifiers EPA qualifier codes assigned to the peak J and N originally When a peak is selected directly or using the Next Peak button the library search hits associated with that peak will be displayed in the right hand list The Assigned Name field will display the current compound name associated with the selected peak The first time the peak is selected that will be the top hit from the right hand list Subsequently the Assigned Name will be that selected by the user which may also be the to
311. ethod Parameters You can print either the specific parameters from a GC method file or the summary information for a method by using the File menu Print or Print Summary commands Two print related dialogs will appear when you print parameters one for method editor options and one for standard printing options Printing the parameters from the method 1 Select Print from the File menu to open the Print Options dialog Print Options x p Print Selection T Audit Trail NONE 2 Select the data to print and click OK 3 Make any changes in the Print dialog and click OK Printing summary information for a method 1 Select Print Summary from the File menu to open the Print dialog 2 Make any changes in the Print dialog and click OK 178 NOTE GC Control Controlling the GC Some GC related menu choices are commands that let you control the GC e Equilibrate e Stop GC and Retry Injection e Take and Release Control Equilibrating the GC GC Equilibration sends the GC method temperature and pressure settings to the GC to enable the GC to reach those setpoints in preparation for sample injection and data acquisition Equilibrating the GC Select Equilibrate from the Method Editor menu The mass spectrometry sends the GC method temperature and pressure settings to the GC and begins equilibration The GC status in the top level window indicates that MS is equilibrating the GC When equi
312. exit and save changes Resetting the toolbar to default settings 1 Click Reset 2 Click Close to exit and save changes Removing the toolbar from the Spectrum display Select Toolbar from the Spectrum Display menu to display hide the toolbar This command is a toggle A check mark will appear next to this menu item when it has been selected Spectrum Displaying Spectra The following procedures describe how to display spectra in the same or separate windows Adding or Replacing Spectra TurboMass gives you a number of options for displaying any new spectrum traces New spectrum traces can be generated by e Opening anew file e Processing spectra subtract smooth center etc e Selecting spectra by double clicking on a chromatogram Once generated you can display spectra in the same or in separate windows When new traces are displayed in the same window you can choose whether to add the new trace to the traces currently displayed or to replace the current trace with the new trace Displaying spectra in a new or in the same window Toggle to display each new spectrum trace in a new or in the same window Adding or replacing spectra in a window Toggle to replace or add each subsequent spectrum or spectrum process in the current window Up to 16 spectrum traces can be displayed in one window NOTE is unavailable when is clicked 431 TurboMass Software User s Guide 432 Manipulating the Display
313. f for example updating the IPM The interface is turned on and connected to computer but is not set up or there is no method downloaded Post run activity is in progress or the autosampler is cleaning up after the previous injection The autosampler is preparing the next injection The interface is ready to collect data and is waiting for the run to start The run is complete The instrument must be initialized again for any future analyses The GC is uploading Run Log information to TurboMass The instrument is being initialized with acquisition information TurboMass is carrying out a system reconfiguration The GC is equilibrating The GC temperature program is in a hold state Not Ready Off Oven Off Pre Run Ready PPC Alarm GC Control The GC is not ready The GC is turned off The GC oven is turned off The GC is executing the pre run events The GC is ready The PPC pneumatics are in a fault condition During the oven temperature program the current program step appears These are Initial temp Ramp 1 Hold 1 Ramp 2 Hold 2 Ramp 3 Hold 3 and Cool Oven Temperature Oven temperature is displayed as an integer and may range from 99 to 450 Viewing Error Messages When an error occurs during configuration method setup or during a run TurboMass displays an error message and saves it in the Error Log 1 Select Error Messages from the GC menu to open the Error Log 2 To print
314. fied then the Sample List title of the tab is displayed in red and all Form tabs are disabled General errors and warnings are displayed in the message pane located on the bottom of the window Error Messages An error is defined as a condition that will prevent the generation of a coherent data set for reporting The Print command remains disabled while such errors exist The following checks are made 1 All sample rows must reference the same Analysis type VOA SV or QA QC If more than one Analysis type is present empty Analysis fields will be ignored for this test an error message will be displayed General Error Sample list contains mixed Analysis types Rows a b x z 2 All sample list rows selected for processing other than Tune Eval types must reference the same Calibration file If more than one Calibration file is referenced an error message will be displayed General Error Sample list contains more than one Calibration file Rows a b xz 3 Ifno Calibration file is included in the sample list rows selected for processing then an error message will be displayed General Error No Calibration file is defined Rows az 4 All sample list rows selected for processing other than Tune Eval types must reference the same Quantify Method If more than one Quantify Method is referenced an error message will be displayed General Error Sample list contains more than one Quantify Method file Rows a b xz 5 Ifno selected rows refe
315. followed by the spectra of the best hits Structure Window Shows the chemical structure of the currently selected hit Delta Window Shows the difference between the unknown spectrum and the spectrum of a particular hit Library also allows you to create your own user libraries that contain spectra from data files in the Spectrum window Library Editor Used to edit libraries Library Locator Used to examine a library and search for library entries that meet various criteria Library Searching a Library The Library Search process has two parts the Presearch and the Mainsearch The Presearch is a faster search designed to select a number of likely candidates from the library These candidates are then passed through to the Mainsearch where they undergo a more rigorous and lengthy comparison TurboMass displays the Mainsearch results in the Hit List Hits Structure and Delta windows The Presearch The unknown spectrum is first reduced to its eight most intense mass weighted peaks This reduced spectrum is then compared to the current library Presearch file The library Presearch file contains a spectrum for each library entry that has been reduced to its eight most intense mass weighted peaks The Presearch process results in a list of the most likely candidates to be passed to the Mainsearch process The most likely candidates are those compounds that have the greatest number of matching peaks with the unknown compoun
316. from sample list If GPC is not performed then Vt 10 000 UL If GPC is performed then Vt 5 000 uL Average relative response factor from calibration file GPC factor derived from setting in sample list GPC Y N GPC 1 0 if water sample was not subjected to GPC GPC 2 0 if water sample was subjected to GPC Dilution factor The dilution factor for analysis of water samples for semi volatiles by this method is defined as follows uL most conc extract used to make dilution uL clean solvent uL most conc extract used to make dilution Dilution Factor from sample list The calculation applies to water low concentration and multi concentration The low concentration calculation will not contain the GPC parameter X is the target amount in nanograms which assumes that the internal standard amount is entered as nanograms in the Sample List If the internal standard amount is entered as a concentration then the user must enter a user multiplier to make the necessary correction 761 TurboMass Software User s Guide Soil Sediment Samples Concentration ug kg Ax Is Vi Dr GPC Xs Vt D1 GPC where Xs is TurboMass concentration Ais RRF Vi Ws D Vi Ws D where Ax Area of the characteristic ion for the compound to be measured from integration results Ais Area of the characteristic ion for the internal standard from integration results ls
317. g the mouse horizontally to the other end As you drag the mouse TurboMass will indicate the range you have selected Do not go beyond the bounds of the axis When the mouse is released the selected range will be redisplayed This operation can be repeated as often as required Altering the range of the mass axis gt Left click at one end of the region of interest and drag the mouse vertically to the other end As you drag the mouse TurboMass will indicate the range you have selected Do not go beyond the bounds of the axis When the mouse is released the selected range will be redisplayed This operation can be repeated as often as required Altering the range of both axes gt Left click at one end of the region of interest and drag the mouse diagonally to the opposite As you drag the mouse TurboMass will indicate the range you have selected Do not go beyond the bounds of the axis When the mouse is released the selected range will be redisplayed Map This operation can be repeated as often as required Restoring the display gt Clicking L amp I toggles from restoring the display to its previous state to displaying the default range Altering the range of the mass axis from the Map menu 1 Select Range from the Map Display menu Map Display Ranges Ea r Vertical Mass Ran Cancel Default Start amu m End amu 300 r Horizontal Time Range gt Start min 11 010 End min 18 000 2 Ente
318. ginning of the peak is subtracted The library reference spectrum for the currently selected plot hit from the compound list This plot is empty when one of the generic compound names is selected Click this button to close the dialog and save the set of selected compound names with each file marked Complete If the last file in the list is selected peaks displayed in the peak list but not yet marked Complete it will be changed to Complete Click this button and a message box with the message Save changes plus Yes No Cancel buttons appears If you click the Yes button the set of selected compound names for each peak will be saved and the dialog closed Clicking the No button causes no data to be saved and the dialog closes If you click the Cancel button the dialog will remain open but no data saved Environmental Reporting To assign the tentatively identified compounds for the selected files l Review the displayed peak plot and spectra associated with the first peak in the selected file and the spectrum for the top hit Click Next Name or click on another name in the right hand list to display the spectrum associated with another plot hit compound When you have decided which compound name should be assigned to the selected peak select that name and click Accept or Having decided that none of the compound names from the plot hits list can be definitely assigned to the peak select one of
319. gn page and click The cursor changes to the following cursor XN kd Move your cursor to a desired spot on the page Click the left mouse button drag the mouse to scale the graphic to a desired size then release the mouse button The graphic appears on the page 565 TurboMass Software User s Guide 35 Lab Name Swed Betreaton oak mime ee er Mace a Sample 1D Sample Devenip tor ay ae tas r 25 Comi tons como GO 35iFllename MO 35 Flename 2 CHROMATOGRAM PLOT GRAPH HEADER 3 i ejeje 5 6 7 8 5 gt PerkinElmer meni Name ACOUISITION PARAMETERS Oven f220 en Program ar aL ler Gar Seleni Delays 17 6 min Trane er Tempel IEBC net meze PERPARA Adding a Data Object to the Template To add a data object to the template follow this procedure 1 Click on Data Objects to display the available data objects 566 Communiqu Reporting K Communiqu Report Creator laj x File Edit View Format Actions Tools Help UAGE o e SoxXagla seuaalaum ae e Ol Mls E Qualitative Report Revision No 1 Page Type 1 TABLE1 ti E Qualitative Report 1 k Data Objects 5 3 Header El oha z TEXT4 f 85 Lab Name S Ua Nare t 23 Full Filename Printed 33 DateTimeReport 3 Softwere Version S texte 24 Creation Date Time Page 34 PageXofY 3 Instrument Type i 25 Sample Description 3 I
320. gram window Click OR Select Combine Spectra from the Chromatogram Process menu to open the Combine Spectrum dialog Enter the peak top scan range either by entering scan numbers separated by a colon for example 619 626 into the Average field or by right clicking and dragging the mouse across the peak Optionally enter one or two background scan ranges Enter the scan numbers into the Subtract field Each range should be in the form of two numbers separated by a colon as above and if there are two ranges they should be separated by a comma for example 606 612 631 637 OR Right click and drag the mouse across the first background scan range Optionally repeat for a second range Optionally enter a background factor in the X field Optionally enter a Peak separation value Click OK Chromatogram Peak Lists The results of the peak integration can be saved to disk as a named Peak List Peak Lists can then be processed using the TurboMass Quantify program Creating and Editing a Peak List Use the following procedures to create a new peak list or edit an existing one l 4 Select Peak List Write from the Chromatogram Edit menu to display the Edit Peak List dialog File Standrd5 Enty 1 Ext Peak Tops Peak List 2 STANDRDS 11 636 Clear All sea l Fie Append Append All Click File to display the File Open dialog and select a file If you want to create a new Peak List file
321. grams for a number of scans equal to the window size around the peak top scan If there is a 447 TurboMass Software User s Guide 448 peak present in this range whose topmost point is within one scan of the peak top scan and more intense than the noise threshold value then this mass will appear in the refined spectrum Note that it is very important to be on the peak apex when using this function Refine is a good alternative to background subtraction Combine when performing library searches or selecting spectra for a Quantify method To refine a scan in a centroid mode data file 1 Identify the scan at the top of the peak you are interested in Display this scan in a spectrum window by double clicking the chromatogram peak Choose Refine from the Spectrum Process menu Enter values for Window size and Noise threshold Window size is the half width in scans at baseline of the TIC peak of interest For the first run set Noise threshold to zero to show all peaks Choose OK If the noise level in the refined spectrum is unacceptable repeat the refine operation with a higher Noise threshold setting Values in the range 0 10 are recommended OR e Refine the current spectrum using the current refine parameters by choosing on the Spectrum toolbar Combine The combine process operates on centroid mode or continuum data Its purpose is to produce a single scan from all the scans across a TIC peak The combined scan exhibits e
322. haracteristic of the compound as high in mass and intensity as possible High mass is desirable to minimize the probability of chemical interference selectivity High intensity is desirable for sensitivity We also try to choose ions with low baselines for these same reasons 1 Click SIR in the Scan Functions dialog The SIR dialog is displayed l Function List Editor r Channels lonization Mode fg Mass Dwell m z Secs nercha nter Chan 0 02 fez 00 0 10 Delay Secs m T Repeats fi 303 00 6 26 Span fo 20 Retention Window Mins Start Time 8 00 End Time Add Change Sort oo Clear All Delete E Cancel Specify your parameters Most of the parameters are the same as those in the MS Scan Editor However the following are different Mass Dwell Inter Channel Delay Specifies the mass to be monitored up to a maximum of 32 A mass can be entered either by entering its value into the Mass field and pressing ENTER or by clicking Add The mass can be calculated if the chemical formula of the ion is known with the MW Calculator function in the top level Tools menu The mass may also be pulled directly from a spectrum displayed in the Spectrum window To do this display the required spectrum in the Spectrum window and right click the ions that you wish to monitor As you select a mass it will appear in the SIR masses table Specifies the length of time in seconds for which the highl
323. hat name in the Project directory then the Report Method Editor will open in the New Method state If the cell contains the name of an existing report method then Report Method Editor will open in the Edit Method state 2 By choosing the Report Method Editor command from the TurboMass Tools menu The default method will be the method most recently used If there is currently no report method of that name in the project directory that is the METHDB subdirectory in the project hierarchy then the Report Method Editor will open in the New Method state Report Method Editor Report Method Editor Toolbar The toolbar displayed at the top of the window lets you perform some common operations with a single click of the appropriate toolbar button The default toolbar contains the buttons listed below You can also customize the toolbar and add additional buttons for other operations File New File Open File Save File Save As File Print File Exit oeM RSLheE Help Contents 551 TurboMass Software User s Guide Selecting an Existing Template 1 Select Report Method Editor from the Too s menu TurboMass TUTORIALQUANT TutorialQuant SPL Report Method Editor The Report Method Editor screen appears a Report Method Editor New Report Method 552 Report Method Editor Click the Browse button to the right of the Template field The Report Template Browser appears R
324. hat you follow a Median smooth with a single iteration of a Mean or Savitzky Golay smooth Center Peak centering uses all the points across a peak in a continuum trace to calculate the mass of the peak center You can use the centering process to either label each peak with the calculated mass or to produce a single stick from each peak in a continuum spectrum The calculation can be performed in three ways e Select the most intense top point on the peak e Calculate the centroid of the peak This is equivalent to finding the vertical line passing through the center of gravity of the peak This will provide a more accurate mass measurement unless the peak contains a coeluting compound e Calculate the median of peak area This is equivalent to drawing the vertical line such that half the area of the peak lies on either side There is little practical difference between the median and centroid methods though it may be the case that the median is a more robust statistic on very asymmetric peak shapes You should not compare masses from different experiments obtained by centering with different methods The centering algorithm looks for the trace rising then falling to indicate the top of a peak You specify how many data points must be visible as a clear peak top before the algorithm turns the peak into a stick 453 TurboMass Software User s Guide 454 For the centroid method you also have the option of using only a spec
325. he columns to appear in the sample list view Both on Sample List tab and Form specific tabs When the dialog is closed the display is updated It is disabled when the Form 6 tab is displayed since there are no selectable columns on the tab Opens this TurboMass Report Generation Help window The following pop up menu appears when you right click on the Sample List tab itself i e the area you click on to select the tab 600 Environmental Reporting v Form 1 TIC v Form2 Form 3 Form 4 Form 5 Form 6 Form 7 Form amp NOTE The symbol in front of an item indicates that this is an on off toggle command The check mark appears in front of the Form when the function is active or selected This applies to all menus described in this document Menu Item Description Y Form X Toggles display of the Form X tab If the change is from Off to On the error warning checks for Form X will be performed If the change is Where X is a Form from On to Off any errors warnings for Form X will be eliminated number 1 through 8 The following pop up menu appears when you right click on the Sample List view pane Select Forms De select All Samples Select All Samples 601 TurboMass Software User s Guide Menu Item Description Select Forms Displays the Select Forms dialog enabling you to change the set of Forms to be generated De select All Samples Removes the checks from all boxes leaving no samples selected
326. he Forms Once the Custom Compound List has been generated it will retain a reference to the Quantify Method from which it was derived It is not part of the method and no automatic synchronizing of the custom list with the compound list in the method will take place When a Custom Compound List is selected the status bar displays the origin of the custom compound list the Project name is displayed in the left hand segment and the Quantify Method name is displayed in the center segment 653 TurboMass Software User s Guide 654 Item Compound list Reporting limits Water Set All Description This list shows all the compounds from the selected Quantify Method Each row has a check box Checked items will be included in the current Submitter Task list and unchecked items will be excluded If the currently selected Task does not have an associated custom compound list then this section of the window is empty It is possible to sort the compound list in one of two ways 1 1 In the order the compounds appeared originally in the main Quantify Method compound list by clicking on the header of the check box column 2 In alphabetical or reverse alphabetical order by clicking on the header of the compound name column An edit box that displays the reporting limit value 0 000 to 999 999 999 for water samples associated with the currently selected compound which may be checked or unchecked A change made
327. he Library Search List dialog Library Library Search List Library Search List Cancel 2 To add a library to the search list click Add The Add Library dialog is displayed Add Library 21x Lookin C aero a a alle al a Nist idb File name I Files of type Library 7 Cancel 3 Select the library you want to add from the Add Library dialog and click Open TurboMass adds the new library to the Library Search List Library Search List x Library Search List C TurboMass IDENDB Nist idb 4 To remove a library from the search list select file you want to remove from the Library Search List and click Remove 5 Click the Close button to return to the Library Hits window 493 TurboMass Software User s Guide 494 Selecting a New Search Spectrum The spectrum currently displayed in the Library window is the current search spectrum From the Library Hits window you can select a new search spectrum scan from one of the following e The data file for the currently displayed spectrum the current data file e 6A different data file e The Spectrum window Selecting a new search spectrum from the current data file 1 Click from the Library toolbar OR Select Spectrum from the Library Display menu Entry f 80 Cancel Update 2 Enter the desired scan number or retention time To obtain the scan number or retention time of a particular peak click to display the total ion
328. he TurboMass View menu Click Ey Enter CTRL S Displaying a particular scan in the current file To display a particular scan in the current file do one of the following Use the mouse to select the required part of a scan in a chromatogram Click from the Spectrum toolbar and enter the required scan number Select Spectrum At from the Spectrum Display menu and enter the required scan number About the Display The spectrum application runs in a top level window that has a menu bar at the top Under each of the headings on the menu bar is a drop down menu and you can 425 TurboMass Software User s Guide 426 access every feature of the Spectrum application from this menu structure The commands and icons are quite similar to those in Chromatogram At the top of the spectrum window is the toolbar The toolbar provides a quick way of performing common operations The top level window can contain one or more spectrum windows and each can contain one or more spectrum traces The current spectrum window is identified by a colored title bar To select another window to be the current one either click in any part of the new window or select one from the bottom section of the Window menu When there is more than one trace in a window the current one is identified by a colored square on the left of the trace To select another trace to be the current one left click any part of the trace select one from the Graphs opti
329. he currently selected chromatogram 1 Select Peak List Read from the Chromatogram Edit menu 2 Click Get All 3 Click OK 417 TurboMass Software User s Guide 418 Automatic Library Searching This option automatically searches the specified library for entries that match the currently integrated chromatogram displayed in the Chromatogram window This process uses your current integration and library search parameters Note that while automatic library searching can work well for chromatographically well resolved peaks complex chromatograms will probably require manual background subtraction and library searching Performing an automatic library search 1 Inthe Chromatogram window set the display range and integration threshold values to limit the integrated peaks to only those you wish to library search See Integrating Chromatograms on page 399 to set up your integration parameters 2 Set up your Library search and display parameters For more information see the fully and semi automatic library search procedures in Library on page 485 3 Click a to initiate the automatic library search process for the first peak in the integrated chromatogram Chromatogram V50 299 12 637 Rf 7 3 000 100 61 Library Search for Compound Name MAN Formula As the search process progresses TurboMass displays a Print dialog where you can specify whether you want to print out the current window
330. he first time you must first configure it or verify that it is configured to interact with the Clarus 500 GC After establishing communication between the instruments in the system and creating your GC method you can develop your TurboMass method The procedure used to configure the GC depends upon whether you are initially configuring TurboMass for GC control or are making front panel changes to the GC e Initial GC Configuration To set up the LINK and GC for TurboMass control for the first time e Reconfiguring the GC To make front panel or hardware changes to the GC without changing the LINK configuration Reconfiguration is also required if you add an autosampler Configuring the GC for the First Time The following steps summarize the procedure for configuring TurboMass for GC control the first time 1 Display the top level main window 2 Select an interface 3 Select Configure from the GC menu 4 Verify the Data Acquisition port 5 Set the LINK Configuration Options 6 Set the GC Configuration Options Appendix B TurboMass Software Installation To configure the Clarus 500 GC In the top level window Select Inlet Interface from the Configure menu 1 Ifthe Clarus 500 is not selected highlighted click to select it 2 Click OK All GC commands are accessible from the GC menu in the top level window From this menu you can set up your GC configuration develop your GC method work interactively with th
331. he spacing between adjacent points on the mass axis for example 0 0625 Da for raw continuum MCA data Mean takes the arithmetical mean of the intensities of the data points in the window Savitzky Golay takes an average of the intensities weighted by a quadratic curve which tends to enhance quadratic shaped features in the data peaks Median takes the arithmetical median of the intensities of the data points in the window This process is unlike the previous two in that the median smooth iterates until the spectrum no longer changes The effect is that the intensity of narrow spikes is reduced on successive iterations to background level on convergence Smoothing a continuum spectrum 1 Expand a section of the spectrum sufficiently to allow you to estimate the width of a peak at half height 2 Select Smooth from the Spectrum Process menu 3 Set Peak width Da according to the value you estimated in step 1 4 Select a smoothing method Spectrum If you have selected Mean or Savitzky Golay you may want to alter the number of times the smooth is repeated by changing the Number of smooths parameter from its default value of 2 Increasing this parameter gives a heavier smooth NOTE This parameter has no effect on Median smoothing which always iterates until the spectrum is unchanged 5 Click OK The Median smoothing algorithm has the side effect of producing peaks with flattened tops For this reason it is recommended t
332. he time at which you want this event to occur during the run From the Event drop down list select the event that you want to add If the event requires a value or setting the Value field becomes enabled 5 Depending on the event use the Value field or list to specify a value for the event 6 Click Add to add this event to the Defined Events list 7 Repeat Steps 2 through 5 to add other events TurboMass list the events in the order of the time at which they occur Changing the time or value of a timed event 1 Under Defined Events select the event that you want to change 2 To change the time enter a new number in the Time field OR 172 GC Control To change the value either select one from the list or enter a value in the field 3 Click Change Deleting a timed event 1 Under Defined Events select the event that you want to delete 2 Click Delete Deleting all timed events Click Clear Entering Descriptive Information for GC Files From the Method Editor you can enter descriptive information about your GC method and or enter audit trail information You may enter descriptive information about a method on the Description tab of the Documentation dialog and you may enter information about changes made in the Audit Trail dialog if auditing is enabled One or the other will appear automatically when you save a file according to the following rules e The Description tab in the Documentation dialog alwa
333. hecked i e selected for processing Analyte or Analyte Dup row in the sample list but you may reassigned this Form 3 reports the recoveries of specific analytes defined as spike compounds in the sample the matrix spike MS and the matrix spike duplicate MSD It flags any compound whose recovery or relative percent deviation RSD is outside of the Quantify Method defined limits 593 TurboMass Software User s Guide 594 Form 4 Method Blank Summary Form 5 Instrument Performance Check Form 6 Initial Calibration Data Form 7 Continuing Calibration Check Form 8 Internal Standard Area and RT Summary Form 4 designates which samples were acquired reporting to a particular method blank Form 5 reports the compliance of the BFB or DFTPP tune evaluation sample instrument performance check and lists all data files acquired while this tune file was valid Form 6 reports the initial calibration of the instrument based on a multi level calibration The average relative response factor RRF and its relative standard deviation RSD are reported for all RRF calibrated target compounds It flags any compound whose response factors or relative standard deviations are outside of the Quantify Method defined limits The r squared correlation coefficient is calculated for linearly calibrated compounds and the Form flags values outside of Quantify Method defined limits You will identify a specific row in the sam
334. ht law and international treaties 15 Click Next to continue the installation The following message appears 698 Appendix B TurboMass Software Installation Setup Installing TurboMass Ver5 2 0 Installing C TurboMass EpcasSystem linemanager pdb E The Communique License Agreement appears ie Communique 2 3 Customer Edition InstallShield Wizard License Agreement Please read the Following license agreement carefully Copyright c 2005 by PerkinElmer LAS Inc All rights reserved PerkinElmer LAS Inc Software License Agreement IMPORTANT Read the terms and conditions of this Software License Agreement Agreement carefully before installing the Programs This Agreement represents the entire agreement between Licensee as defined below and PerkinElmer LAS Inc and its Affiliates collectively PerkinElmer concerning the Programs and the accompanying Documentation This software will not install unless or until Licensee accepts the terms of this Ov accept the terms in the license agreement InstallShield After accepting the terms of the license agreement click Next The Customer Information dialog appears 699 TurboMass Software User s Guide ie Communique 2 3 Customer Edition InstallShield Wizard Customer Information Please enter your information User Name RJB Organization PerkinElmer Inc Install this application For Anyone who uses this computer
335. ialQuant Browse Cancel Integrate Samples Integrates all the sample data files named in the peak list Calibrate Standards Uses Integration results to form Quantify calibration curves from all the data files in the Sample List Quantify Samples Uses Integration results and Quantify calibration curves to calculate compound concentrations from all the data files in the Sample List Print Quantify Produces hard copies of the results of integration and Reports quantification Quantify From Sets the range of samples in the sample list that will be Sample To Sample quantified Using the Quantify Window to Examine Results The Quantify window contains three windows the Summary window the Graphs window and the Peak List window You can turn each of these on and off as required If a peak is missed in Quantify because of retention time or ion ratios it is necessary to manually integrate it before the Quantify View Results Process Update Retention Times Ion ratios can be used for it Displaying the Quantify window gt Select View Results from the top level Quantify menu 295 TurboMass Software User s Guide File Edt Display Process Window Help alaj ajaj BIB ajele Peak Mass 0 000 compound 1 Compound A 430 5 a Name D Type Std Conc Response Cono 2 Default 3 Default 4 Default Graphs METH1 olx Compound 1 name Compound A 430 5 Response Factor 15552555600 Response typ
336. icated by parentheses following the collection name for example Samples 561 TurboMass Software User s Guide Opening a Report Template To open an existing report template follow this procedure 1 Select Report Method Editor from the Tools menu TurboMass TUTORIALQUANT TutorialQuant SPL Report Method Editor NS 2 The Report Method Editor screen appears i Report Method Editor New Report Method 562 Click the Browse button to the right of the Template field The Report Template Browser appears Communiqu Reporting Report Template Browser a 5 1 1 Integra a v5 1 1 Integr 5 1 1 Integra 5 1 1 Integr v5 1 1 Integra v5 1 1 Library v5 1 1 Text re v5 1 1 Display v5 1 1 Option v5 1 1 Table o v5 1 1 Sionr NAENVANNANANGON NWN SpectrumQuant Report v5 1 1 chroma 03 25 2005 11 Select a template name and click OK For example click Qualitative Report This now appears in the Report Method Editor dialog 3 Report Method Editor New Report Method Generate report for every run Move Down Chromatogram Plot 563 TurboMass Software User s Guide 564 5 Click the Edit button This launches the Communique Report Creator K
337. ich the carrier pressure flow velocity changes You can create up to three ramps which are periods during which the pressure flow velocity changes Ramps are shown on the vertical axis of the curve Setpoint Temp Gives the pressure flow velocity to which the carrier is being changed When Oven is selected it displays the temperature for the oven Hold Represents the period for which the pressure flow velocity is held before starting the next ramp The initial setting is the pressure flow velocity of the carrier at the start of the run or throughout the run The Initial Rate field is always 0 0 and you cannot edit this field To edit the other fields click in the field and then enter a value The Setpoint and Hold fields in a ramp are disabled until you set the Rate 1 Select the Carrier tab of the Instrument Control dialog GC Control Instrument Control Lx Autosampler Oven inlets Carer Detectors Instrument Timed Events m Program time min A PFlow He 20 00 B NONE 0 00 Oven time 2000 Data end time 20 00 r Column Length m 25 00 Diameter pm 250 Vacuum comp Off Split Control Ratio n 1 24 0 Elow mL min 50 0 Mode Flow 2 From the available program tabs beneath the table select the tab for the program that you want to display The curve and the table change to reflect the program that you select The curve for the program that you select a
338. ief description of the process you want to save 2 Click OK to save the process and exit Reloading processed data into Spectrum 1 Click Open from the Spectrum File menu 2 Select the raw data file from which the processed data were obtained and click History to open the History Selector dialog Spectrum History Selector GAS2 x Process History 4 Refine 1289 7 3 000 05 Oct 97 21 43 3 Refine 1372 7 3 000 05 Oct 97 21 42 Saved 1 Combine 1372 1386 1373 1339 1353 1376 1382 05 Oct 97 21 42 Saved 2 Refine 1207 5 2 000 22 Sep 97 21 22 Saved Information Sample Unleaded gasoline Function Scan 40 300 El History Raw Data Cancel Devic Delete 3 From the Process History list select the processed data you want to load 4 Click OK to exit the History Selector dialog 5 Click OK to exit the Data Browser and open the processed data Refine The refine process operates on centroid mode data only Its purpose is to identify just those masses that contribute to a specific peak in the TIC Window size i Noise threshold E Cancel You identify a particular TIC peak by specifying the peak top scan You supply two parameters for the process window size based on GC peak width n scans and noise threshold The refine algorithm proceeds by generating the summed mass chromatogram over a range of 1 Da centered on each integer mass in turn It examines these chromato
339. ies Search for User Libraries Copy another copy of selected user MS libraries will be made Old copies will not be used by the newly installed software JT Subtract space to be overwritten lt Back Cancel 13 A prompt appears for the program folder location Accept the default entry and click Next gt 714 Appendix B TurboMass Software Installation Select Program Folder J x Setup will add program icons to the Program Folder listed below You may type a new folder name or select one from the existing Folders list Click Next to continue Program Folders NIST Mass Spectral Database Existing Folders Accessories Administrative Tools Intel Network Adapters Microsoft Hardware NIST Mass Spectral Database Roxio Easy CD Creator 5 Startup TurboMass er5 0 0 User s Guides A final review of the install options is displayed Start Copying Files x Setup has enough information to start copying the program files IF you want to review or change any settings click Back If you are satisfied with the settings click Next to begin copying files Current Settings Typical Setup will install all the components NIST MS Search Program 4832 KB gt c nist02 mssear NIST 02 Main MS Library 149536 KB gt c nist02 mssec MS Interpretation Program 928 KB gt c nist02 mssearc GC MS Analysis Program 25120 KB gt c nist02 amdis Drive Required KB Avai
340. if you want to remove peaks whose height is less than the specified value Relative area Select if you want to remove peaks whose area is less than the specified percentage of the largest peak area Absolute area Select if you want to remove peaks whose area is less than the specified value Setting peak detection parameters 1 You can examine and modify the parameters that control the positioning of baselines and separation of partially resolved peaks by verticals droplines by clicking Peak detect on the Integrate chromatogram dialog 274 Join valleys Reduce peak tailing and Raise baseline Draw vertical Quantify Peak Detect Ea T Baselines Join valleys if peaks resolved to 10 00 above baseline g R Reduce peak tailing until trailing edge is no more than fo 00 wider than leading edge 8 R HE BBB AB BBE Raise baseline by no more than fi 0 00 of peak height T Peak separation Draw vertical if peaks resolved to 20 00 above baseline I Detect Shoulder peaks if slope is less than x 10 0 00 of maximum i Affects how baselines for partially resolved peaks are drawn The larger the value of this parameter the more peak baselines will be drawn up to the valleys between unresolved peaks The default value for this parameter is 30 and normal operating range is 5 75 Allow control over the positioning of baselin
341. ified fraction of the resolved part of the peak This will help to avoid the mass given to the stick being affected by unresolved neighboring peaks Centering a continuum spectrum 1 First background subtract then smooth the spectrum Background subtraction will tell the centering algorithm how much of the spectrum is noise and therefore reduce the amount of noise seen in the resultant stick spectrum Smoothing will help the centering algorithm make sensible decisions about whether groups of data points represent peaks or noise spikes 2 Select Center from the Spectrum Process menu to open the Spectrum Center dialog Spectrum Center x p Centermethd OK Min peak width at halt JE Cancel height channels B z C Top Centroid top 80 00 C Median poe I K Create centered l spectrum C Add amp Heights New window C Areas Replace 3 The Min peak width at half height channels parameter determines how many data points must be visible in the expected shape across the peak top that is minimum width For continuum MCA data setting this parameter to 4 is safe As there are 16 data points collected per Dalton the value 4 is equivalent to 0 25 Da Too low a setting of the peak width parameter will result in the centering algorithm producing sticks from the high frequency noise Too high a setting of the peak width parameter will result in the centering algorithm misinterpreting
342. ighted mass will be monitored This is normally set so that the sum of all the Dwell times for all the target ions gives about 10 scans across the GC peaks Specifies the length of time in seconds between finishing monitoring the highlighted mass and starting monitoring the next mass in the function 203 TurboMass Software User s Guide Repeats Span Add Change Sort Clear All Delete 204 This is only relevant for experiments having more than one function and specifies the number of times we wish to execute this Function per pass For example if we had two Functions defined by their Start Time and End Time to execute simultaneously and the first Function has Repeats 1 while the second has Repeats 3 then the second Function would execute three times for each time the first Function executed once With non overlapped Functions better detection limits will be obtained by increasing the Dwell time rather than the number of Repeats Specifies a small mass window applied centrally about the highlighted mass During acquisition this range will be scanned over the specified Dwell time This minimizes the chance of missing the top of the mass peak A span of zero can be set to simply sit on the specified mass for maximum sensitivity Enter values into the Mass and Dwell fields and then click Add to add the new Mass to the list Left click on a mass in the list and then click Change to change the Mass or Dwell
343. ill be updated to show the current spectrum as the cross hairs cursor is moved across the map display Deselect to remove the link between Map and Spectrum If selected the Chromatogram window will be updated to show the mass chromatogram of the currently selected mass as the cross hairs cursor is moved across the map display Deselect to remove the link between Map and Chromatogram Displaying the Chromatogram and Spectrum windows e Double click the mass chromatogram to display that mass chromatogram in the Chromatogram window e Double click the spectrum to display that spectrum in the Spectrum window Displaying the Status Bar and Toolbar The status bar at the bottom of the Map window displays e The current cursor position in terms of mass and retention time e The status of an ongoing process such as the Create Map process 539 TurboMass Software User s Guide 540 e The function of the currently selected menu item or toolbar button Displaying the status bar and toolbar Toggle the status bar or toolbar display on off by selecting Status Bar or Toolbar from the Map Display menu respectively Selecting the Current Cursor Position You can select the cursor position using the mouse or from the menu Changing the current cursor position gt Double click the required position on the Map display This position will become the current cursor position The Spectrum and Chromatogram displays will be updated a
344. inElmer 03 28 2005 06 Quantitation Report v5 1 1 3ionr 4 PerkinElmer 08 27 2003 03 PerkinElmer 04 04 2005 07 SpectrumQuant Report v5 1 1 chroma 2 PerkinElmer 11 11 2003 06 PerkinElmer 03 25 2005 11 OK Cancel gt To locate a template in a large list Browse through the tree view on the left of the window to find your project folder or 1 Click the Define Template Filter button on the toolbar 2 Set up the desired filter conditions in the Filter Templates dialog 3 Apply the defined filter settings 556 Report Method Editor Filtering the Template List The list of templates may become very large thereby a filtering mechanism helps you locate the template of interest The filter may be defined by accessing the report template filter dialog using the toolbar button The setting of the apply template filter button determines whether or not the filter is active This button can be in the up or down position When the button is down the filter will be active and the list view will display only the templates matching the filter conditions Report Template Filter Toolbar The toolbar displayed at the top of the Report Template Filter window contains the tool buttons listed below The tool button functions are duplicated in the Report Template Filter menus a Displays the Template Filter dialog box io Toggles the defined filter for the template list on and off The filter will be acti
345. indow Description Sample List view This is essentially a read only display No data item in any cell can be directly edited Column widths can be changed in the standard way by dragging the header divider The view cannot be sorted Comment You may enter up to 120 characters which will be printed on the report Message pane This is a read only display window Shows general warnings and all form specific errors warnings 618 Environmental Reporting Row Colors Form 3 shows primary data file in blue which represents the unspiked sample analysis It also uses two unique colors dark green and dark red to indicate the Matrix Spike sample and the Matrix Spike Duplicate samples All the remaining rows are unused for the report and shown in the grey Disregard color Status Column The Status column indicates which rows are currently flagged as the Analyte Spike and Spike Dup samples to be used in generating Form 3 This apparent duplication with the Sample Type column is because it will be possible for you to over ride the Sample List s file Type and assign a different row as one of the three key data files Context Menu A pop up menu appears when you right click on a row in the Form 3 sample list view pane These selections allow you to reassign the Matrix Matrix Spike and Matrix Spike Duplicate samples without returning to the Sample List Note that any reassignments made here are lost after the reports are printed A
346. indow Help la x aHmaiddMErrNNEA AARSE E 50ppm Volatile Organic Analysis Calibration Standard M50 Sb 5 10 00 Scan El 19 61 TIC 100 1 88e5 o 17 00 1750 18 00 18 50 19 00 1950 20 00 ESS sa You can check the operation of the background subtraction process with a given set of parameters by selecting the Make graph of fitted polynomial checkbox This causes the same calculation to take place but rather than displaying a chromatogram with the background curve subtracted the curve itself is displayed Selecting Overlay Graphs and Link Vertical Axes from the Chromatogram Display View dialog creates a display similar to that shown 395 TurboMass Software User s Guide J Chromatogram 50 Of x 8 x E Fie Edit Display Process Window Help S ALD we 2s cB vo aafuz LA Sfee Of A QAY me o s 50ppm Volatile Organic Analysis Calibration Standard V50 Sb 5 10 00 Scan El TIC 106 2 07e5 m Time 1700 1750 1800 1850 1900 1950 20 00 p Chromatogram 50 OF x 5 x E Fie Edit Display Process Window Help e B D wee oa fuz OA la GO AL ne e 9 5 50ppm Volatile Organic Analysis Calibration Standard 50 Sb 5 10 00 Scan El TIC 100 2 07e5 E Time 417 00 1750 18 00 1850 1900 1950 20 00 i Subtracting the background from a chromatogram 1 Select Subtract from the Chromatogram Process menu 2 Set the polynomial order pa
347. ing the From and To values in the grid Report largest n The number of peaks to be reported peaks Exclude target Do not include target compounds in the peak list compounds Coelution window Time window for qualitative and Quantify Trace sec peaks to maximize and still be considered same compound 331 TurboMass Software User s Guide Qualitative Method Editor Search Parameters Tab To define the criteria for library search operation Select the treatment to be applied to the spectrum before initiating the search Select the thoroughness of the search the Spectrum search type and its options More thorough searches take longer Optionally select the Reverse search option to improve the matching capability when there are contaminant peaks in the mass spectrum Optionally restrict the mass range of the searched reference spectra if he has some prior knowledge of the compound molecular weight This will improve matches where the reference spectra may have peaks outside the acquired range Optionally restrict the range of the matched compounds if he has some prior knowledge of the compound molecular weight This will improve the match quality by only returning results with molecular weights within this range F Qualitative Method Editor Untitied MEE Se Hep Ulslels 2 m a General Seach Parameters Libvay Seting Spactum hestment Limits None 4 Apply ents Set Defauls F AutoRigtine M
348. ings Resets the zero level of the instrument and reinitialize the system Activates Standard UltraTune DFTPP BFB Tune Activates Custom UltraTune AutoTune Pauses an acquisition Toggles to continue the acquisition This does not affect the acquisition of data from samples being processed in the Sample List E B Lee E aNg yE u E Stops an acquisition Toggles CI gas on off Toggles reference gas on off BEEE Accesses online Help 85 TurboMass Software User s Guide 86 Changing Tune Parameter Settings Most of the tuning parameters can be set using the slider bar or by editing a text field The tuning parameters can be modified in any of the following ways e by dragging the slider bar using the mouse e by entering a new value directly into the text field e by pressing the left or right keyboard arrows after clicking on the slider bar If you change a tune parameter using the slider bar the value shown in the text field will update as appropriate Other tune parameters only have a text field and can only be changed by direct typing The speed with which the system will respond to changes in parameter settings is controlled by the speed with which the peak display refreshes To get the sliders to be most responsive you should lower the scope scan speed and inter scan time for more information see Setting Scope Parameters on page 103 Instrument Tuning Printing Tune Information A report of the
349. inimum abundance on j fi Pon Minm mig OH fo Spectiun search type Maxine m2 on 1206 G denitp f Sirberty Namal 7 Minimum match on o Spectrum search optiona Molecular weight constet I Reverse sesch Between fi and faco I Penalze sare compound e 5 Reporting Presearch Maxine h s Test 10 C Delad C of z a Mariem hits Plots 3 332 Qualitative Method The Search Parameter Tab Fields Spectrum Treatment None Use original spectrum scan for search AutoRefine AutoRefine the spectrum prior to search Background Average the top 3 apex scans and subtract the scan prior subtracted to GC peak start The Window size and Noise threshold fields are enabled only when AutoRefine option is selected Window size Window size parameter for Refine algorithm scans Noise threshold Noise threshold parameter for Refine algorithm 333 TurboMass Software User s Guide 334 Spectrum Search Type Identity Specifies an Identify type search Similarity Specifies an Similarity type search lt drop down list gt Defines the specific Identify or Similarity search mode Contents of the drop down list change depending on the selection made with the radio buttons Spectrum Search Options Reverse search Use Reverse Search scoring Penalize rare Penalize a match by up to 50 points out of 1000 compounds depending on how common the compound is Default Normal operation use presearch screening before spe
350. integration parameters RelHt AbsHt RelArea Abs Area 0 0 0 0 0 0 0 TIC Window 4 Peak to peak Noise amplitude 2000 00 X Axis units Time mins C Scan Reporting parameters Report largest fi 0 peaks J Exclude target compounds Coelution window sec 1 00 327 TurboMass Software User s Guide 328 Qualitative Method Editor Toolbar The Toolbar is displayed at the top of the Qualify window By choosing the toolbar buttons you can perform some common operations OeaOGthe a Creates a new qualitative method Opens an existing qualitative method Saves the current qualitative method Saves the qualitative method with a new name Prints the qualitative method Closes the Qualitative Method Editor Displays the help associated with this screen Qualitative Method Qualitative Method Editor General Tab To define parameters for creation of a qualitative peak data set e Specify the chromatographic data sets which are to be subject to peak detection and integration The options are The full chromatogram from start to end OR One to four segments with specified start and end times e Each chromatographic data set can be the TIC the BPI chromatogram or a mass chromatogram defined with the usual TurboMass expression e Define the threshold parameters for each chromatographic data set e Define the default peak to peak noise amplitude value e Set the desired number of peaks to
351. ion You can select all the traces by clicking All and then clicking OK Real time Display of Chromatograms If you are acquiring data into a file and displaying el from that file then you can watch the chromatogram build up by clicking or by selecting Real Time Update from the Chromatogram Display menu Each chromatogram window has a separate real time update switch You can see the state of the switch for a particular window by determining if is selected or by making that window current and selecting the Chromatogram Display menu If real time update is enabled Real Time Update has a check mark by it Changing the Order of Displayed Chromatograms When a window contains multiple traces you can change the order in which they are displayed The chromatogram that is first in the list being displayed at the bottom of the screen or on top of the others if graphs are overlaid Select Move To First from the Chromatogram Display menu to display the currently selected chromatogram at the bottom of the screen Select Move To Last from the Chromatogram Display menu to display the currently selected chromatogram at the top of the screen Adding Text to the Chromatogram Display To add text labels to the chromatogram display click A When selected the Text tool button changes color to show that it is active Position the cursor where you want to add text and left click to open the Edit Text String dialog 391 TurboMass S
352. ion defines the security terms used in this appendix Access Rights Privileges By controlling access rights or privileges administrators can control or restrict the actions of a group of users Access rights are assigned to groups and users are members of groups Access rights cannot be assigned directly to individual users Users have the access rights assigned to the group s to which they belong Only users who are members of groups with the Administer User Accounts and Groups access right can assign rights to other groups Administrator The administrator is the person responsible for managing the system adding and removing users and groups and assigning access rights The administrator has unlimited access to TurboMass and to the Security application The Administrator account is always present with full access and only the password can be changed This account cannot be deleted Administrative privileges can be granted to any user by placing that user in the Administrators group Audit Log The audit log file contains a historical list of events showing which users accessed or attempted to access objects covered by the list of access rights Auditing can be customized so that only certain categories of event are included or disabled completely An audit log viewer is provided within the Security Manager Group A group is a collection of TurboMass users A group can have access rights assigned to it to restrict their movements wi
353. ionally enter the number of moments to use and the number of mass spectral peaks to consider 5 Click OK Signal to Noise It is sometimes useful to know the ratio of the peak heights to the level of noise in a mass chromatogram TurboMass provides the Signal to Noise calculation to do this Signal to Noise can be accessed from Chromatogram by selecting Signal to Noise from the Process menu Chromatogram Signal To Noise Lx r Ranges OK O EN Lx 7 Cancel Noise patas m Noise Processing Ignore Zeros M NO Extra Processing e Ignore Worst 5 of Scans Ignore Scans Outside 1 SD C Ignore Scans Outside 2 SD C r Display BMS Q Peak To Peak c The Signal to Noise S N calculations can be carried out to display peak to peak or RMS root mean square values If Peak to Peak is required the greatest height of the signal range above the mean noise value is divided by the variance If RMS is required the greatest height of the signal above the mean noise is divided by the root mean square deviation from the mean of the noise The S N calculated using RMS noise is usually expected to be about 5 times the S N value calculated using Peak to Peak noise Various authorities have different methods for determining what level of noise is taken into account for the calculations of noise variance and RMS deviation A two step process is carried out First the mean should be calculated with or without zeros as normal
354. is released the integration software will calculate the Noise amplitude and update the value Optionally select Enable smoothing and click Smooth to examine or modify the smoothing parameters Optionally set up one or more thresholds to remove small peaks by clicking Threshold in the Integrate chromatogram dialog to open the Response Threshold dialog Click OK to perform the integration The integration software will smooth the chromatogram trace if requested locate the peaks draw baselines and calculate peak statistics Editing Detected Peaks You can use the Edit Integrated Peaks dialog to change the results of integration by changing the position of an individual baseline adding a single peak or deleting one or all peaks Displaying information about an integrated peak gt Left click on a peak to display the peak top position peak height and peak area in the status bar at the bottom of the chromatogram window Peak Annotation can be displayed using any combination of peak top time peak top scan peak response height and peak response area by selecting Peak Annotation from the Chromatogram Display menu Chromatogram Editing a peak baseline 1 Select Integrated Peaks from the Chromatogram Edit menu to open the Edit Integrated Peaks dialog Edit Integrated Peaks x Peak Tops Peak Baseline Edt p Peak Information a OK 9 463 2 3503 Start fo 699 Start 9 699 Epa oes Height 2846
355. is computer O Everyone Just me The following dialog appears ie MATLAB Component Runtime Confirm Installation The installer is ready to install MATLAB Component Runtime on your computer Click Next to start the installation Cancel lt Back 704 Appendix B TurboMass Software Installation 22 Click Next to continue with the installation ie MATLAB Component Runtime Installing MATLAB Component Runtime MATLAB Component Runtime is being installed Please wait Cancel When MATLAB completes the following dialog appears ie MATLAB Component Runtime Installation Complete MATLAB Component Runtime has been successfully installed Click Close to exit 23 Click Close and the following appears 705 TurboMass Software User s Guide Setup Installing TurboMass Ver5 2 0 Restart Computer Setup is complete Before you can configure your system you must restart your computer so that the necessary system drivers are started C No will restart my computer later Remove any floppy disks from their drives and then click Finish to complete Setup 24 The installation process finishes and prompts to reboot the computer Leave the Yes want to restart my computer now option checked and click Finish When the system restarts the TurboMass Software 5 2 startup icon will appear on the desktop Turn on the mass spectrometer and wait 3 minutes for it to boot up D
356. is is scaled from 0 If you select the Baseline parameters and specify an intensity offset in the adjacent text field the vertical axis is scaled from your specified intensity This option can be useful for displaying chromatograms that have a raised baseline If selected the display is automatically scaled such that the lowest point on the trace is at the bottom of the display When comparing two chromatograms by overlaying them it may be useful to plot both chromatograms on the same intensity scale The Link Vertical Axes parameter allows you to do this If selected all axes in the current window will be given a common vertical scale The Horizontal Axis parameter allows you to specify the units of the horizontal axis to be either time or scans If selected multiple traces in the same window will be superimposed on the same axis If not selected the traces will be drawn on separate axes arranged vertically When chromatograms are overlaid only the currently selected trace is annotated If selected the area under the chromatogram trace will be colored If selected then peaks detected by integration are colored Peaks Graph Header Process Description Chromatogram The Graph Header parameter allows you to turn off the header information normally displayed at the top of the chromatogram in order to produce data for publication If selected the header will be displayed if not selected the header will not be
357. ished for the laboratory however when changes are required it involves reviewing a large number of compounds Using the Environmental Parameters dialogs makes interaction more convenient than the main dialog of the Quantify Method Editor by placing all the compound specific environmental parameters in one place for quick viewing and editing The Environmental Parameters dialog displays the parameters based on the type of the currently selected compound Target Compound Surrogate Compound Spike Compound or Internal Standard Compound IMPORTANT Modifying any part of the Quantify Method may cause calculations to be invalid and we strongly advise against doing this without completely reprocessing integrate calibrate quantify the data To set the environmental parameters for compounds 1 Inthe Method Editor select the first compound to be modified and click the Environmental Parameters button OR Choose Environmental Parameters command in the Edit menu 276 Environmental Parameters Compounds Int Std Int Std Int Std Surrogate Surrogate Surrogate Target Target Target Target Spike Target Target Target Target Target Spike Spike Target Target Spike Target Target Target Target Target Target Target Target Target Target Previous Mod Next Pentafluorobenzene 1 4 Difluorobenzene 1 4 Dichlorobenzene D Dibromofluoromethane Toluene d8 Bromoflurorobenzene Dichlorodifluoromethane Vinyl Chloride Bromo
358. isition 353 Multiple Solvent Delays 199 N Noise Reduction 400 O online help 59 output data files 475 oven temperature GC 163 P password change 672 peak centering 455 detection 276 401 767 Index 768 detection flags 315 editing detected 408 integration 313 matching 129 purity 410 printing active spectrum and chromatogram 439 processed data access 42 display 44 processes external 35 processing chromatograms 395 projects create 47 predefined 46 Q QA QC 217 Qualifiers Q Flags 607 Qualitative Method Editor 342 quantification process 258 Quantify application 251 calibration curve graph 306 chromatogram display 299 integration parameters 273 manual peak integration 313 peak list 310 reports 318 results 297 summary results 301 Quick Paths 153 R range adjustment 434 defaults 386 437 magnification 383 435 readbacks 109 real time data 358 reference files 133 Refine search spectrum 514 refine spectra 449 Release Control command 181 Report Method 652 Report Method Editor 551 552 Toolbar 553 Report Method Usage 642 Report Preview Window 245 Report Template Browser 555 558 filtering 559 toolbar 559 Report template new 572 Reporting Calculations 731 run status GC 182 run start 242 294 S Sample Information 221 Sample list editing 239 formatting 231 Sample List Wizard 215 Sample Prep Infrom
359. isplayed When this parameter is set to Normalize all peaks are rescaled relative to the largest peak 103 104 TurboMass Software User s Guide Changing Inlet Heaters The GC Interface Inlet Line Temperature setting on the Tune page is used to set the temperature of the interface between the gas chromatograph and the mass spectrometer Enter the desired temperature C in the text field TunePage d data caltest12_pro z acqudb default ipr olga lt E alal d wej 2 LE EE Instrument Tuning Setting Gas Controls The Gas menu on the Tune page lets you turn gasses on or off Turning a Gas On or Off gt Click the appropriate toolbar button OR Select the required gas from the Tune Gas menu If the gas was previously turned off it will now be turned on A check mark will appear next to a gas if it is turned on Pump out Reference gas should be used for about one minute prior to the first time Reference gas is selected to remove the air from the vial It should also be used whenever the vial is refilled 105 TurboMass Software User s Guide 106 Vacuum The mass spectrometer s vacuum system can be controlled from the Tune page Be sure that this is done in accordance with the information in your Mass Spectrometry Hardware Guide Pumping Down the Vacuum System 1 Select Pump from the Tune Options menu The menu name will change from Pump to Vent and the system will begin
360. isplays the Submitter Task hierarchy as shown in the Submitter Task Data window This includes all of the Submitters and Tasks available with none selected Click in the box to the left of the item you want to select Clicking this button that will applies check marks to all Submitters and Tasks Clicking this button removes any check marks from all Submitters and Tasks Clicking this button displays a File Save As dialog allowing you to enter a file name for the exported data and to select the directory where the file will be stored Clicking this button closes the dialog without exporting any data 647 TurboMass Software User s Guide 648 Import Submitter Task Dialog The Import dialog displays when you select a previously exported Submitter Task data file following use of the Import command from the File menu in the Submitter Task window The form of the Import dialog is similar to that of the Export dialog except for the title and the caption above the tree list are modified appropriately Control Submitter Task list Select All Unselect All Description Applying a check mark to a Submitter will cause all Tasks belonging to that Submitter to be checked Unchecking a Submitter will cause all Tasks belonging to that Submitter to be unchecked Unchecking one or more but not all Tasks under a Submitter will cause the Submitter check box to gray indicating there are some Tasks selected and some unselec
361. ist of generic compound names Choose Generic TIC Names from the Environmental Configuration submenu of the Tools menu Type a generic name into the edit box and click the Add button Repeat step 2 for each generic name required the list is sorted alphabetically as each new name is added Click OK To edit the list of generic names Choose Generic TIC Names from the Environmental Configuration submenu of the Tools menu Edit an existing name by selecting that name editing as required and clicking the Modify button Add a new name by typing the name into the edit box and clicking the Add button Delete an existing name by selecting the name and clicking the Delete button Click OK Appendix A TurboMass Security TurboMass Software User s Guide 661 TurboMass Security The Security application allows a system administrator to control e User access to various parts of the TurboMass system e Which operations can be performed within a given part of the system e Which events are audited Security compliments the Windows protection and adds an extra layer of security that is specific to the TurboMass data system This appendix defines some security related terms provides an overview of the TurboMass security model and explains how to use the Security Manager to configure user accounts user groups and how to assign group privileges TurboMass Software User s Guide 662 Security Terminology This sect
362. ists in the list of users or groups or the password is too short See Setting up an Account Policy on page 669 OR 1 Select an existing user from the list in the Security Manager dialog 671 TurboMass Software User s Guide 672 2 Select Copy from the User menu to open the User Properties dialog and enter the new user information Security creates a new user with some of the User Properties information already entered Until assigned new rights the new user is a member of the same groups as the original user Creating a Group When you create a user group the individual members have those access rights granted to the group You can create a new group by adding members as desired or you can copy an existing group Once you have created a group you will assign access rights to the group Creating a group 1 Create a new group by doing one of the following e Click OR Select New Group from the User menu to open the Group Properties dialog Group Properties x a Description es Cancel _ Members aa Assion _ Goren Assigned Hiahts Appendix A TurboMass Security e Select an existing group from the list in the Security Manager window and select Copy from the User menu to copy the existing group MassLynx Security Manager Jol User Policies Tools View Help ejej P else Username Full Name Description Administrator MassLynx Administrator Built in account for administering M
363. its pump down sequence 2 To monitor the vacuum progress with the optional vacuum gauges select Vacuum Monitor from the Tune Options menu Venting the Vacuum System Select Vent from the Tune Options menu and confirm that you want to vent the system The system will start its automatic venting sequence Instrument Tuning Warning Messages in Tune Select Warnings from the Tune Options menu to display a dialog containing a list of optional warning messages In most cases these warnings should all be selected You can select the following warning messages when exiting Tune under the following conditions e The filament on e The reference gas on e The Pump out reference gas on e The CI gas on You can select the following warning messages when venting the mass spectrometer with e ahot ion source gt 100 C e ahot GC transfer line gt 100 C 107 TurboMass Software User s Guide 108 Resetting the Zero Level The Reinitialize command measures the position of the noise signal so that any baseline offset caused by the electronics or instrumentation can be compensated for It is advisable to reset the zero level whenever the value of the multiplier voltage is changed gt You can reposition the zero level or Baseline by clicking OR Select Reinitialize from the Tune Options menu Instrument Tuning Controlling Readbacks TurboMass allows you to choose how system readbacks will be displayed on
364. ity axis range cy Increases magnification of the current range The current magnification factor is multiplied by 1 5 and rounded up to the nearest even number to give the increased magnification factor If the initial magnification factor is 2 this will give subsequent magnification factors of 4 6 10 16 etc cy Decreases magnification of the current range The current magnification factor is divided by 1 5 and rounded down to the nearest even number to give the decreased magnification factor If the initial magnification factor is 16 this will give subsequent magnification factors of 10 6 4 etc Deletes the current magnification range Where multiple magnification regions have been defined to select the current magnification range click in the magnification description that appears above the range The description will change color to red to indicate the currently selected range Changing the magnification of a particular range Double click on the magnification description of the magnification range The Spectrum Magnify dialog will be displayed Enter the new magnification factor and click OK to exit Deleting Magnification Ranges e To delete a single magnification range select the range you want to cancel and click ey e To delete all magnification ranges select Magnify from the Spectrum Display Range menu Click Default to delete all magnification ranges Click OK to exit Spectrum Changing the Range of Both Axes
365. ity chromatograms The Quantify Trace parameter specifies a chromatogram to be integrated when TurboMass is performing automatic peak detection and is used during the locate phase when TurboMass is matching peak list entries against method compounds 259 TurboMass Software User s Guide 260 Quantification on a selected mass chromatogram is usually preferred for sensitivity and selectivity deally the ion should be e Characteristic of the compound e Have a high relative intensity e A low background level e As high in mass as possible consistent with the previous requirements NOTE TurboMass enters this value automatically if you use the mouse to enter the Peak Location parameters Be sure to verify that it is the best choice for avoiding co eluting compounds See Peak Location parameters in step 7 J For multifunction data select which function number is to be used to quantify the current compound from the Acquisition Function Number drop down list Set the Concentration of Standards parameter to the Sample List column that contains the compound s concentration level within each Standard or QC sample If the compound is an Internal Standard and it is at the same concentration in all samples the Fixed option can be selected The software allows up to 20 concentration levels within a single sample For example if one group of compounds is initially at 50 ppb a second group is at 100 ppb and a third is at 400 ppb
366. k Description Sample Type Submitter Vial Number Injector Inject Volume Process Process Options Process Parameters Spare 1 Spare 2 Spare 3 Spare 4 Spare 5 Job User Name User Divisor Custom Objects la 569 TurboMass Software User s Guide Creating a New Report Template To create a new report template 1 Select Report Method Editor from the Tools menu E TurboMass TUTORIALQUANT TutorialQuant SPL Report Method Editor 2 The Report Method Editor screen appears la Report Method Editor New Report Method 3 Click the New button to the right of the Template field The Communiqu Report Creator appears 570 Communiqu Reporting File Edit View Format Actions Tools Help Jf O6 3 9 e Yoox e a Baaal sagicoe New Template 1 Page Type 1 0 New Template 1 3 Header 2 Foster 2 Page Type 1 Add a Header and Footer 1 Click on Header in the Layout toolbox on the left of your screen The Header appears K Communiqu Report Creator File Edit View Format Actions Tools Help 2 20619 9 hOX 4s nanamn eom New qm leader ETE E TL TP Paala a H n New Template 1 571 TurboMass Software User s Guide If you click on New Template the template description page will be displayed Here you can allow for A4 Letter resizing of your template To properly use the non A4 templates as the only set the
367. k OK to exit and save the changes NOTE f the information in one of the Header Editor areas overlaps another area the overlapped area will not be displayed Removing information from the displayed header 1 Select the Header areas from which you want to remove information 2 Toremove a single field select the information you want to remove in the Format list and click Remove OR To remove all the information from one Header Editor area select the area and click Clear OR To remove all information from all Header Editor areas click Clear All 3 Repeat steps 1 and 2 as required 4 Click OK to exit and save the changes 56 Getting Started Printing Data TurboMass prints data using the Windows Print Manager so any printer supported by your Windows operating system can be used with TurboMass All of the operations involved in setting up your printer are controlled by the Windows Operating System and will be described in the documentation that accompanied that The only TurboMass specific procedures to learn are those involved in selecting what to print You can select the printer that you want to use and specify printer setup by using the Printer Setup command found in each TurboMass File menu or by using the Windows Print Manager Many of the TurboMass Windows have Print buttons on the toolbar Prints current window in portrait format S Prints current window in landscape format Printing a Specific TurboM
368. l 100 478 _ 397 20 4612274 4 73e6 Height Raise baseline is optionally selected in the Peak Detect dialog and prevents the baseline end point from being moved too high up the peak To prevent the baseline endpoints from moving up the peaks reduce the value of this parameter The default value is 5 and the normal operating range is 5 20 This parameter is only relevant when the reduce peak tailing parameter has a small value less than 50 In the example below the reduce peak tailing parameter has been set to 25 403 TurboMass Software User s Guide Chromatogram TDASO922 Miil E3 E Fie Edt Display Process Window Help x e B D wee ea A Hf O Aa ele da and mda TDAS0922 SIR of 2 Channels Cl 100 1446 394 20 519920 6 77e5 Height 1464 249127 1363 1376 1472 160348 185396 108259 Fie Edt Display Process Window Help la x aHmaHAdHMErNANA AASE A da and mda TDA50922 SIR of 2 Channels Cl 100 1448 394 20 556515 6 77e5 Height 1363 1376 1428 181 398 205663 152957 h 1406 54013 Draw vertical is selected in the Peak Detect dialog and determines how well resolved peaks must be before they are separated by a dropline or baselines are drawn up into the valleys depending on the value of the join valleys parameter If you want to separate poorly resolved peaks increase the value of this parameter The default value is 90 and the normal operating
369. l be asked if you want to quantify compounds according to the new calibration curve 5 Click Yes to quantify compounds or No to keep the existing calculated concentrations The calibration curve will be replotted using only the included calibration points Excluded points are denoted by a circle around the point Excluded points are denoted in the Summary reports with an X in the Detection Flags column Excluding a complete sample from being used to form the calibration curve If once the calibration curves have been formed all calibration points from a particular standard sample are seen to be erroneous the sample can be removed from the calibration as follows Quantify 1 Determine which sample produced the erroneous calibration points 2 Inthe Sample List Editor find the row that contains the erroneous sample and set the Type field to Blank Alternatively remove the row from the Sample List 3 Click Start and select the Calibrate Quantify and Print Report options There is no need to integrate again 4 Click OK to start the analysis Performing any of the Quantify processes 1 Select Calculate from the Quantify Process menu to open the Quantify Process dialog Quantify Process x I Calculate calibration curves _Lancel_ IV Quantify compounds IV Blank subtract compounds 2 Select the Quantify processes you want to perform Locate Compounds Locates peaks for all compounds in the current method Calc
370. l be on the menu depending on the units displayed on the horizontal axis 2 Specify the scan number or retention time you want to center on 3 Specify the half width of the display range in the Window text field 4 Click OK Chromatogram Centering the display around a peak list entry 1 2 3 4 Select Range Center Peak List Entry from the Chromatogram Display menu Specify the peak list entry you want to center on Specify the half width of the display range in the Window text field Click OK Altering the Range of the Intensity Axis You can alter the range of the intensity axis with the mouse gt Left click at one end of the region of interest and drag the mouse vertically to the other end A line appears across the range you have selected Do not go beyond the bounds of the axis When you release the mouse TurboMass redisplays the selected range to fill the current window This operation can be repeated as often as required Altering the Range of Both Axes You can alter the range of both axes with the mouse gt Left click at one comer of the region of interest and drag the mouse to the diagonally opposite corner A box appears around the region you have selected Do not go beyond the bounds of the axis When you release the mouse TurboMass redisplays the selected region to fill the current window This operation can be repeated as often as required Setting Magnified Ranges Use the fol
371. l zero SIR Baseline Level sets the baseline position above zero The SIR Baseline Level is typically set to 1 If you want the baseline to appear higher increase the SIR Baseline Level value lon Counting Sets the intensity level below which a data point will be Threshold ignored The lon Counting Threshold can be set to values between 0 and 25 the higher the value the more data will be discarded NOTE To disable the lon Counting Threshold set the value to zero If you want to use the lon Counting Threshold a value of 3 is suitable for most data If you are performing trace analysis or looking at small isotope peaks a value from 1 to 3 may be more appropriate If you are only looking at large peaks you can save disk space with a higher number This threshold is applied to all acquisitions regardless of scanning mode It is also the most significant of all of the data manipulation variables because it is the one applied first to the raw data When an acquisition is started the instrument performs a prescan with the ion beam turned off so that the electronic noise level of the acquisition system and its standard deviation can be measured The lon Counting Threshold level that you enter is multiplied by the standard deviation of the noise to determine the intensity level to be used If you set a value of zero the intensity level is set so that it sits in the middle of the noise range which would mean that roughly half of the nois
372. lable KB Overwrite es 195040 2097151 0 14 Click Next gt to continue The installation of the MS Search program begins and runs to completion 715 TurboMass Software User s Guide A NIST EPA NIH MS Library NIST 02 and AMDIS Setup T EPA NIH MS Library NIST 02 and AMDIS Copying AMDIS Sample Mval126 d c nist2 amdis32 data hp mvall 26 d dete ms 15 When the MS Search software install is complete a screen is displayed prompting you to view Read Me files If you wish to view one or more files at this point check the appropriate box es and click Finish Setup Complete Setup has finished installing NIST MS Search and AMDIS on your computer Setup can let you view Read Me files and start NIST MS Search or AMDIS Choose the options you want below T Yes want to launch NIST MS Search now T Yes want to view the AMDIS Read Me file T Yes want to launch AMDIS now Click Finish to complete Setup The installation process completes and closes Be sure to close all open windows and find the final prompt screen indicating the install process is complete 716 Appendix B TurboMass Software Installation NIST2002 InstallShield Wizard Complete Setup has finished installing NIST 2002 on your computer 16 Click Finish to close the NIST installation process 717 TurboMass Software User s Guide 718 Configuring TurboMass for GC Control Before you begin to use TurboMass for t
373. lank sample the middle trace shows a mass chromatogram from the analyte sample and the upper trace shows the result of subtracting the blank data file from the analyte data file 465 TurboMass Software User s Guide SIR of 2 Chezz Ww SIR of 2 Che gt gt 7 706 SIR of 2 Cher77 706 20 466 Strip and Combine Functions Creating an Enhanced Data File This section describes how to create an enhanced data file and provides examples l 2 Select Enhance in the Strip Datafile dialog To change Input File or to select a subrange click Input Select the input file and function by selecting File to open a browser dialog Set the mass and retention time ranges if required If the default Output file name is not correct click Output and enter the required name Select Enhance Datafile Options from the Strip Options menu to set the Enhance parameters Click Process to start processing the data file The status bar at the bottom of the Strip dialog displays the progress of the current process The following illustration shows two chromatogram traces The lower trace is the raw data file The upper trace shows the same data file after it has been processed using Enhance As you can see the background noise level has been greatly reduced in the enhanced data The original data file size of 19 MB has been reduced to 0 5 MB in the enhanced data file 29 01 20 17 25 87 12 18 16 5247 37
374. lated based on a concentration entered for the internal standard in the Sample List 759 TurboMass Software User s Guide 760 NOTE For compounds designated as Surrogate the Concentration is calculated without including the Dilution Factor This is because in Volatile Analysis the Surrogates are added following dilution and are therefore not affected by it The equation starting from TurboMass concentration for Surrogates therefore becomes Concentration ug Kg SATAY The calculation for results of medium and high level soil sediment volatile organic analyses preserved with methanol is in accordance with EPA SW 846 published Method 8000C Revision 3 03 03 Water contained in a sample mixes with the water soluble methanol preservative to create a greater volume of liquid for analysis To account for the dilution effect of the water to the methanol in the sample a moisture adjustment must be applied This will produce a more accurate quantitation on a sample specific basis for contaminates of concern This moisture adjustment is not the same as reporting the data on a dry weight basis The data must also be adjusted to be reported on a dry weight basis NOTE This calculation will only be performed for Analysis Volatiles Matrix Soil Level Medium and if all required inputs are available The total volume of methanol preservative and sample moisture contribution can be calculated as follows wt of sample wt of d
375. layed RT value will be updated when focus leaves the RRT field If you change the compound defined as the Internal Reference for the current compound then the value in the selected enabled Peak Location field will be used to calculate a new value to be displayed in the disabled field Ifa compound does not have an Internal Reference defined or has one which is then changed to None then the RRT radio button will be disabled and the RRT field will remain disabled and blank Both RT and RRT values will be saved in the quantify method file However when the file is opened again in the editor only the active data value will be read from the file the other value will be calculated as described above 267 TurboMass Software User s Guide 268 Updating of Analyte RTs from Internal Reference To simplify the process of updating retention times of analytes in complex quantify methods this option updates RTs of analytes when the RT of their internal reference peak is modified If the current compound is used as an Internal Reference by other compounds then when its RT is modified and you click the Modify button a dialog will be displayed asking you if the RTs of the associated analytes should be updated as well Update Retention Times Do you want to update the retention times of all the compounds in the method that use this internal standard If you click the Yes button then all compounds that use that Internal
376. le If no peak has been located for a compound entry the peak information fields will be left blank Quantify Summary ANALYSIS METH1 ol x B File Edit Display Process Window Help TEE BALLARE tHE Compound 1 Compound A 430 5 Name ID Type Std Conc RT Area Response Conc 1 STANDRD1 ID Stand 1 00 9 970 17847 17847 025 4515 2 STANDRD2 ID2 Stand 1 00 9 963 17873 17872 848 1745 3 STANDRD3 ID3 Stand 1 00 9 970 14558 14557 564 0 94 4 STANDRD4 ID4 Stand 1 00 9 970 12931 12931 481 0 83 5 STANDRDS IDS Stand 1 00 9 970 14554 14553 860 0 94 Use the Quantify toolbar buttons to display information about a new compound sample e Shows previous compound sample in Summary window gt Shows the next compound sample in Summary window The Quantify Toolbar buttons can be used to display integrated peaks in Chromatogram fa Shows the previous peak in the Summary window E Shows the current peak in the Summary window 299 TurboMass Software User s Guide 300 at Shows the next peak in the Summary window The Summary window format also determines the format of printed Summary Reports Two Summary Reports can be printed the Summary Report listed by sample and the Summary Report listed by compound There are many different columns of quantification information that can be displayed in the Summary window You can select which columns are currently displayed Use the horizontal and v
377. le Area 9814 010 3 Manually adjust the baseline assignment as necessary 4 Add any Comment that you want to store in the peak list for the selected peak For more information see Manual Peak Integration on page 311 File Edit Display Process Window Tools Help x 2 aje welaj ell ealo O Aala lelea Prepared standard 50 Standrd4 Sm SG 2x1 SIR of 2 Channels ES 458 50 6 44e4 Area The Peak List Window Select Show Window from the Quantify Display View menu to display the Peak List window 307 TurboMass Software User s Guide H Eile Edit Display Process Window Help l x aal tjera B alal jej jz Height RT Name 41492 21 987 23491 22 867 68197 24 871 106959 26 121 98029 27 584 71950 30 381 The Quantify Peak List window lists all the peaks in the current peak list with the current peak selected You can configure the columns displayed in the Peak List and the header displayed at the top of the Peak List window The Peak List window displays all the information for a peak list entry To accommodate display space restrictions you can select which columns are to be displayed and the order in which order they are to appear Configuring the displayed Peak List columns To select Configure Peak List columns 1 Select Peak List Display Format from the Quantify Display menu to open the Format DB List dialog and then select the desired column s OR Use the mouse to
378. le Right click Format The Format Table dialog appears x Table Rows Columns Size IV Preferred width inches 6 04 Shape Number of columns Number of rows 4 3 Position In from left inches Down from top inches 05 6 75 Borders Style X E 4 Weight 3 pt ka E Color Automatic bd El 576 Communiqu Reporting 5 Change the Number of columns from 4 to 5 then click OK If necessary click on the Columns tab and change the Column width to 0 5 6 Add text blocks to the top row of the table Label each cell as follows RT Name Match Factor and Area NOTE Remember to first put a Text Block from the Layout Tools in the table so that you can enter a label 7 Under put Peak Number from the Project Samples Qualitative Peaks path in the Data Objects toolbox roject Samples Current QualPeaks Current PeakNumber This information Project Samples Current QualPeaks Current PeakNumber is the source string of the data In this example it will report the peak number of the current QualPeak in the current Sample About Samples Current versus Last The template is used to pull information from the data source during report creation From the point of view of the data source the most recent data e g the current line on the Sample 577 TurboMass Software User s Guide List is the last data entered into the data sourc
379. led YES z Det ECD gt PPC DetB TCD A v PPC Gas leak alarm J Mode z Mode z Aux tmp zone ico gt Out INT hal Out INT fa r inlets m Carrier Pneumatics Pressure units PSIG x PPCA CapillaymodeA MV PPCBIY Capilar modeB I Car B NONE v Valves 3 VALVE gt 4 NONE gt 5 NONE z E NONE m Auxiliary Pneumatics Aux 1 Press PSIG 7 PPC Jv Aux 2 NONE z PPer Aux 3 NONE z Ee ml Aux 4 NONE z nee Select to retrieve the current configuration from the instrument CD E 25 Click Finish Bf Configuration Editor File Instrument User View Help S R m 8 mlz 2 Name Type Acq Port LINK Port Configured IPM PE Nelson Interface Type 680 Eprom 2 0 Memory 244 Kb Serial number None inst AUTOSYSA CLARUS COM2 Instrument Configuration Instrument Type Autosampler Type Injectors Detectors Mode Aux Zone 26 Close the Configuration Editor by selecting Exit from the File menu 728 Valves Output Cartier Pru Aux Pru Clarus 500 GC with Autosampler BUILT IN PSSLPKD ECD TCD R TCD SPLIT NONE VALVE NONE NONE NONE INTNT Press He PPC NONE PPC Press PSIG NONE NONE NONE Appendix C TurboMass Quantify Calculations TurboMass Quantify Calculations Peak Response There are two main methods of calculating peak response value these are External Standard and Internal Standard
380. letter Press ALT key letter to display a drop down menu For example press ALT V followed by C to open the Chromatogram application if TurboMass DEFAULT TutorialQuant SPL Fie Edit Samples Run View Quantify Configure GC Tools Help Spectrum Map Toolbars gt The sample list pane includes a context sensitive menu that allows you to apply options to the queued samples To access the drop down menu right click an item or area The following table describes the options Pause Process Right click an entry and select this option to pause this entry Delete Process Right click the Index of an entry and select this option to Priority Process Refresh Queue Pause Queue Delete Queue Pre emptive Scheduling Getting Started delete the entry from the queue Right click the Index of an entry and select this option to move this entry to the top of the queue If an entry has been deleted or prioritized select this option to refresh the queue display Toggle this option to pause resume all acquisitions A check indicates that a queue has been paused The currently running entry will continue to completion but no new acquisitions will be started The queue can also be paused by selecting Pause Queue from the Run menu or by clicking Select this option to delete all entries in the queue This option allows priority processes to interrupt non priority processes If this option is selected and a non
381. library entry number and the compound name The mass axis can be zoomed to expand a region of particular interest these changes are also reflected in the Delta window 507 TurboMass Software User s Guide 508 M750 316 13 351 Cm 314 318 306 310 322 326 100 a 47 37 4042 48 54 98 TEE R 974 Nist 3439 CHLOROFORM 100 435 37 47 48 72 82 odil ama gs 60 siea 70 27 S R 849 Nist 18134 METHANE OXYBIS DICHLORO 100 8 47 PE Sa 37 40 ao 4851 ae 35 40 45 50 55 60 65 70 75 30 95 117418 120 117418 172122 Hit 2 19 Pal 100 105 110 115 120 126 1174 You can manipulate the display in a number of different ways Determine which hits are displayed Change the range of the mass axis Restore the display Determining which hits are displayed l Changing the range of the mass axis zoom The first hit displayed is always the current hit which is the hit selected in the Hit List window To change the number of hits displayed select View from the Library Display menu and change the No Hits value The Hits window displays up to four of the next best hits gt Left click at one end of the region of interest and move the mouse horizontally to the other end TurboMass indicates the range you have selected Do not go beyond the bounds of the axis When you release the mouse button TurboMass redisplays the selected range to fill the current window OR
382. libration is complete the GC status changes to Ready Stopping and Restarting the GC If there is a problem with the GC setup after a run is started the Stop command lets you stop the analysis Once you have corrected the problem Retry Injection lets you restart the GC without stopping and restarting your mass spectrometer method Stopping the GC from the GC menu does not stop MS data acquisition Selecting Stop from the GC menu stops the method that is in the inlet file cell of the Sample List however the mass spectrometer is still acquiring data To stop MS data acquisition select Stop from the TurboMass top level window Run menu and respond whether you want to stop the GC as well 179 TurboMass Software User s Guide 180 If you started the MS data acquisition from the Tune page Window menu stop the MS data acquisition and select Stop GC from the Configuration Editor GC menu if you want to stop the GC also Releasing and Taking Control of the GC The Release command lets you release the GC from mass spectrometer control to change a setting from the GC keypad or to make a hardware change to the GC Once you have completed your change s you must re establish Take control of the GC Releasing control of the GC gt From the GC menu select Release Control The Take Control command in the GC menu allows you to take control of the GC if its current GC status is Released Usually you do not have to select Take Contr
383. lick Change or Remove E Microsoft NET Framework 1 1 5 Microsoft NET Framework 1 1 Hotfix KB886903 wi msn 12 Click on Yes The following appears MATLAB is removed Appendix B TurboMass Software Installation 13 Delete the Desktop icon 14 Reboot the computer 691 TurboMass Software User s Guide Installing the TurboMass software 1 Verify that all pre installation tasks are done See the IMPORTANT information on the first page of this section 2 Save all data and close all Windows programs 3 Insert the TurboMass compact disk in the CD ROM drive The installation program automatically starts and guides you through the installation process with a series of dialogs that prompt you for your choices The following three buttons are always displayed at the bottom of each setup dialog e Back Go to the previous screen e Next Go to the next screen Click this button when you have completed a dialog e Cancel Stop the installation process and quit the setup program The rest of this procedure describes the TurboMass installation process and shows the corresponding screens The installation process begins automatically with the Software Licence Agreement 4 Click Yes to accept the agreement or click No to cancel the setup procedure 692 Appendix B TurboMass Software Installation Installing TurboMass Software License Agreement Please read the following license
384. lick OK TurboMass updates the Library display to show the results of the comparison in the Hit List Hits Delta and Structure windows if these windows are currently displayed The format of the display is the same as for a normal search except of course there is only one hit Using the Library Subtract Process The Subtract process allows you to subtract the spectrum of a particular hit from the search spectrum The resulting subtracted spectrum becomes the new search spectrum and the library search can be repeated 513 TurboMass Software User s Guide 514 The Library Subtract process can be useful if you suspect that the search spectrum is a mixture of more than one compound A mixture is indicated by a high Reverse Fit and low Forward Fit value If you subtract the spectrum of one of the hits from the search spectrum and repeat the library search the other component of the mixture now appears high on the Hit List For mixtures that contain more than two compounds this process can be used to identify compounds one at a time Subtracting a hit from the search spectrum gt Select Subtract Hit from the Library Process menu enter the number of the hit you want to subtract and click OK The subtracted spectrum becomes the new search spectrum Subtract Hit Bpo Cancel Library Creating User Libraries In addition to the libraries available from PerkinElmer you can create your own user libraries that contain your own
385. ll Line 1 Left aaa Group RawFileHeader z Format annie Getting Started Adding information to the displayed header 1 Select the Header areas in which you want to display information 2 Select the Group from the drop down list that contains the information you want to append to the displayed header 3 Select the information required in the Element list 4 Select the field before which you want to insert the information in the Format field and click Add To add information at the end of the currently displayed information select End and click Add 5 To add your own text to the header select Text in the Element list and click Add The User Text dialog is displayed 6 Enter your text and click OK Your user text will be shown in the Format list and will be displayed in the header when you exit the Header Editor dialog 7 Ifyou want to format the information in the header select the relevant field in the Format list and click Format Format RawFileHeader SampleT ext iia i Textual EE ancel Numeric Decinaliplaces i For numeric information you can select the number of Decimal places displayed in the 0 to 6 range Some Elements have sub elements that may be selected by the Field list 55 TurboMass Software User s Guide 8 Repeat steps 1 to 6 as required A maximum of eight areas can be used at one time to display header information 9 Clic
386. ll be displayed in a new window of its own if the Chromatogram toolbar button is activated Removing chromatogram traces and windows e To remove a particular chromatogram trace select the trace to make it the currently selected trace and then press DELETE Click OK to confirm the deletion e To close a particular chromatogram window click the Windows close button x 53 TurboMass Software User s Guide 54 The Header Editor The Header Editor is used to determine the information displayed in the header for each of the TurboMass windows The TurboMass Window Header can be thought of as a table that has six rows and three columns Various pieces of information can be displayed in the header including your own text Information can be displayed in lines 1 to 6 On each line information can be displayed in three positions left center or right There is a graphical representation of the current header at the top of the Header Editor dialog The Header Editor areas that are currently displaying information are shaded in gray A maximum of eight areas can be used at one time to display header information Determining the Header Information in a TurboMass Window gt To open the Header Editor dialog in most TurboMass windows double click the Window header OR Select Header from the Display View dialog Header Editor ChrHeader x r Header areas r Ce
387. llation The MATLAB screen appears ie MATLAB Com ponent Runtime MATLAB Component Runtime Cancel 20 Click Next to continue with the installation ie MATLAB Component Runtime Welcome to the MATLAB Component Runtime Setup Wizard The installer will guide you through the steps required to install MATLAB Component Runtime on your computer NOTE THIS INSTALLATION SHOULD TAKE ABOUT 5 MINUTES TO COMPLETE WARNING This computer program is protected by copyright law and international treaties Unauthorized duplication or distribution of this program or any portion of it may result in severe civil or criminal penalties and will be prosecuted to the maximum extent possible under the law 21 Click Next to continue The Select Installation Folder dialog appears 703 TurboMass Software User s Guide NOTE Do not change the folder path MATLAB components only work when MATLAB is installed in the default path NOTE The default install for MATLAB specifies Just Me Change the default setting to Everyone and click Next to continue ie MATLAB Component Runtime Select Installation Folder The installer will install MATLAB Component Runtime to the following folder To install in this folder click Next To install to a different folder enter it below or click Browse Folder C Program Files MathWorks MATLAB Component Runtimes Install MATLAB Component Runtime for yourself or for anyone who uses th
388. log Set the Mass and Retention Time ranges if required 3 To change Background File or Scan number click Background Select the Input File and Function by clicking File Enter Background scan number or select Use all background file if the entire file is to be used If a previously generated spectrum process is to be used click File to open the browser and click History within the browser Strip and Combine Functions 4 Ifthe default Output file name is not correct click Output and enter the required name 5 Set the Subtract parameters by selecting Subtract Datafile Options from the Strip Options menu 6 Click Process to start processing the data file The status bar at the bottom of the Strip dialog displays the progress of the current process The lower trace shows the TIC chromatogram of the V50 data file The upper trace shows the TIC chromatogram of the same data file after a background scan scan 761 at retention time 32 min has been subtracted 50ppm Volatile Organic Analysis Calibration Standard Scan El I 7 67 19 61 7 58 T ag 13 351410 35 98 21 99 24 87 26 20 27 58 39 3g 34 0536 06 37 85 Scan EI I 19 61 26 20 37 58 24 87 30 38 3 20 ioga 13351410 a ee ala I A 3408008 27 8 2 03 gt j 10 00 15 00 20 00 25 00 30 00 35 00 5 00 rt The illustration shows an example of subtracting a complete data file from another data file The lower trace shows a mass chromatogram from the b
389. log opens TurboMass Path Select C Shutdown E Structdb TurboMass 153 TurboMass Software User s Guide 3 Select a path and click Select TurboMass will add the path as a quick path and list it in the Quick Paths dialog If you want to set a quick path to your project directory specify the following quick path to the project subdirectory that contains the GC method lt project path gt acqudb For example c TurboMass myproject pro acqudb If you do not specify a project directory TurboMass creates the following project directory as a default which you can specify as one of your quick paths c TurboMass Default pro Inserting a path in the Quick Paths list 1 Inthe Configuration Editor select Quick Paths from the User menu to open the Quick Paths dialog 2 Select the path above which you want to insert a new quick path and click Insert 3 Inthe Path Select dialog select a path and click Select TurboMass will add the path to the Quick Paths list Removing a quick path from the Quick Paths list 1 Inthe Configuration Editor select Quick Paths from the User menu to open the Quick Paths dialog 2 Select the path you want to delete from the Quick Paths list and click Delete 154 GC Control Removing all paths from the Quick Paths list 1 Inthe Configuration Editor select Quick Paths from the User menu to open the Quick Paths dialog 2 Click Clear 3 Ifyou change your mind click
390. lon Counting Threshold 2 AB0010 2 0 128 Sm SG 2x1 00 Cm 1 18 Scan El 100 614 06 4 3004 lon Counting Threshold 1 ABO000 2 0 128 Sm SG 2x1 00 Cm 1 Scan El 6 100 4 48e4 lon Counting Threshold 0 625 630 635 640 645 Figure 5 Effect of increasing Ion Counting Threshold on low intensity peak in Heptacosa spectrum 78 Instrument Data Thresholds Changing Lab and User Information TurboMass can save management information with a data file The information saved is Laboratory Name Instrument Identification and User Name This information is entered into the Lab and User Info dialog This information will be stored with any data that are acquired and can be displayed as part of the header information of a chromatogram or spectrum when displayed or printed l On the Tune page select Instrument Name from the Options menu The Lab and User Info dialog appears Lab And User Info x L La User Administrator Cancel Instrument ID nst Make required changes to the information Click OK 79 TurboMass Software User s Guide 80 Communications Status and Diagnostics Communications Status Select Communications Status in the Tune Options menu A dialog indicates if the computer and the TurboMass instrument are in communication and the number of hours The version of the communications protocol software is displayed In this dialog clicking Reboot will download the c
391. loropropane Chloroform Benzene Trichloroethene Dibromomethane 1 Bromo 2 chloroethane Toluene trans 1 3 Dichloropropene 1 1 2 Trichloroethane Ethylbenzene p m Xylene o Xylene Type CAS number Abbreviation Maximum in blank MDL Water Soil Response Factors Minimum RRF Maximum RSD Init Cal Maximum Difference Surrogate 5MC Concentration Recovery Limits Water Soil Surrogate y 1868 53 7 BFM Target Isopropylbenzene Target Bromobenzene Target n Propylbenzene Target 1 3 5 trimethylbenzene Target sec Butylbenzene Previous This dialog contains all of the above parameters plus the following Concentration An edit box that defines the amount of the compound used to spike the sample Low Recovery limits Water and Soil An edit box that defines the minimum acceptable recovery percentage for the compound spike or surrogate in a Water sample and a Soil sample High Recovery limits Water and Soil An edit box that defines the maximum acceptable recovery percentage for the compound spike or surrogate in a Water sample and a Soil sample 282 Matrix Spike Environmental Parameters Compounds Type Name Int Std Int Std Int Std Surrogate Surrogate Surrogate Target Target Target Target Target Target Target Target Target Spike Spike Target Target Spike Target Target Target Target Target Target Target Target Target Target Previous P
392. lowing procedures to set the magnification ranges 381 TurboMass Software User s Guide 382 Creating single or multiple magnification ranges To create single or multiple magnification ranges do any of the following If you have a three button mouse middle click at one end of the region of interest and drag the mouse horizontally to the other end A line appears across the range you have selected When the mouse is released TurboMass redisplays the selected range with an initial magnification factor of 2 Hold down the SHIFT key and left click and drag the mouse across the region of interest To expand the chromatographic range of interest left click and drag the mouse and click as many times as required to achieve the desired magnification Click E to restore the original chromatographic range Set parameters from the Chromatogram Magnify menu Creating single or multiple magnification ranges using the Magnify menu Select Magnify from the Chromatogram Display Range menu to open the Chromatogram Magnify dialog Chromatogram Magnify xi ae p Settings Cancel By m Default Eom foao m Io fi 4 986 OR Double click the magnify range indicators for an existing magnified range Enter the range to magnify in From and To Enter the magnification factor you want to apply in By Chromatogram To define more than one magnification range select a new range in Range and repeat step 2 You
393. lt 473 TurboMass Software User s Guide 474 Peak Width This parameter is the spectral peak width in amu It is only used when subtracting centroid data The peak width can be determined from inspection of the tune peaks on the Tune page The peak width is used to determine if peaks present in the input and background data represent the same peak Background This is applied to the intensities of the peaks in the multiplication background spectra before they are subtracted from peaks in factor the input spectra This provides a method of adjusting the height of the subtracted background 2 To set parameters to their default values click Default Setting Enhance Datafile Options Enhance operates on continuum data only It works by examining each spectrum data sample to determine if it is a noise spike or part of an actual peak This is achieved by looking at neighboring samples on the mass scale and at the same area in the preceding and following scans For example using the values in the Enhance Datafile Options dialog two samples either side of the current sample will be examined including the current sample This makes five in all One scan either side of the current scan will be used so including the current scan three scans will be used Multiplying the number of scans by the number of samples in each scan shows 15 samples are examined in all Consequently for a sample to be accepted 60 of these samples nine samples
394. lue fT 000000 User Peak Factor 1 000000 Reporting Threshold 0 000 i H mi Standard 43 63 83 123 143 163 Concentration Factor 7 900 258 Quantify Setting method parameters l Enter the name of the compound in the Name field The compound name can be up to 30 characters in length The names of the compounds in the method appear in the Compound list Select the internal reference compound in the Internal Ref field Set this parameter to None if the compound is not using an internal reference standard Only compounds that appear in the compound list can be selected Select the Data Source of the peak for the selected compound e MS Mass spectral data will be used e GC A The GC detector from channel A will be used i e a raw data file from this detector e GC B The GC detector from channel B will be used i e a raw data file from this detector If a GC detector is selected most of the MS specific options will be deactivated for For example Quantity Trace Acquisition Function Number Relative Retention Time REV Fit Threshold and the Spectrum display Set Quantify Trace to the trace descriptor of the chromatogram being used to quantify the compound as follows e A single decimal number for mass chromatograms e A range of masses for example 280 286 will sum the intensity of m z 280 to m z 286 e TIC for total ion current chromatograms e BPI for base peak intens
395. m quantification This can be achieved by selecting Save from the File to update the current method file or Save As to save to a new method file When opened the Quantify Method Editor contains the current TurboMass method If the current method is not available the editor will contain default values and the name of the current method in the editor title bar will be set to Untitled The current method becomes the current system method file that is used when performing quantification gt To open the Method Editor dialog select Edit Method from the Quantify menu Method Editor 8260b_Tutorial J sioj xj File Edit Help Compound 2 1 4 Difluorabenzene Name Pentafluorobenzene 3 1 4 Dichiorobenzene D4 4 Dibromofluoromethane Internal Ref 1 Pentafluorobenzene z 5 Toluene d8 6 Bromoflurorobenzene 7 Dichlorodiluoromethane pascor G MassSpec C GCA C GCB 8 Vinyl Chloride 3 Bromomethane Rises Tinos 168 10 Trichlorofluoromethane A 11 1 1 Dichloroethene Acquistion Function Number One X Concentration of Standards conce E Peak Location Retention Time mins 6 302 Relative Retention Time oo 20 1 Bromo 2 chloroethane i ee 21 Toluene Time Window mins 22 tans 1 3Dichloropropene eer el gan 23 1 1 2 Trichloroethane E Peak Matching 24 Ethylbenzene z d 2 Peak Selection Spectrum y Append Insert REY Fit Threshold g Mody Delete Spectrum 168 General Parameters 100 Integrate Parameters Environmental Parameters F UserRF Va
396. m the Library Edit menu 8 Print the results of the Library search by clicking or OR Select Print from the Library File menu All the above settings are retained for future searches and need to be edited only if you want to change them You do not need to edit them each time you do a search Library Toolbar At the top of the Library window is a set of buttons called the library toolbar The toolbar allows you to perform some of the most commonly used actions with the click of a button E Selects a data file Prints the current window in portrait format S Prints the current window in landscape format Copies the bitmap of current window to the clipboard 491 TurboMass Software User s Guide 492 Copies the current hit list to the clipboard g Refines the current search spectrum e Searches the current search spectrum against the current library Arranges the windows in a tiled view Arranges the windows in a cascaded view Arranges the windows in a stacked view Selects a new scan number as the search spectrum E Toggles to restore the previous display range or to display the default axis range Selecting Which Libraries to Search The Library application searches one or more Libraries specified in the Library Search List These can be standard Libraries such as the NIST or Wiley libraries or user libraries Building a search list 1 Select Search List from the Library File menu to open t
397. many peaks to produce a single stick 4 Select a centering method Spectrum If you have selected Centroid top you may want to alter the fraction of the resolved portion of the peak that is used to calculate the centroid from its default value of 80 Values in the range 60 95 are reasonable If you want to generate a stick spectrum select Create centered spectrum The height of the sticks can either represent the intensity of the continuum trace at the mass of the stick select Heights or the sum of the intensities of the points across the peak in the continuum trace select Areas The stick spectrum can be added to the current spectrum window replaced with the current spectrum or be placed in a new window Select Add Replace or New window as appropriate Click OK 455 TurboMass Software User s Guide 456 Copying to and from the Windows Clipboard The Windows Clipboard provides temporary storage for information that is being transferred between application programs word processors spreadsheets TurboMass etc You can use the Clipboard to move data in or out of the Spectrum window either as a picture or as a text list For example you can paste spectra or chromatograms into reports written with a Windows compatible word processor TurboMass can copy a Spectrum picture to the Clipboard as a metafile giving greatly improved resolution When the metafile is pasted into another windows application it can
398. mass chromatogram centered around the selected peak and 1Da wide OR Click to display the Mass Chromatogram dialog Enter the mass required in the Description field and click OK Chromatogram TUT01 BEE E File Edit Display Process Window Help la x 2 alal wee a a A ala l La elle 1 0 Scan El 6 64 164 TIC 3 63e6 367 TurboMass Software User s Guide 368 The Chromatogram Display The chromatogram application runs in a window that has a menu bar at the top Under each of the headings on the menu bar is a pull down menu and every feature of the chromatogram application can be accessed from this menu structure At the top of the chromatogram window is the toolbar The toolbar provides a quick way of performing common operations The top level window may contain one or more chromatogram windows and each can contain one or more chromatogram traces The current chromatogram window is identified by having a colored title bar To select another window to be the current one either left click on any part of the new window or select one from the bottom section of the Window menu When there is more than one trace in a window the current one is identified by a colored square to the left of the trace To select another trace to be the current one left click on any part of the trace select a trace from the Traces option on the Chromatogram Display menu or use the up and down arrow keys on the keyboard
399. mation and Peak Information options you want to print 4 Click OK to exit and print the report Printing with Chromatogram This prints the active spectrum and chromatogram on the same page to the default printer To Print the Active Spectrum and Chromatogram on the same page 1 Open the raw file and selected function in the Chromatogram window 2 Scale the chromatogram as desired 3 Set up peak annotations as desired 437 TurboMass Software User s Guide 4 Select the scan desired or perform a Combine operation background subtraction 5 Set up annotations in the Spectrum window as desired 6 Choose the Print With Chromatogram command from the File menu in the Spectrum window Controlling the Appearance of the Display Each spectrum window has its own set of Display Parameters which determine the appearance of the spectrum display You can inspect and alter the parameters for the current spectrum window from the Spectrum Display dialog Changing the display parameters 1 To display the Spectrum Display dialog select View from the Spectrum Display menu m Normalize Data To Style Largest Peak on Display T Overlay Graphs C Base Peak in Spectrum T Fill Trace C Mass 0 00 Graph Header C Intensity 0 I Process Description Baseline at Zero Split Axis 1 gt Baseline fo Osasta fj Grid Off x T Link Vettical Axes r Data Threshold FullScale foo C Intensity 0 Cancel Hea
400. me The current cursor position is given by a pair of cross hairs The mass chromatogram for the currently selected mass is displayed at the top of the Map window The spectrum at the currently selected retention time is shown at the bottom of the Map window The Map program provides the ability to overview a complete data file very quickly This is particularly useful for complicated GC MS data files The data file can be rapidly searched for particular masses with the simultaneous display of mass chromatograms and spectra 527 TurboMass Software User s Guide How to create a data file map l 3 528 Select Map from the TurboMass top level Process menu OR Click EJ The first time the Map program is loaded the Map window will initially be blank Click OR Select Open from the Map File menu or select Create Map from the Map Process menu The Create Datafile Map dialog is displayed r Static File C TMintro PRO Data G4S2 Function 1 rm Retention Time Resolution Mass Range Start min 1 01 Mass amu 1 000 Start amu 40 0 End min 18 00 Scans fi End amu 300 0 OK Cancel Default If you wish to change the data file select File to open the Map Data Browser dialog Map Map Data Browser cs amp TMintro PRO E Data Scan 40 300 El foe 4 Select the new data file from the File Name list You can access a data file on a different
401. menu to open the Mass Chromatogram dialog Mass Chromatogram x Fie vso Description m z Cancel File Function Scan 35 260 El z C Addtrace Replace trace New window 2 Ifrequired select a function from the Function drop down list 3 Enter the description of the mass chromatogram you want to generate using one of the following formats The summed chromatogram of masses 109 5 to 110 5 110 340 The summed chromatogram of masses 109 5 to 110 5 and 339 5 to 340 5 110 340 The summed chromatogram of masses 339 5 to 340 5 subtracted from the summed chromatogram of masses 109 5 to 110 5 110_ 340 The summed chromatogram of all masses from 110 to 340 inclusive 375 TurboMass Software User s Guide 376 You can generate more than one mass chromatogram trace at a time by separating individual descriptions with commas For example 110 150 The two mass chromatograms centered around 110 and 150 110_150 340 The summed mass chromatogram of all masses from 110 to 150 and the mass chromatogram centered around 340 4 Ifyou want to add the mass chromatogram to the current chromatogram window select Add trace If you want the mass chromatogram to replace the currently displayed chromatogram trace select Replace trace If you want the mass chromatogram to have its own chromatogram window select New window 5 Click OK 6 Mass Chromatograms can also be generated from a spectrum display A single
402. methane Trichlorofluoromethane 1 1 Dichloroethene Methyl Tert butyl Ether Methylene Chloride 1 1 Dichloroethane 2 2 Dichloropropane Chloroform Benzene Trichloroethene Dibromomethane 1 Bromo 2 chloroethane Toluene trans 1 3 Dichloropropene 1 1 2 Trichloroethane Ethylbenzene p m Xylene o Xylene Isopropylbenzene Bromobenzene n Propylbenzene 1 3 5 trimethylbenzene sec Butylbenzene a v Type CAS number Abbreviation Maximum in blank MDL Water Soil Quantify Surrogate bd 1868 53 7 BFM 0 500 0 0500 Response Factors Minimum RRF Maximum RSD Init Cal Maximum Difference Surrogate SMC Concentration Recovery Limits Water Soil If the compound Type setting is not correct select the appropriate value from the drop down list on the right side of the dialog In the above example the Type is Surrogate Modify numeric parameter fields as required Click Modify to accept the changes for the current component but leave it selected or click Previous or Next to accept the changes and move to a new component After making all required modifications click OK to save the revised method or Cancel to abandon all changes and leave the method unchanged 277 TurboMass Software User s Guide Environmental Parameter Settings The Environmental Parameters dialog displays when you click the Environmental Parameters button in the main Quantify Method Editor window or choose the Environment
403. mple List see Creating and Editing Sample Lists on page 211 2 Create a Qualitative Method A Qualitative Method is required for most Communiqu reporting an exception is when you just report the chromatogram plot or acquisition conditions The Quantify Method is required for Calibration and Quantification curves The Qualitative method describes how a data file is processed to produce calibration curves and qualitative information Details must be entered into the method for each of the compounds being used in the analysis The Qualitative Method specifies information for performing the following tasks 339 TurboMass Software User s Guide 1 Qualitative Peak integration and Reporting parameters 2 Library Search parameters Spectrum treatment search type search options and limits molecular weight constraints and reporting parameters 3 Library Selections To create a Qualitative Method follow this procedure 1 Select Qualitative Method Editor from the Tools menu i TurboMass TUTORIALQUANT Untitled Qualitative Method Editor be The Qualitative Method Editor appears Qualitative Method Editor Untitled Dlglala 2 m a 340 Qualitative Method The General parameters are needed for all qualitative reports that require a peak data set Since Search Parameters and Library Settings are only required when a library search is to be performed the
404. mple list Errors If no Meth Blank sample was located in the rows selected for processing according to the rules given above then an error message will be displayed Form 4 Error No method blank sample identified Warnings If no rows selected for processing excluding the Meth Blank row are of sample type other than Tune Eval Init Calib or Cont Calib then a warning message will be displayed Form 4 Warning Sample list contains no sample types reported in Form 4 summary Form 5 Primary data for Form 5 will be taken from a Tune Eval sample with summary information from other samples types other than Tune Eval The default Tune Eval to be used as the primary data set will be the last Tune Eval sample row selected in the sample list 637 TurboMass Software User s Guide 638 Errors If no Tune Eval sample was located in the rows selected for processing according to the rules given above then an error message will be displayed Form 5 Error No tune evaluation sample identified Warnings If no rows selected for processing are of sample type other than Tune Eval then a warning message will be displayed Form 5 Warning Sample list contains no sample types reported in Form 5 summary If the Analysis type is Volatiles and the specified Tune Eval file references DFTPP or Analysis is Semivolatiles and Tune Eval references BFB then a warning message will be displayed Form 5 Warning Tune evaluation sample references the wrong compound
405. n dialog displays the COM port and instrument name LINK Configuration m Jal eote mote ort Confirming the LINK configuration 1 Select the LINK port for the GC For an integral Link you must select Port A 2 Select AutoSystem With or Without Autosampler or Clarus 500 With or Without Autosampler in the Instrument module drop down list according to your GC configuration 146 GC Control You must select AutoSystem With Autosampler or Clarus 500 With Autosampler if an autosampler is installed on your GC You may exclude use of the autosampler in the GC Method Editor If you make a mistake click Restart to disconnect the GC and clear the LINK port Click Reset to clear all changes and return this dialog to the state it was in before it was opened Setting the GC configuration options l In the LINK Configuration dialog click Configured next to the port selection to open the GC Configuration dialog To rename the GC to something other than its default name enter the new name in the Name field Under Options select whether or not you have PPC Programmable Pneumatic Control installed Selecting YES activates the other PPC options Under Inlets select the Injector setting that matches your GC for Channel A and or B Select the valve type for each valve in the GC The PPC split vents will be configured automatically Select PPC for detector A and or B if detectors and PPC are installed Under De
406. n is replace the currently selected trace Note that chosen B Toggles real time chromatogram update on and off Bel swi Switches between overlay and non overlay mode cy Increases the magnification of the current range cy Decreases the magnification of the current range IQ ae Deletes the current magnification range E i Resets the display to a TIC trace e Decrements the currently displayed scan in the spectrum window gt Increments the currently displayed scan in the spectrum window EJ Toggle between the previous display range and the default display range Chromatogram Customizing the Chromatogram Toolbar The Chromatogram toolbar can be customized to e Add other buttons for the operations that you use most frequently e Remove buttons you do not require e Determine the order in which the toolbar buttons are displayed Customizing the Chromatogram toolbar gt Select Customize Toolbar from the Chromatogram Display menu and add or remove buttons as appropriate Customize Toolbar Available Buttons Toolbar Buttons e Display TIC trace SJE it integrated peaks E Decrement E Display analog chromatograr S Jincrement E smooh iEMOyE E peisut range Zsubtice Separate EB Tite windows X q uu The additional buttons that can be added to the default Chromatogram toolbar are SA E Edit integrated peaks Display analog chromatograms E Smooth cs Subtract Tile windows
407. n is always enabled and valid Using the Move Up and Move Down command buttons reorders the Reports in the list Reports will be processed by report number i e in the order in the list 7 Select Save As from the Report Method Editor File menu 554 The Save Report Method As dialog appears Save Report Method As 2 x Save in Ga REN File name Qualitative Report rme Save as type Report Method Files rme 7 Cancel 4 Report Method Editor Type a File name for your Report Method for example Qualitative Report then click Save This Report Method is now available for the Report Method column of the Sample List Double click in the Report Method field and select Qualitative Method from the drop down list E TurboMass TUTORIALQUANT TutorialQuant SPL 5 x File Edit Samples Run View Quantify Configure GC Tools Help alsm a 2 gt man waa taa GC i Ryritions uantify Method oOo 1 T40 525 525d Tut02 525 525d 2 Oven Temp orc w ry Tut03 525 525d 3 A General Status GC Status p MS Operate ed Pressures Filament Ready 0 0 Shutdown Enabled No Instrument hand corner of the screen 10 Close the Report Method Editor by clicking the Close box in the upper right 555 TurboMass Software User s Guide Report Template Browser In the Report Method Editor dialog click the B
408. n tds 292 TurboMass Software User s Guide Quantify the Data cceccccccesscesscessceesceeeeeeseeeseeeseecaeecsaecaecnseceseenseenes 294 Using the Quantify Window to Examine Results eeeeseeseeeeeees 295 The Summary Window ccccccccssecssecsteceseceeceeeceeeeeeeeseneeseeeeseeesaeenaees 299 The Graphs Window ccccccccsscesseestecsteceeceseceseceeeeseeeeeseesseeeseeesaeesaees 304 The Peak List Window ecceceseeseeeeceseeseeeceseeeeeeeceaecaeeeeeeseceeeaeenees 307 Manually Changing Quantify Results 00 0 eeeceeeceseereeteceeeeeeeeeeees 311 Controlling Quantify Reports ccceecceescseceeeseeeseeeseeeseeeseeeseeneenaeees 316 Files Used During Quantify ccccccesccesecessceseceeeeseeeeeseeeseeeseeeeeensees 319 Qualitative Meth Od s iccc sccisscsessccvsosceteessonnectsossessesbestactsesvessescasessessevessseess 323 Introduction to Qualitative Processing cccceeseeesceeseeeteeeseeeseeesseenseenseens 325 Qualitative Integration and Peak Selection eceeceeseeseeeeeteeneeeeees 325 Qualitative Method Editor 00 0 0 cccccccsscecssecesscecseeeesseceeseecseeeesseeeesseeees 327 Qualitative Method Editor Toolbar cccccccccscecsscceseceessseeesseceeseeenseeees 328 Qualitative Method Editor General Tab cccccccccceseceesseceesseceseeeesseees 329 The G n ral Lab Fields t sseievisses catdeneai ods ninaa i A asr 330 Qualitative Method Editor Search Parameters Tab cceeccecsceesee
409. n the Current Settings spectrum display This gives you the opportunity to experiment before making your changes permanent 31 TurboMass Software User s Guide Click OK to exit the dialog Any TurboMass displays affected by these changes are updated The Font Editor The Font Editor allows the font font style font size color effects and script to be changed Any changes can be viewed in the Sample text To change fonts select the required colors and fonts and click OK NOTE Selecting Cancel in the Colors and Fonts Editor will disregard these changes Font x Eont Font style Size farial Regular E Cancel Arial Black Effects Sample T Strikeout T Underline AaBbYyZz Red Script Westem x To change data colors select the required colors and click OK NOTE Selecting Cancel in the Colors and Fonts Editor will disregard these changes The color editor displays 48 basic colors Data colors to 5 are used for chromatogram traces and spectra Data colors 6 to 10 are used in the Map program Data color 5 is also used to set the color of tune peaks on the Tune page 32 Getting Started To define custom colors 1 Click Define Custom Colors on the Color dialog L 2 To define the colors either drag the cross hairs a and the arrow 4 OR Enter Hue Sat Lum Red Green and Blue values until the required color appears in the Color Solid field Color IEEE H
410. nalysis Data can be acquired processed and reports printed without user intervention The whole process is controlled from the Sample List Editor which is a very important part of the Quantify system You provide a list of the samples and a Quantify method describing how to process each of the compounds within these samples Quantitative Processing for Environmental Analysis Quantitative processing for environmental analysis is an extension to the TurboMass Quantify environment The Communiqu data model is enhanced to support the additional data items required for environmental calculations It is also important to note that not all the calculations are performed by TurboMass Quantify and some calculations are specific to certain sample types Some calculations are only be performed when environmental reports are generated These exceptions will be specifically noted 249 TurboMass Software User s Guide 250 Two principal categories of calculations can be identified for both volatile VOA and semi volatile SV organic compound analyses e Matrix specific concentration calculations e QA QC calculations values associated with spiked samples TurboMass Automated Quantification an Overview There are six basic stages in automated quantification 1 Creation ofa list of samples using the Sample List Editor 2 Acquisition of each sample in the analysis 3 Integration of data file chromatograms 4 Formation of Q
411. nd button that causes the preview window to close without printing the current report Furthermore future reports from the sample list will be neither previewed nor printed A command button that closes the preview window without printing the current report However the next report generated from the sample list if any will be previewed 245 TurboMass Software User s Guide 246 Quantify 10 Quantify Introduction This section describes how to use TurboMass to perform quantitative assays Many parts of the system are used to automate the acquisition integration quantification and reporting of data The Quantify window is used to view the summary of Quantify results calibration curves and lists of integrated chromatography peaks TurboMass enables you to form Quantify calibration curves using Standard samples containing compounds of known concentrations The calibration curves can then be used to calculate the concentrations of compounds in Analyte samples For more information see Appendix C TurboMass Quantify Calculations The results of Quantify can be viewed in the Quantify Summary window Calibration curves can be viewed on the display and a number of Quantify Reports can be produced Facilities are also provided for writing Quantify information to the Windows Clipboard for use by other Windows applications The TurboMass automated quantification provides a simple way of quantifying large numbers of samples within an a
412. ndard Concentration Factor will be defined for each compound it is requirement that the standards will be prepared by serial dilution Example of usage Compound A specifies Concentration of Standards Conc A and has a Standard Concentration Factor of 1 1155 The Calibration type is Linear Fit The processed sample list includes four Standard rows for which the contents of column A are 10 20 50 and 100 The actual concentration values used in generating the calibration curve for graphic displays and for calculating the linear equation will be 11 155 22 31 55 775 and 111 55 Setting General Parameters 1 From the Quantify Method Editor dialog click General Parameters to display the General Method dialog poo o _ f Calibration Curves Type intemal relative ad Polynomial Type Linear zii Areas C Heights Point of Origin Exclude Eit Weighting 1 X pe Axis Transformation None Cancel 264 Quantify To use the General Parameters for all compounds in the method select Propagate General Parameters from the Quantify Method Editor Edit menu A check mark will appear next to this option and the general parameters will be copied to all compounds in the method Response Response parameters in the General Method dialog determine how the response value of a located peak is to be calculated The response values are used to form calibration curves for compounds f
413. ndow size parameter to the half width of the smoothing window in scans by right clicking and dragging the mouse across a chromatogram peak or by entering a value in the field Set the number of times the smooth is repeated by editing the Number of smooths parameter Increasing this parameter gives a heavier smooth Select a Smoothing method Two types of smoothing are available for chromatograms Moving Mean and Savitzky Golay Both methods slide a window along the chromatogram averaging the data points in the window to produce a point in the smoothed spectrum Moving Mean takes the arithmetical mean of the intensities of the data points in the window Savitzky Golay takes an average of the intensities weighted by a quadratic curve This tends to enhance peak and valley shapes as well as preserving the height of the peaks better than the Moving Mean However Savitzky Golay does tend to produce small artifacts on either side of the real peaks Setting peak thresholds l Click Threshold on the Integrate chromatogram dialog to open the Response Threshold dialog and examine or modify these parameters 273 TurboMass Software User s Guide i i fiso ox I Absolute height fo Cancel IV Relative area 200 I Absolute area fo 2 Set the required parameters and click OK Relative height Select if you want to remove peaks whose height is less than the specified percentage of the highest peak Absolute height Select
414. nds calibration points Quartic Performs a fourth order regression on the compounds calibration points NOTE There must be one more calibration level than the order of the curve For example a linear curve needs two points a quadratic curve needs three points and so on An Included or Forced origin counts as one calibration level 5 Select Point of Origin to Exclude Include or Force At the point of origin it is assumed that zero concentration has a response of zero If Polynomial Type is set to RF this parameter is not used Force The calibration curve will always pass through the origin Include The point of origin will be included in the calibration curve regression the curve will not usually pass through the origin Exclude The origin will be ignored when forming the calibration curve 6 Set the calibration Fit Weighting to None 1 X 1 X 2 1 Y or 1 Y 2 This parameter is used to give higher priority to calibration points with a low concentration or response when using regression to fit a calibration curve This generally results in the calibration curve being fitted closer to points at low concentrations thereby reducing the relative error at these points Normally this parameter is set to None 7 Set the Axis Transformation parameter to the required option The available options are None LN Natural Log Log Base 10 Log and Square Root The transformation is applied to the concentration and response values before
415. negative Baseline Level value to reduce the amount of noise seen and apply thresholding to 1 16th Dalton type samples This thresholding occurs after ion counting and therefore has a less significant effect If you want to see more noise use a positive value Do not use a positive Baseline Level value with lon Counting Threshold Can be set to one of three values 4 8 or 16 Selecting 8 points will allow you to acquire data twice as quickly as selecting 16 and will in continuum mode result in data files that are approximately half as big as those acquired at 16 points per Dalton Selecting 4 points will allow you to acquire data twice as quickly as selecting 8 and will result in data files that are approximately half as big as those acquired at 8 points per Dalton Acquiring data at 16 points per Dalton gives the greatest possible resolution Acquiring data at 4 points per Dalton gives data with a smoothed appearance For centroided data the type most commonly used for GC MS there are two parameters that you can set The Intensity level below which peaks detected will be ignored Typical value is 2 Should not be changed The minimum mass peak width Typical value is 10 for 16 points per Dalton Should not be changed NOTE Data is acquired according to the Profile Data criteria before it is centroided 72 Instrument Data Thresholds SIR Data SIR Used when lon Counting Threshold is not enabled set to Baseline Leve
416. ng maintenance operations on TurboMass Back Cancel X 8 Click on Finish 9 On the Add or Remove Programs dialog select Communiqu 2 3 Customer Edition and click on Remove 688 Appendix B TurboMass Software Installation F Add or Remove Programs ae 5i Currently installed programs 7 Show updates Sort by Name 7 Change or Remove Programs c aty ij Communique 2 3 Customer Edition Add New Programs E am Add Remove Windows g Dell Wireless WLAN Utility 8 Broadcom Gigabit Integrated Controller 5p C Major Audio Click here for support information To remove this program from your computer click Remove 8 Dell ResourcecD Components The following appears Add or Remove Programs p xt YD Are you sure you want to remove Communique 2 3 Customer Edition from your computer Cey e 10 Click on Yes The following appears Communique 2 3 Customer Edition A Please wait while Windows configures Communique 2 3 Customer per Edition Gathering required information Uninstall runs when complete uninstall MatLab 11 On the Add or Remove Programs dialog select MATLAB Component Runtime and click on Remove 689 TurboMass Software User s Guide 690 a Logitech Camera Driver Size 26 79MB MATLAB Component Runtime Size 75 92MB Click here For support information rarely is program or remove it From your To change th computer c
417. nges and Yes and No buttons Clicking Yes saves the data Clicking No closes the dialog and any changes to the data will be lost Displays the New Submitter dialog to enter a new Submitter After entering a new submitter Name the OK button will be enabled Each submitter name must be unique independent of case If the entered name is valid the dialog will close and a new submitter node will added to the tree If the entered name already exists an error message is displayed Displays the New Task dialog to enter a new task for a submitter 645 TurboMass Software User s Guide 646 Load Compound List Select All Unselect All Rename Delete Help Help Topics New Task Dialog Displays the Load Compound List dialog When you have selected a method the compound list is read from the Quantify method and assigned to the selected Task Initially all compounds are selected for use Puts a checkmark next to all compounds in the current compound list Removes checkmarks from all compounds in the current compound list Allows you to change the name of the selected node Ifa Task node is selected it deletes the task node and its associated data compound list and or report methods If a Submitter node is selected all Tasks associated report methods and custom compound lists for this submitter are also deleted You can recover deleted data by closing the window without saving the data Di
418. nhanced signal to noise and improved mass accuracy File V50 Function 1 Average fos2es2 Peak separation fio Cancel Subtract_ 633 646 668 702 X foo Reset Spectrum You specify three scan ranges and a background factor One range contains the scans across the peak top and the other two ranges contain scans from the background on each side of the peak The scans across the peak top are averaged together and the average of all the background scans multiplied by the background factor X is subtracted from the result Peak separation is the spectral peak width in Da For centroided data the peak width can be determined from inspection of the tune peaks on the Tune page The Combine algorithm combines peaks within a Peak separation window into a single peak Clicking Reset will remove all values that have been entered into the dialog Combining scans in a centroid mode data file 1 Display the chromatogram peak of interest in a chromatogram window 2 Select Combine from the Spectrum Process menu 3 Enter the peak top scan range either by entering scan numbers separated by a colon for example 619 626 into the Average field or by right clicking dragging the mouse across the peak 4 Optionally enter one or two background scan ranges Again you can do this either by entering scan numbers into the Subtract field or by right clicking and dragging the mouse If you enter the values each range should be in the form of two num
419. niqu and MATLAB using the Add Remove Programs function in the Windows XP Control Panel When installing TurboMass v5 2 it will automatically detect a Communiqu 1 x database from TurboMass v5 0 and export those templates to c turbomass clExportedTemplates directory After installing v5 2 you can go to that directory and import the templates Upgrading from TurboMass v5 1 will save a backup copy of your templates database We strongly recommend that you manually export all user modified templates from TurboMass to your hard drive using the Communiqu Utilities or the Communiqu Report Creator Template Designer before uninstalling TurboMass v5 0 or v5 1 After installing TurboMass v5 2 use the Communiqu Utilities or the Communiqu Report Creator to Import the templates into v5 2 All v5 0 and v5 1 TurboMass templates have been updated in v5 2 so do not import your modified templates using the same names After installing the software and rebooting the computer cool the transfer line and ion source to below 100 C then you must turn the MS power off then back on again after at least 5 seconds to ensure correct installation of the updated software into the instrument 683 TurboMass Software User s Guide Installation Summary l Uninstall the TurboMass 5 X software and all its components Install the TurboMass v5 2 software Reboot the Clarus MS Install Clarus 500 MS NIST EPA NIH Library 2002 Configure Tu
420. ns menu select the items that you want to be included in the experimental record display When an item has been selected a check mark will appear next to its name The options available for inclusion in the experimental record display are Header Tune parameters Function description and GC Information Printing a report of the Experimental Record Select Print Report from the Experimental Record File menu The currently displayed Experimental Record will be sent to the printer Deleting a Raw Data File 1 Select the data file you want to delete and click Delete A dialog will be displayed asking you to confirm that you want to delete this particular data file 2 Click Yes to delete the file History Selector The History Selector dialog allows you to access processed data If no processed data are selected raw data is the default Processes are saved to disk when you select Save spectrum from the Spectrum File menu The History Selector also allows you to delete from disk processes that are no longer required Process History Sample Function History OK Cancel Delete Delete All Getting Started History Selector GAS2 E Process History 2 Refine 1207 5 2 000 22 Sep 97 21 22 Saved 1 Smooth 0 Mn 1x3 22 Sep 97 21 22 Information Sample Unleaded gasoline Function Scan 40 300 El History Raw Data Cancel Delete Delete All Displays the full history of
421. nsity Spike Percentage Ratio Sets the intensity threshold below which spikes will be ignored Take this value from the Tune page intensities A very low intensity signal may include single ion events that can be combined to produce significant peaks For this type of data you should set the Minimum Spike Intensity to a suitable value such that these single ion events are not discarded as spikes Sets the ratio used to determine whether a data point is a spike This determination is made by comparing the data point to its immediate neighbors If the Spike Percentage Ratio is set to 30 then if at 30 of its full intensity the data point is still more intense than both its immediate neighbors it will be regarded as a spike To express this as a ratio the maximum allowed intensity ratio between a data point and its immediate neighbors is 3 1 Spike Percentage Ratio set to 50 is equivalent to a ratio of 2 1 Spike Percentage Ratio set to 20 is equivalent to a ratio of 5 1 75 TurboMass Software User s Guide 76 The following examples show the effects of changing the Baseline Level and lon Counting Threshold parameters A series of acquisitions were done using Heptacosa FC 43 PTA PFTBA and acquiring continuum data Each data file contains 18 scans The data file AB0000 is not thresholded both Baseline Level and lon Counting Threshold were set to zero This first example shows the effect of increasing the Baseline Le
422. nstrument Name a Standard Footer 1 es conuhlcrat TEXTI 3 Inlet Interface Tye S a Page Type 1 3 LabName Eg Chromatogram Plot CHROMATOGRAM PLOT 5 3 Project LJ OBJECTFRAM GRAPH HEADER 3 Project Name amp Chromatog 3 Project Directory Grmi 3 Project Date Time Txe 3 Samples i 3 Sample ID TEXT10 E 3 Concentratior TEXT11 3 Conditions TEXTS 3 Sample Desc D Peak Number a Task Desciip 3 Retention Tit 3 Sample Type 2 TAS 3 Submitter re D Acs DATAM 3 Vial Number L 3 Noim DATAd 3 Injector 3 Inject Volume 3 Process 3 Process Optic Process Para 3 Spare1 3 Spare 2 7 3 Spare 3 Spare 4 3 Spare 5 3 Job 3 UserName le Saas 4 Custom Objects Position 1 65 3 75 Width 4 4 Height 0 6 2 Move the table see above and then the Chromatogram Plot down the page to make room at the top of the Chromatogram Plot e To move the table and Chromatogram Plot move your cursor over the table e It turns into Now hold the left mouse button down and move your mouse to move the table e Next move the Chromatogram Plot the same way 567 TurboMass Software User s Guide 568 F Communiqu Report Creator 218 x Fie Edit View Format Actions Tools Help UGG s e YsoxX aan a a m a ale e olls z Qualita e Repo Re o o Page pe Chromatogra Plo Layout a Layout Tools 1 Qualitative Report 1 Data Objects El 2 Header a Global a TEXT4 35 Lab Name t 3
423. nt access to the Form tabs nor do they prevent reports being generated although there is no guarantee the results will be complete or entirely valid The following checks are made 1 Ifsample list rows selected for processing specify a sample type other than one of those listed plus Analyte a warning message will be displayed General Warning Sample list contains nonenvironmental sample types Rows a b xz NOTE The display of row numbers exhibiting the warning should be determined as described in the previous section 2 A sample list row selected for processing should not be reassigned as different sample types on different Form tabs with the exception of Tune Eval Form 5 and Cont Calib Form 7 or Form 8 which is valid For example assigning the same row as Meth Blank for Form 4 and as Tune Eval for Form 5 would cause a warning message to be displayed General Warning Sample list contains invalid multiple sample type assignments Rows a b xz 3 Ifthe injection time of any rows selected for processing is more than 12 hours after the injection time of the tune evaluation sample 633 TurboMass Software User s Guide 634 Form Specific Checks The sample list is checked when it is opened and whenever the state of any row is changed All selected rows of the sample list will be examined to identify errors or warnings If any errors related to a specific Form are identified then the title of that Form tab will be displayed in
424. nt command from the Report menu The TurboMass software then queues the selected rows of the sample list for processing for all selected reports Customized Field Display You are able to define which data columns are displayed using the Options menu item Customize Field Display dialog to appear in the sample list view both on Sample List tab and Form specific tabs where applicable The display is updated when the dialog is closed This dialog is disabled when the Form 6 tab is displayed since there are no selectable columns on this tab but enabled at all other times fea Customize Field Display v Sample ID ID Sample Type TYPE v File Name FILE_NAME v Matrix MATRIX vV Level CONC_LEVEL v Vial SAMPLE_LOCATION Canca v Quantify Method QUANT_METHOD Canca Qualitative Method QUAL_METHOD Submitter SUBMITTER Z Task TASK v Analysis TYPE_ANALYSIS Auto File AUTO_FILE Case No CASE_NUMBER Cleanup CLEANUP_DESCR Cone A CONC_A Cone B CONC_B 603 TurboMass Software User s Guide Sample List Tab The Report Generation window is displayed when the Continue button is clicked in the Select Forms dialog The Sample List tab is selected initially An additional tab will display for each of the Forms selected in the Select Forms dialog The following screen shows all forms selected d Report Generatio m Sample List Forms Options Help
425. ntrol and develop your GC method before you execute your MS method The GC Menu All GC commands are located in or are accessible from the GC menu in the TurboMass top level window and Sample List From the GC menu you set up your GC configuration develop your GC method work interactively with the GC and perform all other GC related procedures cig Tools Help Details Real Time Plot Method Editor Modify Active Hands On Retry Injection Take Control Release Control Stop Run Configure Change Acquisition Port Eror Messages The GC Status Box You can monitor the GC status from the TurboMass top level window GC Status box The GC Status box displays the GC oven temperature and the general GC status The general GC status indicates the run status or the GC operational status 141 TurboMass Software User s Guide 142 For information on GC status messages see Understanding GC Status Messages on page 185 i TurboMass 4 2 DEFAULT Default spl a jeju waa tem e a e E E E ST Fe Nave MS Method GC Method Vel Infect Semple IO Fe Tet Conetions Dele E Ae e EL 1 Pear foerat The GC Editor Toolbars and Status Bars There are two GC editors the Configuration Editor and the Method Editor Each GC editor has a toolbar with buttons that give you quick access to commonly used commands When you point to a toolbar button a tool tip will appear beneath the
426. ntrol the amount of data collected during a continuum data acquisition By default TurboMass collects one data point every 16th of a Dalton For example if you scan from mass 50 to mass 1200 you will collect and save 18 400 data points per scan As each point requires 6 bytes of disk space every scan will require 55 2 KB of disk space in this example So if you use this type of scanning in conjunction with chromatography the data file sizes will grow to be enormous In addition to the disk space issue collecting this amount of data puts a heavy demand on the transputer system which will ultimately affect the scan rates at which you can collect data The ability to use a threshold with continuum data is therefore highly desirable as it lets you disregard data that is noise yet save the complete peak profile for the real data The use of a threshold with continuum data retains the information in the data while reducing disk space requirements 71 TurboMass Software User s Guide Baseline Level Points per Dalton Centroid Data Minimum centroid height Minimum points per peak Raises or lowers the baseline to see more or less noise The Baseline Level parameter sets the baseline position above zero when lon Counting Threshold is not enabled set to zero The Baseline Level parameter is typically set to 0 If you want the baseline to appear higher increase the value of the Baseline Level parameter You can use a
427. nty No 2of2 Library Name test Name f s Text Value1 0 00 cas 0 00 0 Formula Molwt fo Delete Entty EEEE Value 2 fo 00 Flags File View Flagged 2 Select the entry that contains the data you want to enter or modify and then enter the data Name CAS Formula The compound name for the entry up to a maximum of 128 characters The Chemical Abstracts Sequence CAS number for the compound The CAS number is used to link library entries to their chemical structures in the Structures Library for display in the Structures window The CAS number has the format x yy z where x is a string of numbers for example 12398 or 6 yy is a two digit number string for example 23 or 07 z is a one digit number string for example 7 or 0 The elemental formula for the compound Elemental formulas are entered in standard format as an element symbol followed immediately by its count if greater than one and then immediately by another symbol as relevant For example consider Formula set to C6H20NCIBr2 Enter in the standard upper and lower case format Note that Cl does not need a 1 after it and that there are no spaces The specific order of elements is irrelevant Formula and Mol Wt are compared within an entry and you are warned if there is a 4 Mol Wt Text Value Flags Library discrepancy The molecular weight of the compound that is entered as an integer based
428. o re index it before you use it for searching 519 Indexing a user library 1 Select Index Library from the Library Process menu The Library Reindex dialog is displayed Hroces eating temporary mass file NG ES Elapsed Tine Elapsed Approy Hemenma lime O0000g 2 Click Start to begin the indexing process A display keeps you updated on the indexing progress and gives you an 0 Library indication of the remaining time required When indexing starts the Start button changes to the Stop button You can cancel indexing at any time by clicking Stop 3 When the indexing is complete click Close Deleting Library Entries You can only edit the text associated with a library entry you cannot edit the spectrum itself If you want to change the spectrum associated with a library entry you must delete the entry and then create a new entry by appending the correct spectrum to the library 520 Library Deleting a user library entry 1 Select Library from the Library Edit menu to open the Edit dialog 2 Select the entry to be deleted 3 Click Delete Entry and confirm the deletion 4 To view deleted entries select View to open the View dialog You see the text DELETED above the top left of the spectrum and all input fields are unavailable Restore Entry has replaced Delete Entry and can be used to restore this entry At this point the entry has been Flagged as deleted
429. o reconfigure your LINK and GC to reflect your new instrumentation see Configuring TurboMass for GC Control on page 144 Changing Your Acquisition Port You can change the serial port without reconfiguring your LINK and without opening the Configuration Editor Before starting this procedure be sure to reconnect the serial cable to the appropriate port on your PC 1 Select Release Control from the GC menu to release the GC from TurboMass control 2 Select Change Acquisition Port from the GC menu to open the PortSwitch dialog GC Control P PortSwitch x This application allows you to change the acquisition port The COM port highlighted below at startup is the one that is currently configured Simply change the COM port then click OK to change the acquisition port Gk Exit Configure acquisition port to be COM2 3 Select the appropriate port and click OK 4 Inthe GC menu select Take Control to re establish TurboMass control of the GC TurboMass changes the selected COM port and updates your configuration Configuring TurboMass without GC Control You can configure TurboMass for data reprocessing only or for use with a GC that is not under TurboMass control 1 Select Configure from the GC menu to open the Select Interface dialog 2 To configure TurboMass for data reprocessing only select None OR For data acquisition but not GC control select Contact Closure Configuring User Options From
430. o the new user library by selecting Library Get Spectrum from the Spectrum Edit menu enter the number of the library entry you want to display and click OK Fie NIST Entry 3243 Cancel Addtrace al Replace trace C New window Select Library Append from the Spectrum Edit menu The Append Spectrum dialog is displayed Append Spectrum x Append spectrum to Library LIB1 Cancel File If the current library is the one you want click OK If not click File to display the Append File Select dialog enter or select the desired library file and click OK to add the first spectrum into the new user library Library Append File Select Lookin Ey Idendb 1 elles Files of type Library 7 Ta 5 Enter a new file name for the user library and click Open 6 Click OK to add the first spectrum into the new user library Adding Text Data to the Library Entries Once you have appended a spectrum to a user library you need to edit it to add text data such as Compound Name Text CAS Number Formula and Molecular Weight You can also add two numerical User Values and User Flags for the entry These can be used to hold information about the compound These fields can then be used as library search filters Entering text data for a user library entry 1 Select Library from the Library Edit menu to display the Edit dialog 517 TurboMass Software User s Guide 518 4 Sa gt E
431. ob it may be possible to simply accept all the default compounds names offered i e the highest rated hit For this reason the software provides for a simultaneous display of the current tentatively identified compound setting for each peak in a selected sample This display also allows reviewing the final set of selections to ensure consistency e g the same compound name has not been used twice The following screen is a general layout of the Tentatively Identified Compounds dialog prior to your interaction other than selecting a file Environmental Reporting Assign Tentatively Identified Compounds Sampie D Fle Nome Assigned Nome Compound Nome MethodBionki B10040510 Carbon dioxide Butane 2 methy i 201 But nethyh BM Fentane Ethane 1 2 dichloro Nitroxide bis 1 1 cim Chliorobenzene c5 Hexone 2 Pentanone 3 met Propane 2 methyl 1 Heptone Fentane 2 4 dimeth 1 1 Disobutoxy buta 13002 Pentone 2 bromo 107 81 3 Next Peak Qualifiers IN NextName _ New Name 2 01 Butane 2 methy Raw Spectrum Parameter Description File list This list displays the files for which TICs must be identified It also displays the TIC status as Pending or Complete Sample ID The Sample ID field from the selected sample list row this can be left empty File name The raw file name for the selected sample row this cannot be left empty Status Indicates wh
432. od Report 1 Select the field you want to insert in the Available Fields list 2 Select the field before which you want to insert the new field in the Displayed Fields list and click Insert 3 Repeat steps 1 and 2 as required 4 Click OK to save the changes Removing a field from the Method Report 1 Select the field you want to remove in the Displayed Fields list 2 Click Remove To remove all the fields in the Method Report click Remove All 3 Repeat steps 1 and 2 as required 4 Click OK to save the changes 291 TurboMass Software User s Guide Formatting the display of a field in the Method Report Select the field whose display settings you want to change in either the Available Fields or Displayed Fields lists 2 Change the Header field to display the heading you want to display above this column 3 Change the Justification setting to Left Right or Center as required 4 Change the Field Width and Decimal Places as required 5 Repeat steps through 4 as required 6 To change the settings for all fields back to default values click Default 7 Click OK to save the changes Starting the Analysis gt Before starting an analysis save any changes made to the Sample List by selecting Save from the Sample List File menu NOTE The GC status must be either No Method or Run Done to successfully set up Otherwise GC communication lockups may occur Acquiring data 2 292 Select Start f
433. of mL of the original water sample used for purging from sample list Dilution Factor Dilution Factor from sample list NOTE For compounds designated as Surrogate the Concentration is calculated without including the Dilution Factor This is because in Volatile Analysis the Surrogates are added following dilution and are therefore not affected by it The equation starting from TurboMass concentration for Surrogates therefore becomes 1 Xs is the target concentration amount This is calculated based on a concentration entered for the internal standard in the Sample List Area is referenced here since it is specified by the EPA methods but the software will actually use whatever response mode area or height is specified in the Quantify Method This applies to all the environmental calculation defined in this document Appendix F Environmental Reporting Calculations Xs Concentration ug L ion ug L Vo The average relative response factor RRF is the average of the relative response factor values calculated at each calibration level Relative reponse factor Be x Ge Ais Cx where Ax Area of the characteristic ion EICP for the compound to be measured in the calibration standard Ais Area of the characteristic ion EICP for the specific internal standard in the calibration standard Cis Concentration of the internal standard in the calibration standard Cy Concentration of the compound to
434. oftware User s Guide 392 Edit Text String x 7 Border Justification Cc J Vertical Left Cancel 9 I Autosize Center IV Attach to axis Right F Text Enter the text in the Text field select desired options and click OK You can change the position of the user text by dragging it to a new position Use the handles at the sides or corners of the text box to size the box If you want to edit the text double click it to redisplay the Edit Text String dialog The font and color of the user text can be changed in the Colors and Fonts option on the TurboMass Tools menu Any changes made to fonts or colors will only apply to text added after the changes If you want to change existing text you must delete and reinsert it Other formatting options available for user text are as follows Justification Aligns text to the left right or center of the text area Border Draws a box around the user text Vertical Displays text vertically rather than horizontally Autosize Defines the text area to be just large enough to hold the user text If not selected use the handles that appear to size the text area as required Attach to If selected user text can be positioned only within a box axis defined by the intensity and time scan axes If it not selected user text can be positioned anywhere on the display The current formatting options are saved as the default options each time you exit from the Edit Text
435. ol because this occurs automatically when you start your MS data acquisition However you may need to select Take Control if you previously selected Release Control Taking control of the GC gt From the GC menu select Take Control GC Control The Details Window The Details command lets you see the GC run and interface status information The specific contents of the Details window depend upon whether you are collecting data from a Clarus detector Text appearing in blue on your screen represents information that is changing dynamically as the GC status changes Text appearing in gray represents information that does not apply to this setup Viewing detailed status and run information gt Select Details from the GC menu to open the Details window N ASXL Details Jol File View Help 2 Al IF Status Released Viewing a Real Time Plot of GC Detector Data You can view a real time plot of GC detector data for example a plot from a flame ionization detector FID 181 TurboMass Software User s Guide 182 NOTE To display the real time plot e Select Real Time Plot from the GC menu The GC method file must be available in order for the software to display the real time plot Viewing Data Acquisition Information The information that appears in the Details window is grouped into several categories Sample Information Vial Number Number of the sample as specified in the Sample List
436. ol buttons e To show the previous calibration curve 305 TurboMass Software User s Guide gt To show the next calibration curve To open a dialog where you can enter the number of the desired calibration curve Curve number is for the first compound curve number 2 the second and so on Changing the display range of the calibration curve Both the horizontal and vertical display ranges of the Graphs window can be expanded 1 Left click and drag the mouse horizontally vertically or diagonally from one end of the region of interest to the other As you drag the mouse TurboMass indicates the range you have selected When you release the mouse the selected range will be redisplayed to fill the current window Repeat this operation as often as required 2 To restore the display to the default range click E Viewing another calibration curve file 1 Select Calibration from the File menu to open the File Open dialog 2 Select a file and click Open Displaying more information about a particular calibration point 1 Select a calibration point to update the Summary and Peak List windows to display the calibration point as the current entry 2 Double click on a calibration point to display the peak list entry display the corresponding chromatogram and open the Edit Quantify Peak dialog 306 Quantify Peak Information Lox Top 11 628 a Start 11 438 2 End 11 885 lete Height 60657 De
437. om the Spectrum Display menu 2 Make any changes 3 Click OK TurboMass Software User s Guide Spectrum Peak Annotation x r Annotation Type Decimal Places io v MV Mass T Intensity Annotation Threshold Full Scale foo C Intensity pO Level Hion v Cancel _ Annotation Type Decimal Affects the precision to which mass labels are displayed Places You can select between zero and four decimal places on masses This parameter does not affect intensity labels which are always displayed as integers In general only one decimal place is significant for quadrupole GC MS data and usually none are displayed There are several types of peak labels Some are always available others are the result of a specific process All can be controlled separately by means of a set of checkboxes Mass If selected peaks in the current spectrum window will be labeled with their masses to the specified number of decimal places Intensity If selected peaks in the current spectrum window will be labeled with their intensity as an integer value Annotation Threshold checkboxes allow you to specify a minimum intensity for a peak to be labeled Full Scale Allows you to set a threshold as a percentage of the base peak intensity Intensity Allows you to set an absolute intensity threshold 442 Spectrum Level Determines the number of labels that appear on the chromatogram The level
438. ommunications protocol from the computer to the TurboMass instrument This is used only for service diagnostics purposes When done do not close the System Manager dialog Click Hide to return to the Tune page view Do not click Exit Diagnostics Select Diagnostics Page a checkmark appears in the menu in the Tune Options menu to display diagnostic information This information includes turbomolecular pump speed voltages to vacuum gauges reference voltages 5 and 0 volts and the prefilter bias reference voltage Instrument Tuning 5 Instrument Tuning The Tune Page Before acquiring data you may need to check the tuning conditions of the instrument and if necessary modify one or more of the instrument tuning parameters The instrument can be tuned either manually or automatically from the instrument Tune page The Tune page is a configurable paneled display Use the lon Mode menu to display parameters for EI electron ionization CI positive chemical ionization or CI negative chemical ionization depending on your ionization source The left side of the window contains the mass spectrometer tuning parameters TE TunePage c turbomass default pro acqudb default ipr of gt File lonMode Calibration Gas Options Help ojslala fm alles l wli 2 El Source Diagnostics Mass Span Gain GC Interface i g m2 fxn f 3 Inlet Line Temperature 5 0 Pa as k P een Pa 502 po Source Paramete
439. on VOA_Tutori VOA TiCsearchi0 9 SpikeDup2 Spike Dup _ B10040512 Water Mediu 8260b_Tutorial VOA_Tutori VOA_Tutori VOA TiCsearcht0 10 MethodBlank2 Meth Blank B10040513 Wate Mediu 82606_Tutorial VOA_Tutori VOA_Tutori VOA TlCsearcht0 11 00123 Analte B10040514 Water Mediu 8260b_Tutorial VOA_Tuton VOA_Tutori VOA TlCsearcht0 2 00124 Analyte B10040516 Water Mediu 8260b_Tutorial VOA_Tuton VOA_Tutori VOA TlCsearcht0 13 50ua L Cont Caib 810040506 ater edu 8260b_Tutorial VOA_Tutori VOA_Tutori VOA TiCsearchT0 lt gt Deactivate Q flags reporting for Form 1 M Bflag D Eflag M Jflag M Uflag J Allflage Entors Wamings for Form 1 Organics Analysis Data Sheet Qualifiers Q Flags In addition to the concentration of a compound the Form 1 also contains a column labeled Q for qualifier A qualifier provides additional information about the compound IMPORTANT If you change the quantitative results at the report generation time for example you select a different method you must reprocess otherwise the qualifier flag assignments may be invalid The EPA defined qualifiers are U This flag indicates the compound was analyzed for but not detected or below the MDL 606 Environmental Reporting NOTE For the purpose of environmental reports the term MDL is used to indicate the threshold value for the U qualifier flag Values below this threshold value will flag the compound with a U in the F
440. on Gas Options Help olsla a l mlale lt 2 El Source Diagnostics Pirani Penning GC Interface Inlet Line Temperature 799 200 M Source Parameters Electron Energy hh EE Trap Emission a0 F Bepeler Lane fos so lt Lens 2 jz 500 m F F SouceTempiC fied fa Filament Current ea Source Current 320 x men i 87 5 1 M MS Parameters LM Res 2S E HM Res EE len Ecce mm meeste i CE Muti V m e F aio 180 2050 280 3090 320 34 Press for Standby i Vacuum OK Operate Vi Figure 6 Tune Page showing instrument pressure information Displaying the Tune Page 1 Click in the MS portion of the instrument status panel in the TurboMass top level window 2 From the Tune Options menu select either Peak Editor to show peak information or Vacuum Monitor to show instrument vacuum pressure information Instrument Tuning The Tune Page Toolbar The toolbar is displayed at the top of the Tune page and allows you to perform some common operations with a single click of the appropriate Toolbar button Loads the default file Selects a data file Saves current Tune parameters to disk Prints current window in portrait format Displays Tune peak information Displays instrument vacuum pressure information Edits scope sett
441. on on the Spectrum Display menu or use the up and down arrow keys on the keyboard The spectra in each spectrum window share a common mass axis To display spectra on different mass axes you must put them in separate windows ua Spectrum 50 OO x EJ File Edit Display Process Tools Window Help l x S aa wle ula Alole o alal x SOppm Volatile Organic Analysis Calibration Standard V50 180 7 671 Scan El ia 9 4 22e4 M50 624 26 204 Scan El 91 5 56e4 89 93 85 7_98 119131 150 169181193205 219231243255 40 60 80 100 120 140 160 180 200 220 240 260 Spectrum The Spectrum Toolbar The toolbar displayed at the top of the spectrum window lets you perform some common operations with a single click of the appropriate toolbar button The default Spectrum toolbar contains the buttons listed below You can also customize the Spectrum toolbar and add additional buttons for other Spectrum operations Opens a data file Prints the current window in portrait format A Prints the current window in landscape format Sends a picture of current window to the Clipboard Copies a list of points in the spectrum to the Clipboard Pastes the contents of the Clipboard onto the display Identifies the current scan using the library search facility Toggles between processing all traces in the current window and the current trace in the current window Writes text onto a
442. or acquisition or processing could lead to invalid or misleading results Form1TIC_SV Form1TIC_VOA Form2_SV_soil Form2_SV_Water Form2_VOA Soil Form2_VOA_ Water Form3_SV_Soil Form3_ SV_Water Form3_VOA_ Soil Form3_ VOA_ Water Form4 SV Form4 VOA Form5 SV Form5 VOA PKIITIC_SV PKIITIC_VOA PKI2_SV_soil PKI2_ SV_water PKI2_VOA soil PKI2_VOA water PKI3_SV_Soil PKI3_ SV_Water PKI3_VOA Soil PKI3_ VOA_ Water PKI4 SV PKI4 VOA PKI5_SV PKIS5 VOA The following report methods can be included in a sample list Report Method column to generate reports during acquisition or reprocessing Where the report method is specific to a particular sample type the required sample type is indicated in parentheses Other specific limitations are also indicated in parentheses 640 Forml SV Form VOA Form6 SV Form6 VOA Form7 SV Form7_ VOA Form8 SV Form8 VOA ICV_SV ICV_VOA LCS SV LCS VOA PKI LCS SV PKI LCS VOA PKI6 SV PKI6 VOA PKI7 SV PKI7 VOA PKI8 SV PKI8 VOA PKIEnvQuant Environmental Reporting a valid calibration file must be specified on the sample list row a valid calibration file must be specified on the sample list row Cont Calib samples only Cont Calib samples only report method must appear only on the last row and the first row must be a Cont Calib report method must appear only on the last row and the first row must be a Cont Calib Cont Calib samples only Cont Calib samples only La
443. or Form 1 check boxes enabling you to deactivate specific Q flag reporting Any Q Flags selected will not be printed in the Q column of Form 1 for any compound The All flags selection will prevent any Q flags from being reported Message pane Shows general warnings and all form specific errors warnings NOTE The row numbers appearing for each sample on this tab and all Form tabs will be the same as those from the Sample List tab 608 NOTE Environmental Reporting Form 1 TIC Tab Tentatively Identified Compounds The Status column of the Form 1 TIC Tentatively Identified Compounds indicates whether or not the qualitative results have been reviewed and a Tentatively Identified Compound selected for each peak even if this was just an implicit acceptance of the default top hit Pending indicates that the file has not yet been fully reviewed Complete indicates that TIC selection has been completed for the file When using TurboMass to run Environmental Reports in the Qualitative Method Editor Exclude target compounds must be checked so that Form 1 TIC reports the proper results Section of the Window Description The spreadsheet displays selected information from the Sample List view Sample List Column widths can be changed in the standard way by dragging the header divider The selected columns can be changed using the Options Customize Display Message pane This is a read only display window di
444. or Injectors A and B POCO and PSSO track the oven program temperature 5 C 13 If the option is available enter an Auxiliary zone temperature GC Control Setting GC Carrier Parameters You can use the Carrier tab of the Instrument Control dialog to set carrier parameters such as the inlet pressure or flow rate for carrier gas If the GC has neither carrier nor auxiliary zone configured as a PPC Zone you can enter only the pressure and flow values for inclusion in the instrument s Ready logic You must set the actual pressure and flow rate on the GC itself Setting carrier parameters without PPC zones 1 Select the Carrier tab of the Instrument Control dialog Instrument Control 2 Enter the Pressure or flow rate for carrier A and B Enter 0 0 if you do not want the actual pressure or flow setting to prevent the instrument from becoming ready 165 TurboMass Software User s Guide 166 Setting GC Carrier Parameters with PPC Zones If the GC has either carrier or any auxiliary zones as a PPC zone you can enter information about the column program inlet split controls and auxiliary pneumatics setpoints The Carrier tab also includes a pressure flow velocity curve that reflects the values that you enter in the table beneath it You can switch among different carrier programs by selecting the program tabs at the bottom of the table The table has the following columns Rate Represents the rate at wh
445. or all windows for that peak C2H2C12 156 59 2 ETHENE 1 1 DICHLORO C2H2C12 75 35 4 PROPANOIC ACID 2 2 3 TRICHLORO C3H302C13 3278 46 4 CARBONIC ACID ETHYL 2 MERCAPTOETHYL E C5H1003S 5628 96 6 PROPANOIC ACID 2 2 3 TRICHLORO METHYL C4H502C13 4749 35 3 ETHANE 1 1 2 TRICHLORO C2H3CI3 79 00 5 FLLIQRATHINPHOSGENE S aasar TurboMass continues to search the specified library for consecutive peaks in the integrated chromatogram and prints the results of each search 419 TurboMass Software User s Guide 420 Copying to and from the Windows Clipboard The Windows Clipboard provides temporary storage for information that is being transferred between application programs word processors spreadsheets TurboMass etc You can use the Clipboard to move data into or out of the Chromatogram window either as a picture or as a text list For example you can paste spectra or chromatograms into reports written with a Windows compatible word processor TurboMass now copies a Chromatogram picture to the Clipboard as a metafile giving greatly improved resolution When the metafile is pasted into another Windows application it can be rescaled if required without distorting the original image as long as the original aspect ratio is maintained When you use the TurboMass Edit Copy Picture command both a metafile and a bitmap are copied to the Windows Clipboard Copying a chromatogram as a picture to the Clipboar
446. or enter your project name in the Project Name field Click OK For TurboMass to change to a new project it must close any TurboMass applications that are currently running If you are currently running any of the TurboMass such as Spectrum or Chromatogram a message will appear informing you that all applications will be closed Click Yes to close any open applications and change to the new project Getting Started Directory Structure When TurboMass is opened a number of default folders will be created that contain information for different parts of the application Files can be opened from and saved to any location that you specify but TurboMass will look in the default folders for the information first The following is a list of folders created in the TurboMass directory Folder Name Type of information stored in the folder IdenDB Libraries against which searches are performed Mass Spectral NIST and user defined libraries Macro Macros Peak list information for Calibration reference files Shutdown Shutdown parameters MS methods for startup before and shutdown after acquisition Library chemical structures The following table lists the folders that are created within projects Folder Name Type of information stored in the folder AcquDB Acquisition defaults and saved Tune page settings calibrations etc Inlet method files Quantify calibration curve data Raw data files 49 TurboMass Software User s Guide
447. or the match The REV Fit Threshold control will be enabled and the spectrum display will be visible NOTE Quantify does not perform background subtraction or AutoRefine during Spectral peak matching For example when using spectrum data objects in a Communiqu report template check the Spectrum Properties to make sure the Background treatment is set to None to match this behavior e When you select Multiple lon Ratio to Quantify Trace the spectrum plot is hidden The Qualifier Ion table the Tolerance and the Coelution window controls will be visible The REV Fit Threshold is enabled e When you select Multiple Ion Ratio to Base Peak the spectrum plot control is hidden The Qualifier Ion table the Tolerance Coelution window Quantify Trace Target Ratio and Tolerance controls will be visible The REV Fit Threshold is enabled e any other selection The spectrum plot will be visible and the multiple ion controls hidden but REV Fit Threshold will be disabled 11 Optionally specify the User RF Value The User RF Value is used in cases where there are no calibration standards to plot a calibration curve It represents the gradient of a curve and is used as a multiplication factor that will be applied to peak responses for the current compound to determine concentrations 12 Optionally set the User Peak Factor This value is a multiplication factor that will be applied to all calculated concentrations for the current compound If
448. or the Mass Range and Retention Time range that you wish to process These ranges can be set from Spectrum and Chromatogram respectively by right clicking and selecting the desired range To set the Mass Range parameters right click at one end of the Spectrum region of interest and drag the mouse horizontally to the other end TurboMass indicates the range you have selected The Combine Datafile Functions Input Datafile dialog will be updated to show the new mass range To set the Retention Time parameters right click at one end of the Chromatogram region of interest and drag the mouse horizontally to the other end TurboMass indicates the range you have selected The Combine Datafile Functions Input Datafile dialog will be updated to show the new retention time range Selecting an Output Data File The Output section of the Combine Datafile Functions dialog identifies the data file that will be created by Combine Functions when processing When an Input file is selected the Output file defaults to the same directory and a name based upon the Input name with an extra letter appended For example if the input file was mldata1 davlc7 raw the default output file might be mldata1 davlc7a raw When defaulting the output name TurboMass attempts to choose a name that does not already exist Changing the default output file and directory 483 TurboMass Software User s Guide 1 Click Output in the Combine Datafile Functions
449. or the first Analyte sample following the Spike Dup If no Analyte or Analyte Dup can be located an error condition exists see below If no Spike Dup was located look for the first Analyte or Analyte Dup sample preceding the Spike in the sample list If one is not found look for the first Analyte or Analyte Dup following the Spike If no Analyte or Analyte Dup can be located an error condition exists see below Environmental Reporting Errors e Ifno Spike sample was located in the rows selected for processing according to the rules given above then an error message will be displayed Form 3 Error No matrix spike sample identified e Ifno Analyte or Analyte Dup sample was located in the rows selected for processing according to the rules given above then an error message will be displayed Form 3 Error No Unspiked sample identified Warnings If no Spike Dup sample was located in the rows selected for processing according to the rules given above then a warning message will be displayed Form 3 Warning No matrix spike duplicate sample identified form will be incomplete This is a valid condition since Spike Dup samples are not always run Form 4 Primary data for Form 4 will be taken from a Meth Blank sample with summary information from samples types other than Tune Eval Init Calib or Cont Calib The default Meth Blank to be used as the primary data set will be the last Meth Blank sample row selected in the sa
450. orm I report and no concentration values will be printed J This flag indicates an estimated value This flag is used in the following circumstances e When estimating a concentration for Tentatively Identified Compounds where a 1 1 response to the total ion current of the nearest internal standard is assumed Form 1 TIC e When the mass spectral and retention time data indicate the presence of a compound that meets the volatile and semivolatile GC MS identification criteria and the result is between the compound s MDL and Reporting Limit Form 1 IMPORTANT The Reporting Threshold value will be used as the Reporting Limit for the purpose of Setting flags on Form 1 and determining what Compounds to show on the general environmental Quantitative Report PKIEnvQuant template if no Custom Compound List which includes Reporting Limits is defined N This flag indicates presumptive evidence of a compound This flag is only used for Tentatively Identified Compounds where the identification is based on a mass spectral library search It is applied to all Tentatively Identified Compounds results For generic characterization of a Tentatively Identified Compound such as chlorinated hydrocarbon the N flag is not used This flag is used when the analyte is found in the associated method blank as well as in the sample It indicates probable blank contamination and warns the data user to take appropriate action This flag is used for
451. ory The mass spectral structures library is stored in the Structdb sub directory in the TurboMass installation directory Automatic Library Search The library search application used for identifying spectra by matching them with a standard library for example NIST works on a single spectrum when started from the Spectrum display Chromatogram has an automated library search facility to automatically search a number of spectra in a chromatogram Note that while automatic library searching can work well for chromatographically well resolved peaks complex chromatograms will probably require manual background subtraction and library searching Using automatic library search in fully automated mode 1 Inthe Chromatogram window set the display range and integration threshold values to limit the integrated peaks to only those you wish to library search 2 Inthe Chromatogram window click l or select Lib Search Peaks from the Process menu 3 The Library search process performs a search for the first peak in the list and displays the Print dialog 4 To print results for all currently displayed Library windows select All Windows 5 To print results for the currently selected window select Current Window and click OK 6 All other spectra matches will also be printed out in this format Library Using automatic library search in semi automated mode 1 Inthe Chromatogram window set the display range and integration threshol
452. ouble click on the TurboMass icon and then pump down the mass spectrometer 706 Appendix B TurboMass Software Installation Installing Clarus 500 MS NIST EPA NIH Library 2002 If the NIST Library is currently installed you do not need to reinstall These instructions are provided for those who have not yet installed NIST After installing the TurboMass software you can install the NIST Library option next The NIST Library software is sold and licensed separately from the TurboMass software NOTE Always refer to the Release Notes supplied with the NIST Library for the most up to date information Installing the NIST Library 1 Insert the NIST install CD in the CD ROM drive 2 Right click Start and Explore to use MS Explorer to display the contents of the CD drive Click on Setup exe to begin the install process NIST2002 PerkinElmer precisely InstallShield Wizard NIST2002 Setup is preparing the InstallShield Wizard which will we guide you through the program setup process Please wai Checking Operating System Version _ The setup splash screen and setup screen are displayed 707 TurboMass Software User s Guide NIST2002 Welcome to the InstallShield Wizard for NIST2002 The InstallShield Wizard will install NIST 2002 on your computer To continue click Next 3 Click Next gt to continue NIST2002 all Ix License Agreement y Please read the following license agreement ca
453. ough to include the mass ranges of all the spectra or the current spectrum only Automatic If enabled the display range will return to the specified default see range default Default range and Default graph when a new spectrum is added to a spectrum window If Automatic range default is disabled the display range will remain unchanged when a new spectrum is added Displaying a Spectrum as a List You can replace the display in the current spectrum window with a list of masses and intensities of the peaks in the currently selected spectrum Select List Spectrum from the Spectrum Display menu A check mark is placed next to the List Spectrum menu item You can use most of the menu commands and the spectrum toolbar Restoring the graphical display Select List Spectrum from the Spectrum Display menu The check mark is removed from the List Spectrum menu item 436 Spectrum Printing a report of the spectrum listing 1 Select Print Report from the Spectrum File menu Spectrum Print Report x Cancel m Header Information MV Sample Description Process information IV Date printed m Peak Information IV Peak numbering I Absolute intensity Intensity relative to BPI I Intensity relative to TIC 2 Select the data range you want to display Select Data to print a listing of the whole data file Select Display to print a listing of the current display range Select the relevant Header Infor
454. ow ccccesccesscessceseceeeeeeeeeeeeeeeeeeseeeseeeseeeseeenaees 642 S bmitter Fask TiSi ieas tta aa aa aaa aa aS ias 644 Report Method Tabing a A E a need R axe 650 Custom Compounds Tab cccccccesscssseesneeeeeeeeeeecseecaecnsecnseeseeseeesnneeaes 653 Generic TIC Names Dialog ccccecccesscesceeseesseeeseecscensecnseceseeseeeeeeeseneeeaes 657 Appendix A TurboMass Security sesssesssessosssesssessseosseosseossoossosssoossoosso 659 TurboMass S Curity cotsc tessvesiecct lenveestoniscel aaa aetan ean iaae n TEES 661 Security Terminology cccccccccssecssecsseceseceeceecseeeseeeseeeeeseseseeeseeeeeesaeeaees 662 Access Rights Privileges ccccccsecsseestesseceeeeeeeeeeeeeeseeeseeeseecseeeaeenaees 662 Administrator aessa annn ameo neee Aae deze A E aest 662 A dit Log aenar a a E E AE E a y 662 GT OUP eeta a a a a a 662 GTOUP Rights aerias taa a aa aaa ade oes 662 Logon Name ig ssiazeczsdetive corsdctdateise cevnneteasbiadancevied sha sbivgn cdosdeteaneaenstevte 663 PASS W OTC orare n Sresnonsaseunyni A a T 663 ETAn o bA Oe EE EA 663 Security Mana p T irnir a a a cashes 663 OE E EE EA E E E EAE 663 User Account e e Aata aeaaea aaae aaa ataei i ia aaea 663 Username oe en a ets EA EEE E leat OE E AEs 663 Security Modelni irani anea aa ET E Erao E RE A EESE 664 Validate Username and Password ccccccccccccessessssscescscceseesssssesseees 664 TurboMass Software User s Guide Access Validation esa e a aaa
455. p Init Set Setpoint temperatures for detectors A and B Actual Current temperatures of detectors A and B 183 TurboMass Software User s Guide 184 Ready Whether or not the temperature zone is ready Carrier Pressure Flow Init Set Actual Units Ready The initial carrier setpoint for channels A and B The current actual carrier pressure flow of channels A and B Units configured for the carrier Whether or not the carrier zone is ready Detector Flow Init Set Actual Ready The setpoint detector flow two flows can be associated with each injector The current actual detector flow of detectors A and B Whether or not the detector flow zone is ready Auxiliary Pressure Flow Init Set Actual Units Ready Split Flow Init Set The initial setpoint pressure flow for auxiliary zones 1 through 4 The actual value might differ from the Init value due to timed events The current actual pressure flow of auxiliary zones through 4 Units configured for the carrier Whether or not the pressure flow is ready for the auxiliary zones The setpoint displayed as either flow or ratio depending on which mode you are using The actual value might differ from the Init value due to timed events NOTE GC Control Actual The current actual flow Ready Whether or not the split flow zone is ready Understanding GC Status Messages The status is displayed in the top level TurboMass window in
456. p Move Down 3 Report Method Editor New Report Method Generate report for every run E 1 Click the Browse button The following dialog appears Cea E All Templates PerkinElmer Accelerants Chroms v5 1 1 Six sum 2 PerkinElmer 03 18 200 Chromatogram v5 1 1 Chroma 3 PerkinElmer 04 04 200 Chromatogram Spectru v 5 1 1 Chroma 2 PerkinElmer 03 18 200 Default v5 1 1 Display 2 PerkinElmer 03 25 200 Integration Summary R v 5 1 1 Integra 9 03 28 200 Integration Summary R v5 1 1 Integr 3 03 28 200 Integration Summary R v5 1 1 Integra 2 03 28 200 Integration Summary R v5 1 1 Integr 4 03 28 200 Ton Ratio Intg Summary v 5 1 1 Integra 2 PerkinElmer 03 25 200 LibSearch 3 v5 1 1 Library 8 _ PerkinElmer 04 04 200 LibSearch Text v5 1 1 Textre 2 PerkinElmer 03 25 200 ualitative Report v5 1 1 Display 2 PerkinElmer 03 21 200 Quant Report Table v5 1 1 Option 6 PerkinElmer 04 04 200 Quant Report Table 2 v5 1 1 Table o 27 00 Quantitation Report v5 11 Sonn 4 PerkinElmer ties 04 04 200 t Report v5 1 1 chroma 2 11 11 2003 06 PerkinElmer 00 PerkinElmer 581 TurboMass Software User s Guide 2 Select your template for example Qualitative Report and click OK Qualitative Report appears as shown below 4 Report Method Editor Ne
457. p hit A single row in the list can be selected which causes the library search results from the associated qualitative file to be displayed along with predefined generic compound names list 612 Compound list Qualifiers Next Sample below file list Next Peak below peak list Next Name New Name Environmental Reporting This list view displays the top hits from the library search with a predefined generic compound list at the bottom Compound Name The names from the plot hits list plus the generic names CAS The Chemical Abstracts Service number for the compound for NIST hits only Match The Match factor for this compound as returned by the NIST library search A single row in the list can be selected which causes that compound name to be assigned to the currently selected peak and displayed in the Assigned Name column for that peak If the selected item is one of the predefined generic names and the current Qualifier string contains the N flag the N will be eliminated from the string A text box indicating the EPA qualifier codes applied to the selected peak This field is enabled when a peak is selected in the peak list and you have permission to edit qualifier codes Click this button to mark the currently selected file as Complete and select the next file in the list Click this button to select the next peak in the currently selected file If the curren
458. page 423 Setting Library Search Parameters The Library Search parameters control how many library entries are passed from the Presearch to the Mainsearch exactly which entries are used and how the results are reported Editing the Library Search parameters 1 Select Library from the TurboMass Process menu to open the Library Hits window 2 Select Parameters from the Library Edit menu to open the Library Search Parameters dialog 3 Edit your library search parameters and click OK Match By These parameters determine how many candidates or entries are passed from the Presearch to the Mainsearch Level Sets the number of matching peaks that the library entry must have to be passed to the Mainsearch You can enter a value from eight to zero matching peaks The higher the value the fewer entries are passed to the Mainsearch Library Viables Sets the number of matching peaks to the minimum number of entries to be passed from the Presearch to the Mainsearch For example if you enter a value of 8 Library first takes all entries that have eight matching peaks If the number of entries is less than the Viables value Library takes all entries that have seven matching peaks adds these to the previous entries and compares the new total to the Viables value This process is repeated until the number of entries passed to the Mainsearch is greater than or equal to the Viables value In practice the number of entries passed to the M
459. peak width at half height for the Low and High Masses being monitored Typical values are 0 6 for both but applications requiring higher mass resolution for example the environmental BFB tune or more accurate isotope ratios may need higher resolution for example 0 55 or 0 50 SIR sensitivity may be improved by selecting a number larger that 0 6 but care must be taken to avoid nearby eluting peaks with ions one m z above or below the target ion 99 TurboMass Software User s Guide 100 3 Click OK When you are satisfied with the AutoTune setup parameters click OK to exit Click Start to start AutoTune TheAutoTune status bar is updated to show the progress of AutoTune AutoTune has seven stages The AutoTune stages are listed here 1 Checking instrument conditions Attempting to detect initial beam Rough tuning focus lenses at low mass Tuning ion energy and ion repeller Tuning for good peak shape Fine tuning focus lenses at high mass Tuning multiplier for good sensitivity AutoTune checks that Tune page readbacks are within acceptable tolerance AutoTune looks for an initial beam by increasing the value of the multiplier Values of lenses are ramped to see where the low mass peak intensity maximizes Ramps values for ion energy ramp ion energy and repeller for best sensitivity consistent with lowest values for these parameters Checks peak width at half height and height of valley bet
460. ple list to be used as the source of the Form 6 header data This will default to the first checked i e selected for processing Analyte or Analyte Dup row identified as referencing the calibration file to be used as the source of the Form 6 data Form 7 compares the daily calibration check continuing calibration data against the initial calibration data of the instrument Compounds whose relative response factors or differences exceed Quantify Method defined limits are flagged Linearly or quadratically calibrated compounds are flagged if their drifts exceed Method limits Form 8 reports the retention time and area reproducibility for the internal standards for all data selected Environmental Reporting Continue This button opens the main environmental reports generation window Cancel This button closes the Generate Forms dialog NOTE Whenever you select a new sample list and click Continue the main environmental reports generation window will open with the Sample List tab selected If the sample list is the same one you had previously been working with in the current session and the Select Forms dialog was only used to change Forms selected then Continue will return to the previously selected Form tab unless this is no longer present in which case the Sample List tab will be selected 595 TurboMass Software User s Guide 596 Report Generation Window In this window you can select the Forms you want printed and
461. plies to the current TurboMass Project and the configuration file is copied to a new Project as part of the New Project Wizard functionality In TurboMass terms the Forms are a combination of single run reports and summary reports The Environmental Reporting environment automatically generates one or more temporary Sample Lists based upon the needs of each report and adds them to the Communiqu report generation queue The normal Communiqu report generation procedures can be used to produce most of the non summary Forms automatically after data acquisition Non environmental Communiqu reports e g chromatogram plots library search results quantitation plots can also be produced in the same manner The selections in the Select Forms dialog are described below Parameter Description Sample list The name of the sample list to be processed You type it in or select it from the current project only using the Browse button Browse A button when clicked displays a standard File Open dialog with the Title Select Sample List allowing you to select a stored sample list SPL file Form 1 Organics Selecting this check box indicates that Form 1 report is to Analysis Data Sheet be generated for each applicable sample in the sample list Form 1 reports the concentrations of target compounds in the sample 592 Form Tentatively Identified Compounds Form 2 SMC Surrogate Compound Recovery Form 3 Matrix
462. port Methods allows Form customization by providing a translation between the EPA Forms and Communiqu templates referenced in TurboMass report methods This translation enables the environmental report generation process which is driven from the selection by the user of the Forms to be printed to assemble the appropriate set of report methods templates automatically The Status Bar When a Custom Compound List is displayed the status bar located on the bottom of the window displays the exact origin of the Custom Compound List the Project name is displayed in the left hand segment and the Quantify Method name along with the time and date the compound list was imported is displayed in the right hand segment At all other times the status bar will be left empty 643 TurboMass Software User s Guide 644 Submitter Task List This window is displayed when the Submitter Task Data command is chosen from the Environmental Configuration submenu under the Tools menu in the main TurboMass Sample List window The following Submitter Task pane on the left side shows a Submitter and Task selected This pane is a hierarchical tree view showing clients Submitters and their projects Tasks displayed in alphabetical order The tree view can be expanded and collapsed by clicking on the or nodes next to the Submitter names Nodes can be renamed by using the right click context menu You can also associate a Custom Compoun
463. ppears as a solid line The curves for all other programs appear as dashed lines The information under Program time also changes to reflect the selected carrier values The color coded carrier time fields show how much time is required to complete the pressure flow velocity program Aux Time appears instead of the carrier time for certain instruments Oven time shows how much time is required to complete the oven program 3 Inthe Initial Setpoint field of the table set the flow pressure velocity for the start of the run 4 Ifthe program you are editing is a constant flow pressure velocity program then you can only enter an initial Setpoint value in the table 167 TurboMass Software User s Guide 9 10 11 12 168 In the Initial Hold field enter the length of time to hold at the final flow pressure velocity for this program step To hold the flow pressure velocity until the end of the temperature program enter 999 Set the Rate Setpoint and Hold values for the other ramp levels You can also change the values directly on the curve by dragging the points associated with each ramp level When you release the points after dragging the new values appear in the table e To change the rate flow pressure velocity of a level select the point that represents the setpoint and drag it horizontally e To change the setpoint value of a level select the point that represents the setpoint and drag it vertically e To
464. pped gt Click Stop in the Strip Datafile dialog Confirmation of the action will be requested 480 NOTE Strip and Combine Functions Combine Functions The Combine Functions application provides a way of combining all functions in a data file to produce a new data file containing a single function which is the sum of the multiple functions The Combine Functions option is particularly useful for combining functions acquired with CI and CI in the same chromatogram To use the Combine Functions option all the functions in the data file must have been acquired using the same scan range and scan rate or must contain the same SIR ions The Combine Functions application cannot be accessed while the Strip application is opened Likewise the Strip application cannot be accessed while the Combine Functions application is opened Creating a Combined Datafile 1 Select Combine Functions from the TurboMass top level Tools menu OR Click to open the Combine Datafile Functions dialog mm Combine Datafile Functions BBE File Help a i Process File v50 Function 1 2 To change the Input File or to select a subrange click Input Select the input file by clicking File to open a browser dialog Set the Mass and Retention Time ranges if required 481 TurboMass Software User s Guide 482 3 If the default Output file name is not correct click Output and enter the required name Click Process
465. pper trace shows the same data file after it has been processed using the Cluster option to show pairs of peaks differing in mass by 2 Da The illustration shows the spectrum of a mixture of chlorinated and non chlorinated compounds V50B Scan El TIC 100 8 36e4 26 00 27 58 N 11 89 413 35 14 14 18 23 19 61 v50 Scan El TIC 6 69e5 19 61 26 20 27 58 24 87 ra 30 3 38 14 10 15 98 47 98 34 05 36 06 Fiad 7 67 10 43 13 35 Time 5 00 10 00 15 00 20 00 25 00 30 00 35 00 Creating a CODA Data File The following describes how to create a CODA data file and provides examples 469 TurboMass Software User s Guide 470 Select CODA in the Strip Datafile dialog To change Input File click Input to open a browser dialog Note that input mass range cannot be changed and all functions are processed irrespective of function selected If the default Output File name is not correct click Output and enter the required name Select CODA Options from the Strip Options menu to set the CODA options Click Process to start processing the data file The status bar at the bottom of the Strip dialog displays the progress of the current process 30 40 38 06 44 04 44 42 7 45 10 52 38 TiC 6 4868 53 44 56 54 60 86 64 57 67 53 69 12 21 61 16 00 19 42 11 54 835 14 42 24 64 29 57 N 38 13 37 15 38 89 S17 44 04 6761 TIC 6 480
466. previous compound in the list Click this button to set the reporting limit values of the currently selected compound to the values in the Reporting limits edit box boxes Water and Soil Click this button to set the reporting limit values of the currently selected compound to the values in the Reporting limits edit box boxes Water and Soil and then selects the next compound in the list To create a Custom Compound List To create a Custom Compound List for a new Task of an existing Submitter 1 Choose Submitter Task Data from the Environmental Configuration submenu under the Tools menu in the main Sample List window is to be generated In the Submitter Task Data window select the Submitter for whom the new Task 655 TurboMass Software User s Guide 656 3 Choose New Task from the Edit menu or the context menu for the tree list which will display the New Task dialog Enter a name for the new Task and select the Quantify Method from which the compound list is to be imported The compounds are displayed and initially each one is checked Click on the check box to deselect a compound that is not required to be reported for this Submitter Task Repeat as required Select a compound for which a different reporting limit Water or Soil is required Enter the new value in the appropriate edit field below the list and click Modify to save the change or Next to save the change and select the next compound
467. priority process is acquiring data when a priority process is added to the queue the current sample will be acquired the current process will then be paused and the priority process will start acquisition When the priority process has finished acquiring data the previous process will continue If selected a check will appear next to the process To open a recently used sample list select one of the four sample lists displayed at the bottom of the File menu 29 TurboMass Software User s Guide 30 The TurboMass Desktop TurboMass uses a multiple window system that is controlled from the TurboMass top level window Each component of the system such as the Chromatogram display or the Tune page has its own window and menu bar These frames can be independently positioned and in some cases resized The different components can be linked together to allow easy data flow around the system The desktop can be automated to provide a complete turnkey custom application When you exit TurboMass the current layout is saved in the Username ini file and reopened the next time you open TurboMass Chromatogram GAS2 oR B Fie Edit Display Process Window Tools Help la x e ala wee ea eaaeo aay jele nleaded gasoline 5 45 180 10 Split 50 1 843870 973 1085 44 46 2 00 4 00 6 00 8 00 10 00 12 00 14 00 Spectrum File Edit Display Process Tools Window Help 2j alaj sloe ules ela el xaa leleii S Ill ez 93 95
468. r User Factor 1 3 Spare 1 5 Quantify Method Calibration Curve Qualitative Method Report Method User comment on analysis and or sample preparation conditions Recorded in data file header Divisor used during concentration calculation stage of Quantify Defaults to 1 if not specified Multipliers used during concentration calculation stage of Quantify Defaults to 1 if not specified General purpose fields to store extra information about the sample The selectable method from the drop down list The list is populated with mdb files from the lt Project gt METHDB directory The selectable calibration curve file from the drop down list The list is populated with cdb files from the lt Project gt CURVDB directory The selectable method from the drop down list The list is populated with qlm files from the lt Project gt METHDB directory The selectable method from the drop down list The list is populated with rme files from the lt Project gt METHDB directory 3 To change the order in which the fields are displayed select the name of the field and click or L until a field is in the required position a 4 To view field properties select a column heading and click OR Select Properties from the Field in the Samples menu to display the Field Properties dialog 234 Sample List Field ID FILE_NAME i Field name Fie Name Cancel Alignment Left X 5 To chang
469. r limit on the number of atoms of this element that may appear in the library entry If an element appears only in the Max field there is no lower limit on the number of atoms of this element that may appear in the library entry Include If selected other elements may be present in the library entry Other If not selected the library entry must contain only the Elements elements specified in the Min and Max fields Flags Specifies a range of values within which a library entry Flags parameter must lie in order for the entry to appear in the Hits List The Flags parameter is only relevant to user libraries User These are strings of one or more characters that have been flags entered in the user library Enter the required text in the User flags field The search for the User flags text is always case sensitive If Apply exact is not selected the library entry must contain the characters specified in the User flags field These characters can appear in any order in the matching library entry Apply If selected the library entry needs to contain the characters Exact specified in the User flags field in the exact order in which they are entered For example if the Flags parameter is set to Bv BpKv vKpB and KBvp will pass a nonexact search only KBvp will pass an exact search User These parameters specify a range within which a library entry Values User Value must fall in order for the entry to appear in the Hits List The User Valu
470. r mass spectrometer system refer to the User s Tutorial supplied with the mass spectrometer Starting TurboMass 1 To start TurboMass double click the TurboMass icon on the Windows desktop If TurboMass Security is enabled the TurboMass Login dialog will be displayed 2 Enter your Logon Name and Password TurboMass will start and communications with the instrument will be initialized Configuring the Inlet System 1 Select Select Inlet Interface from the Sample List Configure menu and select your interface 2 Configure your GC as described in the GC portion of the documentation Preparing the Mass Spectrometer for use Prepare the mass spectrometer for operation as described in the Hardware Guide for your mass spectrometer If in a vented state it should be pumped down Then switch it into the Operate mode Tuning the Mass Spectrometer The instrument must be tuned to obtain the best conditions for ionization according to the instructions in the Hardware Guide for your mass spectrometer 63 TurboMass Software User s Guide 64 Calibrating the Mass Scale gt The mass scale must be correctly calibrated so that the masses reported for acquired data are correct Calibration of the mass scale involves introducing a reference compounds into the system acquiring initial data and then comparing the result with the expected masses for the reference compound A calibration curve is produced and used to corr
471. r new Start and End values for the mass and time axes as required 3 Click OK Restoring the display to the default range gt Select Default from the Map Display menu Changing the Map Intensity Scaling To enhance features within the data file it may be necessary to experiment with the map intensity scaling Each mass intensity is compared to the most intense mass in the data file range that is being mapped Each mass is then mapped according to its comparative intensity to the corresponding color 535 TurboMass Software User s Guide 536 The value of Start corresponds to the intensity at which the color mapping starts and the value of End corresponds to the intensity at which the color mapping ends In the example all masses with intensities less than 20 ona logarithmic scale of the most intense mass would be shown in the first user color All masses with intensities greater than 80 on a logarithmic scale of the most intense mass would be shown in the last user color All masses with intermediate intensities would be mapped to the other user colors Changing the map intensity scaling 1 Click OR Select Scale from the Map Display menu Map Intensity Scaling x Map Intensity Range gt Start 120 00 Cancel Endi feo 00 Color Palette Moming Frost Intensity Mapping Mode flea X r Palette 2 Set the Intensity Mapping Mode The options available are Lin
472. r to environmental report generation In the Report Generation window you can select the Forms you want printed and the data set to be used as input Also the selection of Tentatively Identified Compounds TIC from the initial library search qualitative processing is made within this environment IMPORTANT If you change the quantitative results at the report generation time for example you select a different method you must reprocess otherwise the qualifier flag assignments may be invalid Report generation is a daily operation within the environmental laboratory and TurboMass Environmental Reporting is designed to streamline the process TurboMass Environmental Reporting supports e Efficient environmental report generation based upon environmental QA QC sample batches e A powerful interactive data review environment e Custom per client and per project compound lists e Automatically report only client requested compounds e Does not need a new Quantify method and Calibration curve 589 TurboMass Software User s Guide 590 e Do not need to manually delete target compounds for TIC searching and reporting Intelligent errors and warnings report of missing information during file selection Intelligent default selection of files for QA QC reports Optional reporting of J flagged compounds Easy review and selection of TIC compound name results Easy to customize reports without programming Environmental Reporting
473. ram Combine Spectra The Combine process also called spectral background subtraction can be accessed from either Chromatogram or Spectrum by clicking or by selecting Combine from the Process menu The combine process operates on centroid mode or continuum data Its purpose is to produce a single scan from all the scans across a TIC peak The combined scan exhibits enhanced signal to noise and improved mass accuracy Combine Spectrum x File V50 Function 1 Average 547 667 Peak separation 7 0 Cancel Subtract 636 647 668 669 x fi o00 Reset Specify three scan ranges and a background factor One range contains the scans across the peak top and the other two ranges contain scans from the background on each side of the peak The scans across the peak top are averaged together and the average of all the background scans multiplied by the background factor X is subtracted from the result The Peak separation parameter is the spectral peak width in Da amu For centroided data the peak width can be determined from inspection of the tune peaks on the Tune page It is typically 1 0 for GC MS data The Combine algorithm combines peaks within a Peak separation window into a single peak Clicking Reset will remove all values that have been entered into the dialog 413 TurboMass Software User s Guide Combining scans in a centroid mode data file l 414 Display the chromatogram peak of interest in a chromato
474. ram select the desired entry in the Summary window or the Peak List window entry B Chromatogram STANDRD4 _ oj x I File Edit Display Process Window Help 1 2 x AAS Se 213 14 eAlae15 S919 ells Prepared standard 50 STANDRD4 Sm 8G 2x1 SIR of 2 Channels ES i00 11 63_ 458 50 9814 6 44e4 Area T TT T TTT T T TTT T Time 10 00 10 50 11 00 11 50 12 00 12 50 13 00 13 50 Figure 9 Chromatogram showing peak used for a calibration point 311 TurboMass Software User s Guide 312 2 To display calibration standard peaks double click on the desired calibration point in the Calibration Curve window TurboMass opens the Chromatogram window with the relevant peak displayed Also the Edit Quantify Peak dialog is opened This displays detailed peak information and from which you can manually adjust the baseline Peak Information Cox Top 11 628 Ca Start 11 438 cca End 11 885 Delet Height 60657 Area 9814 010 Comment To modify the peak baseline select the handles that appear at either side of the baseline and adjust the baseline as required TurboMass will update the Peak Information displayed in the Edit Quantify Peak dialog When you are satisfied with the manual integration click OK to save the new peak integration information Optionally add a Comment to be stored in the peak list for the selected peak The comment can be include
475. rameter as described above 3 Set the below curve parameter as described above 4 Click OK 396 Chromatogram The Subtract dialog indicates the progress of the subtract algorithm After every iteration TurboMass updates the convergence value in the dialog The algorithm terminates when convergence is less than tolerance With higher order polynomials background subtract will sometimes have difficulty converging on a solution There is a preset upper limit of 300 iterations If background subtract does not seem to be making progress click Cancel in the Background Subtract dialog and try again with a lower order polynomial Smoothing Chromatograms and or Reducing Noise Smoothing improves presentation and aids interpretation of a chromatogram by increasing the apparent signal to noise ratio NOTE In some instances if your chromatogram has very small peaks you may want to turn smoothing off to accurately define the valley of overlapping peaks Two types of smoothing are available for chromatograms Moving Mean and Savitzky Golay Both methods slide a window along the chromatogram averaging the data points in the window to produce a point in the smoothed chromatogram Moving Mean takes the arithmetical mean of the intensities of the data points in the window Savitzky Golay takes an average of the intensities weighted by a quadratic curve This tends to enhance peak and valley shapes as well as preserving the height of the peaks
476. rboMass for GC control Uninstalling the TurboMass Software and all of its Components 1 684 From the Windows XP desk top click on Control Panel i Internet J My Documents Internet Explorer A iJ My Recent Documents gt E mail w Yahoo Mail a My Pictures fa Notepad a My Music e Fr My Computer nag ak e My Network Places gt Ya Snagit Studio 6 A WordPad Set Program Access and Defaults w Connect To 5 k 2 Printers and Faxes Help and Support Search All Programs gt I Run Log Off iO Shut Down The Control Panel dialog appears Appendix B TurboMass Software Installation lolx File Edit View Favorites Tools Help a Qe gt z 5S JO search gt Folders EI Address e Control Panel z Go a amp amp w G Accessibility Add Hardware Administrative Automatic G Switch to Category view Options Tools Updates P p w B See Also a Date and Time Dell Wireless Display Folder Options Fonts A Windows Update WLAN Utility 9 Help and Support m a a togtech Game Internet Keyboard Logitech Mouse Controllers Options Came amp e 8 b 2 Network Network Setup Phone and Power Options Printers and Connections Wizard Modem Faxes 4a 3 QuickTime Regionaland Scannersand Scheduled Security Language Cameras Tasks Center zj Click on Add or Remove Programs The Add or Remove Progeams dialog appears F Add or
477. rd Concentrations A to T identical with the Conc A to T values shown in the sample list spreadsheet display These concentrations levels are defined for the standard compounds in the Quantify method Sample Tracking Submitter Drop down list of the Submitters previously entered in the Submitter Task Data window Task Drop down list of the Tasks previously entered in Submitter Task Data window Optionally defines the list of compounds to be reported reporting limits and 223 TurboMass Software User s Guide 224 NOTE NOTE printouts report methods Job Text field describing the job the sample is associated with Contract Text field describing the contract under which the sample is being analyzed EPA sample No Text field defining the EPA sample number Case No Text field defining the case number SAS No Text field defining the Special Analytical Services SAS number SDG No Text field defining the Sample Delivery Group SDG number Lab Code Text field containing the laboratory code Files GC Method A drop down list enabling you to select the GC Method to be used for the analysis MS Method A drop down list enabling you to select the MS Method to be used for the analysis Quantify Method A drop down list enabling you to select the Quantify Method to be used for the analysis Calibration Curve A drop down list enabling you to select the calibration file to be used for the
478. rd if the sample is to be used to form a calibration curve Analyte if the concentration of the compounds within the samples is to be calculated QC if it is a quality control sample or Blank if the sample does not contain any analyte compounds Concentration Only required if the sample is a standard and is optional for QC samples Specifies the known concentrations of the compounds within the standard This does not apply to compounds whose concentration has been specified as being constant fixed within all samples The Sample List files are normally stored in the SAMPLEDB directory The Quantify Method MDB File The Quantify Method contains an entry for each of the compounds being analyzed determining how the data are to be processed The same method is applied to all the samples in the analysis For more information see Creating a Quantify Method on page 257 The Method files are normally stored in the METHDB directory Peak Lists PDB File A Peak List contains peaks that were detected when integrating chromatograms Further information gathered as a result of running Quantify such as compound name and concentration is also saved in the peak list Peak lists are produced as a result of running the TurboMass automated Quantify software or by the Chromatogram application One peak list should be formed for Quantify each of the samples in the analysis The peak list will have the same name as the sample from which it w
479. rea 5 0 NPKAREPER N 10 2 Normalized Quantify Mass chromatogram Integrated Peak Area 5 0 QNTRATIO N 19 9 Quantify Mass chromatogram Ratio to Largest Peak area 5 0 QNTLOWLIM N 19 9 Quantify Mass chromatogram Ratio Low Limit 5 0 QNTHIGLIM N 19 9 Quantify Mass chromatogram Ratio High Limit 5 0 QNTPERTOL N 19 9 Quantify Mass chromatogram Ratio Tolerance 5 0 QNTMLTPAS L TRUE if within the limits 5 0 IONIMASS N 10 2 Qualifier Ion 1 Mass 5 0 IONIRT N 8 3 Qualifier Ion 1 Mass Chromatogram Peak Top Retention Time 5 0 IONIAREA N 16 3 Qualifier Ion 1 Mass chromatogram Integrated Peak Area 5 0 ION1HEIGHT N12 Qualifier Ion 1 Mass chromatogram Integrated Peak Height 5 0 ION ST RT N 8 3 Qualifier Ion 1 Mass chromatogram Integrated Peak RT of Baseline Start 5 0 IONI_ EN RT N 8 3 Qualifier Ion 1 Mass chromatogram Integrated Peak RT of Baseline End 5 0 Qualifier Ion 1 Mass chromatogram Integrated Peak Height of Baseline ION1_ST_HT N12 Start 5 0 Qualifier Ion 1 Mass chromatogram Integrated Peak Height of Baseline ION EN HT N12 End 5 0 IONIRATIO N 19 9 Qualifier Ion 1 Ratio 5 0 IONILOWLIM N 19 9 Qualifier Ion 1 Ratio Low Limit 5 0 ION1HIGLIM N 19 9 Qualifier Ion 1 Ratio High Limit 5 0 745 TurboMass Software Guide 746 Version Field Name Format Description Added IONIPERTOL N 19 9 Qualifier Ion 1 Percent Tolerance 5 0
480. red The error will be displayed in the message pane on the Form tab as well as on the Sample List tab Form specific warnings will also be displayed in both places Form specific errors warnings follow General errors warning in the message pane on the Sample List A Form specific error is defined as a condition that will prevent the generation of that Form The Print command will remain disabled while such errors exist A Form specific warning is defined as a condition that does not meet the strict rules of CLP reporting but may be valid in the context of CLP like reporting Warnings do not prevent reports being generated although there is no guarantee the results will be complete or entirely valid Form 1 The sample list is checked for the existence of sample types reported on Form 1 Errors If no rows selected for processing are of sample type other than Tune Eval Init Calib or Cont Calib then an error message will be displayed Form 1 Error Sample list contains no sample types reported on Form 1 Form 1 TIC The sample list is checked for the existence of sample types reported on Form 1 TIC Errors If any rows selected for processing of sample type other than Tune Eval Init Calib or Cont Calib have no associated qualitative results saved then an error message will be displayed Form 1 TIC Error No qualitative data found for some selected samples Rows a b x z Environmental Reporting If no rows selected for pro
481. refully Press the PAGE DOWN key to see the rest of the agreement These databases and software are produced and licensed by the government of the United States of America s National Institute of Standards and Technology NIST THEY RE PROVIDED AS IS WITHOUT WARRANTY OF ANY KIND PERKINELMER INC DISCLAIMS ALL WARRANTIES EITHER EXPRESS OR IMPLIED INCLUDING THE ARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 1 The entire risk arising out of use or performance of this database and software product remains with you ha Do you accept all the terms of the preceding License Agreement If you choose No the setup will close To install NIST2002 you must accept this agreement InstallShield lt Back tio o 4 Click Yes to accept the terms of the licensing agreement and continue 708 Appendix B TurboMass Software Installation A screen indicating the install destination folder is displayed NIST2002 xi Start Copying Files Review settings before copying files Installshield A prompt next appears to install the NIST search click Yes 709 TurboMass Software User s Guide Question i xj Q Would you like to install NIST Search A warning is next displayed reminding the installer to close any open windows when the installation completes These windows are left open by the install process and will cover the final prompt to close the NIST software installation
482. rence environmental sample types e g all set to Standard an error message will be displayed General Error Sample list contains no environmental sample types 631 TurboMass Software User s Guide 632 NOTE 6 7 8 11 All sample list rows selected for processing that specify a matrix type must specify the same type or an error message will be displayed General Error Sample list contains mixed matrix types Rows a b xz All sample list rows selected for processing that specify a concentration level low med must specify the same level or an error message will be displayed General Error Sample list contains mixed matrix concentration levels Rows a b xz A sample list row selected for processing cannot be reassigned as different sample types on different Form tabs with the exception of Tune Eval Form 5 and Cont Calib Form 7 or Form 8 which is valid For example assigning the same row as Meth Blank for Form 4 and as Tune Eval for Form 5 would cause an error message to be displayed General Error Sample list contains invalid multiple sample type assignments Rows a b xz If the calibration file identified in the sample list does not exist in the Project CurveDB directory then an error message will be displayed General Error Calibration file cannot be found Rows az Selected rows other than Tune Eval or Calib types must contain values for Analysis and Matrix General Error Sample list contains sample ro
483. rence number of internal standard Pee e Found retention time of internal standard Ena compound o l pe E paea fpo o peee p e perm fpe fe freee fars FEE Modify Comment MOD_TEXT Modification description entered for last peak baseline modification Modify User MOD USER C 16 Name of user who last manually modified peak baseline This is the user login name Peak Height Height of the target compound Predicted RRT Ll Calculated relative retention time RE Predicted RT Compound retention time from Quantify Method 744 Sample CONDITIONS Sample TASK Sample Text FILE_TEXT Char 255 Char 255 Condition information from Sample List Recorded in data file header Task description from Sample List Recorded in data file header Sample text description from Sample List Recorded in data file header USER FACTOR 3 Appendix D Sample and Compound Table Output Fields Double Multipliers used during concentration calculation stage of Quantify Defaults to 1 if not specified USER_DIVISOR_1 Double Divisor used during concentration calculation stage of Quantify Defaults to 1 if not specified USER_FACTOR 1 fuseereacricor fF pee ee ee a fee User Peak RF i User RF Value set in the Quantify method Version Field Name Format Description Added PKAREAPER N 10 2 Quantify Mass chromatogram Integrated Peak A
484. reverse alphabetical order if clicked again Type A drop down list that indicates the nature of the compound Target SMC Surrogate Spike or Internal Standard 279 TurboMass Software User s Guide 280 NOTE NOTE NOTE NOTE A compound cannot be designated as an internal standard within this dialog The use of a compound as an Internal Reference within the main Quantify Method Editor window defines it as an internal standard and will cause the Int Std selection to be displayed in this control as read only CAS number An edit box specifying the Chemical Abstracts Service number for the compound Abbreviation An edit box specifying the abbreviation to be used for the compound on Forms 2 and 8 1 e this is only used for Surrogates and Int Stds Maximum in blank An edit box that indicates the maximum amount permitted 0 0000 to 9999 9999 or left empty in the method blank before a B flag will be assigned If the concentration is larger than this value a B flag will be assigned on Form 1 and Form 1 TIC B flags indicating blank contamination are not set when the compound concentration is less then the MDL If you do not wish to see the B flag you may set the Maximum in blank value equal to the Reporting Threshold MDL Water An edit box to indicate the MDL minimum detection limit for the selected compound in water samples Concentrations below this value will not be reported This
485. rface including the type model number EPROM version number memory size available in the interface in bytes and serial number On the right is a summary of the GC configuration Configuring TurboMass for GC Control The procedure used to configure the GC depends upon whether you are initially configuring TurboMass for GC control or are making changes from the GC keypad Initial GC Configuration Use to set up the LINK and GC for TurboMass control for the first time Reconfiguring the GC Use to make changes from the GC keypad or hardware changes to the GC without changing the LINK configuration Reconfiguration is also required if you add an autosampler Initial GC Configuration There are four steps to configuring TurboMass for GC control for the first time Confirm a data acquisition port Confirm the LINK configuration Set the GC configuration options Save the configuration GC Control Each step is described in a separate procedure Confirming a data acquisition port 1 Open the TurboMass application to display the TurboMass top level window 2 Select Configure from the GC menu to open the Configuration Editor 3 Inthe Configuration Editor select Configure from the Instrument menu to open the Serial port connected to the GC dialog 145 TurboMass Software User s Guide Serial port connected to GC GUM 9 4 Select the serial port and click Continue The LINK Configuratio
486. ribe how to complete each of the tabs in the Instrument Control dialog The possible tabs in the Instrument Control dialog are Autosampler Oven Inlets Carrier Valves Detectors Instrument Timed Events For a complete definition of each GC parameter refer to your GC hardware manual GC Control Setting autosampler parameters for the GC l Select the Autosampler tab of the Instrument Control dialog Instrument Control x Autosampler Oven iniets Carrier Detectors Instrument Timed Events r Injection Source A Manual Autosamplet r Sample Injection Syringe capacity pL fao z Sample pumps fe zl Iniection volume uL 10 OF Viscosity delay p x Injection speed Noma Wash waste vial set fx p Washes Pre injection solvent washes 2e H Pre injection sample washes R Post injection solvent washes A e Post injection solvent washes B es Cancel a The autosampler will be used If you are using manual injection select Manual OR If you are using an autosampler continue with Steps 3 through 9 Select the Syringe capacity for the syringe in the autosampler Select the actual Injection volume and an Injection speed Select the number of Sample pumps that you want to use This value specifies the number of times the syringe is filled and emptied before the final load If you are injecting a viscous sample set the Viscosity delay Select the Wash
487. rivileges A user cannot be directly given an access privilege The Security system performs tasks such as user account management group management and audit log maintenance and logs users in and out and verifies their access privileges TurboMass or TurboMass Security Manager area Login TurboMass Sechrity Subsystem Vv i Access Validation Audit Log Validate username and password Management Validate Username and Password The system within Security that verifies a username and password TurboMass against the existing user accounts If Security finds an account for the specified username and the password is correct the user is allowed to proceed All subsequent access requests can then be validated Any information written to the audit log contains a reference to the username Access Validation When a user attempts to enter a TurboMass or a Security Manager protected area the Access Validation subsystem determines the access rights of the groups to which the user belongs An entry is also written to the audit log to reflect the outcome of the access attempt Audit Log Management The audit log management system maintains the audit log NOTE Appendix A TurboMass Security Security Manager The Security Manager is used by an administrator to assign access privileges and set up user accounts and groups Specifically an administrator can perform the following tasks Create
488. rom standard samples and to calculate the concentration of compounds within analyte samples Set the Response Type to Internal relative or External absolute Select Internal relative if a compound s response is to be calculated using an Internal Standard in which case the Internal Ref parameters in the Quantify Method Editor must have the Internal Standard compound selected Select External absolute if compound does not have an Internal Standard the response is then taken as the absolute peak height area Select Response Areas or Heights to specify whether the responses for the compound of interest will be based upon peak heights or areas Calibration parameters in the General Method dialog determine how a compound s calibration curve is to be formed Select the type of calibration curve Average RF Linear Quadratic Cubic or Quartic from the Polynomial Type drop down list Average RF Produces a calibration which is a straight line through the origin and through the mean response factor of the calibration points A response factor is the response of a calibration point divided by its concentration This option should be selected for compounds with a fixed concentration Linear Performs a linear regression on the compounds calibration points Quadratic Performs a second order regression on the compounds calibration points 265 TurboMass Software User s Guide Cubic Performs a third order regression on the compou
489. rom the TurboMass top level Run menu OR Click gt to open the Start Sample List Run dialog Project Acquire Sample Data Auto Process Samples Auto Quantify Start Sample List Run xj r Project C TurboMass DEFAULT PRO AS IV Acquire Sample Data zh I Auto Process Samples Bre d alp T Qualitative Calculations L IV Generate Communiqu Reports I Preview Reports Run From Sample fi IoSample 4 r Quantify Qualify and Generate Reports J C After Each Run At End of Sample List r Process I Pre Run I Post Run Cancel Quantify The name of the current project appears in this field To acquire data to a different project click OK or Cancel to exit this dialog open another project and restart data acquisition Selecting this option will acquire data for the specified samples in the list See the Acquisition Help file available in the Help menu for more information on data acquisition Samples quantification at the end of the Sample List Qualitative Calculations Generate Communiqu Reports Selecting this option will automatically start sample Selecting this option will process the acquired data as specified in the Process column of the Sample List Selecting this option enables Qualitative Method Processing Selecting this option enables Communiqu report generation 293 TurboMass Software User s Guide 294 Preview Repo
490. rowse button to the right of the Template field The Report Template Browser appears x 2 All Template Template Name Description Rev Author Date Time Crea Editor Date Time Edited PerkinElmer accelerants Chroms v5 1 1 Six sum 2 PerkinElmer 08 07 2003 04 PerkinElmer 03 18 2005 06 Chromatogram v5 1 1 Chroma 3 PerkinElmer 10 14 2003 0 PerkinElmer 04 04 2005 08 Chromatogram Spectru v5 1 1 Chroma 2 PerkinElmer 08 07 2003 1 PerkinElmer 03 18 2005 07 Default v5 1 1 Display 2 PerkinElmer 10 14 2003 01 PerkinElmer 03 25 2005 12 Integration Summary R v5 1 1 Integra 9 10 19 2003 12 PerkinElmer 03 28 2005 11 Integration Summary R v5 1 1 Integr 3 10 19 2003 12 PerkinElmer 03 28 2005 06 Integration Summary R v5 1 1 Integra 2 10 19 2003 12 PerkinElmer 03 28 2005 11 Integration Summary R v5 1 1 Integr 4 10 19 2003 01 PerkinElmer 03 28 2005 11 Ton Ratio Intg Summary v5 1 1 Integra 2 PerkinElmer 08 21 2003 04 PerkinElmer 03 25 2005 10 LibSearch 3 v5 1 1 Library 8 PerkinElmer 08 07 2003 04 PerkinElmer 04 04 2005 07 LibSearch Text v5 1 1 Textre 2 PerkinElmer 09 14 2003 0 PerkinElmer 03 25 2005 12 Qualitative Report v5 1 1 Display 2 PerkinElmer 08 25 2003 0 PerkinElmer 03 21 2005 02 Quant Report Table v5 1 1 Option 6 PerkinElmer 10 07 2003 04 PerkinElmer 04 04 2005 05 Quant Report Table 2 v5 1 1 Table o 27 10 19 2003 05 Perk
491. rs Electron Energy z g aa 5 z 2190 x 5020 X o 2 2 s xj 0 0 0 0 Trap Emission Repeller Lens 1 Lens 2 Source Temp C Filament Current Source Current MS Parameters LM Res HM Res lon Energy lon Energy Ramp Multiplier V ne m maLa eee 68 0 70 0 130 0 132 5 217 6 220 0 oo 502 5 Press for Operate Standby A Vented The panel in the top right of the window can display either the tune peak information or instrument pressure information The display can be switched between tune peak information and instrument vacuum pressure information using the and toolbar buttons A toolbar displayed at the top of the Tune page allows you to perform some common operations with a single click of the appropriate toolbar button 83 TurboMass Software User s Guide 84 At the bottom right of the window is the Tune peak display You can display up to four masses to tune on The number of tune peaks displayed is controlled by the four checkboxes in the top right panel Any one of the tune peaks can be zoomed so that it occupies the entire tune peak area When a tune peak has been zoomed the controls for the mass and span for that peak are displayed at the top of the display window TunePage d data caltest12 pro acqudb default ipr BEE File lon Mode Calibrati
492. rst row The data inserted into these new rows will continue the series from the row above For example selecting the two highlighted rows in the figure on the left below and clicking Insert will result in the figure on the right o Bone 1 ld Bottle 2 ID1 Bottlel Battle2 ID3 Bottle3 5 jD Bottle3 amp jon Bottle4 ope 1 ID Bottle ID1 Bottlel 2 D 0 Bottle3 za ID11 Bottled If there is more than one number in a field only the last number is incremented when Fill Series is selected For example if the ID is Samplelrun1 when Fill Series is selected the next field will be Sample 1run2 etc The Cut Copy and Paste commands can also be used to enter data Select an area Cut or Copy the data and Paste to a new area NOTE The Paste area must be same size as the Cut or Copy area 238 Sample List Replacing data in a cell Use one of the following methods to replace data in a cell Use the mouse or the arrow keys to select the cell and enter or paste new data into the cell to replace the previous contents Use the Cut Copy Paste and other editing commands or right click to display the following pop up menu Open Cut Copy Paste Delete Contents Add Insert Clear Selected Propertie Renove Eolumr Customize Display Double click on a cell and select an entry from a drop down list displayed For Sample Type select one of the displayed options
493. rts Check this box to specify that the Communiqu reports generated during processing will be displayed in a preview window prior to printing or saved to a file or database The options above allow you to acquire and immediately process and quantify data as desired Or you may choose to process or quantify data at a later time Run From Sample Sets the range of samples in the sample list that will be To Sample acquired and or analyzed If you highlight a range of rows before starting the analysis the first and last rows of the highlighted region will be displayed here Quantify Qualify and Generate Reports After Each Run This indicates specified processing will occur after each row in the sample List At End of Sample Indicates specified processing will occur only after the Sample List List is complete Process Pre Run Specify the name of the process that will be run before the acquisition of files in the Sample List Post Run Specify the name of the process that will be run after the acquisition of files in the Sample List Quantify the Data To quantify data after it has been acquired select Process Samples in the Sample List Quantify menu 2 Select the options required and click OK to start the analysis NOTE Quantify Project C TurboMass QUANTIFY PRO Quantify From Sample hn ToSample 3 B v il eee al Sameiet Method TutorialQuant Browse R I Print Quantify Reports Curve Tutor
494. rum by dividing the mass axis into segments then arranging the segments vertically For example if a spectrum from 40 to 340 amu is on display and you select 3 from Split Axis the display will show three axes one from 40 to 140 amu one from 140 to 240 amu and one from 240 to 340 amu 440 TurboMass Software User s Guide 441 Overlay Step Grid Header The Overlay Step X and Overlay Step Y parameters are enabled when Overlay Graphs is selected Overlay Step allows you to offset each subsequent spectrum trace by a percentage of the corresponding axis which can make it easier to examine overlaid traces Entering a value in the X field will offset each new trace horizontally Entering a value in the Y field will offset each new trace vertically Entering values in both will offset each new trace diagonally Allows you to fit a grid to the Spectrum display The pattern of the lines that make up the grid can be chosen as Dot Dash or Solid Clicking Header displays the Header Editor which allows you to edit the header information displayed at the top of the window Controlling the Appearance of Peak Labels Each spectrum window has its own set of Peak Annotation parameters that determine the appearance of peak labels You can inspect and change the parameters for the current spectrum window from the Spectrum Peak Annotation dialog Changing the peak annotation parameters 1 Select Peak Annotation fr
495. run sequentially 352 Data Acquisition 7 The sample in the Sample List that is currently being acquired will have a green next to it NOTE Filenames in a Sample List must not be duplicated and Sample List names in a queue must not be repeated Process The Process parameters allow you run processes before and after the Sample List Pre Run Specify the name of a process that will be run before acquisition of the files in the sample list Post Run Specify the name of a process that will be run after acquisition of the files in the sample list for example to switch the instrument out of the operate mode and to turn off various gases If you want to run a process after each sample in the sample list has been acquired format the Sample List to display Process and enter the name of the process to be run for each of the samples If you want the process to automatically operate on the data file that has just been acquired select Options from the Sample List Tools menu then deselect the Use Acquired File as Default parameter on the System tab Automated Analysis of Sample List 1 Select Process Samples from the Quantify menu to display the Quantify Samples dialog 2 Select the checkboxes required and click OK E r I Calibrate Standards p Quantify From Sample Ho ToSample 3 z v i AST aas a a K lauari areis Method TutorialQuant Browse 72 I Print Quantity Reports Curve TutorialQuant Browse Cancel
496. running the Oven temperature and status information e The MS panel below the GC pane displays the status of the mass spectrometer e The currently selected Sample List appears in the main pane e An Index of acquisitions queued on the mass spectrometer and the status of each appears on the lower portion of the screen E TurboMass Tutorial Default SPL File Edit Samples Run View Quantity Configure GC Tools Help alem a gt s n waa taae 2 e a ea 212 E sz a FileName MS Method GCMethod Vial injector Sample ID File Text I A Pead DEFAULT Defaut 1 A mm Conditions Index ID Description Status Not Scanning 00 Shutdown Enabled Ui 27 TurboMass Software User s Guide 28 The TurboMass Toolbar The TurboMass toolbar includes buttons that allow you to quickly access a variety of common tasks and options To see the function of a particular button roll the mouse pointer over the icon to display a pop up definition For example to access Chromatogram from the toolbar click a Accessing Menu Commands All TurboMass menu commands are accessible by the mouse or keyboard commands according to standard Windows conventions For example to select the Chromatogram Using the mouse From the TurboMass View menu select Chromatogram to open the Chromatogram application Using the keyboard Each top level menu will have one underlined letter the key
497. rward Fit value The Reverse Fit value shows how likely it is that the search spectrum contains the library entry In this case the search spectrum may be a mixture of compounds Any peaks present in the library spectrum but not present in the search spectrum decrease the Reverse Fit value However peaks that are present in the search spectrum but not present in the Library spectrum have no effect on the Reverse Fit value An Overview of Library Searching This section lists the steps in a library search Each step is described later in this chapter 1 Select the library or libraries that you want to search by selecting Search List from the Library File menu 2 Select the search spectrum scan from the Spectrum or Library windows e To select a scan from a new data file from within Library click or select Open from the Library File menu to open the Library Data Browser OR e To select a new scan from the current data file click or select Spectrum from the Library Display menu 3 Edit the Library search parameters by selecting Parameters from the Library Edit menu 490 NOTE Library 4 Apply any search filters by selecting Filters from the Library Edit menu 5 Initiate the Library search from Library or Spectrum by clicking OR Selecting Search from the Library Process menu 6 Adjust the Library display by selecting View from the Library Display menu 7 Format the Hit List window by selecting Format List fro
498. ry sample ii 100 Sample solid wt of sample 100 Moisture Vt Ve Moisture x wt of sample x 1000uL mL where Moisture The Moisture value from the sample list expressed as a fraction i e Moisture 100 Vi Total volume of methanol plus water in the sample container for analysis Ve Total extract volume usually assumed to be only the volume of methanol This adjusted value for Vt will then be used in the equation shown in section Soil Sediment Samples Medium Level in place of the nominal extract volume Appendix F Environmental Reporting Calculations Semi Volatile Organic Compound Analysis Water Samples Concentration ug L where Ax Ais ls Vo Vi Vi RRF GPC Df _ Ax Is Vi D GPC Xs Vt Di GPC Ais RRF Vo Vi where Xs is TurboMass concentration Vo Vi Area of the characteristic ion for the compound to be measured from integration results Area of the characteristic ion for the internal standard from integration results Amount of internal standard injected in nanograms ng from appropriate Concentration column of the sample list as defined in the Quantify Method Volume of water extracted in milliliters mL Sample Vol from sample list Volume of extract injected in microliters uL Injection Volume from sample list Volume of the concentrated extract in microliters uL Concentrated Extract Volume
499. s 56 then there should be 56 entries after Data 1 On the Sample List page select Import Worksheet from the File menu The Worksheet Names dialog appears 2 Click the drop down button next to Look in and search for the directory containing your files 3 When you find your desired file click open We have provided a sample worksheet for import Templates _LIMS import txt in the C TurboMass TutorialReports pro SampleDB directory If an error occurs during generation of the sample list rows read from the text file that were valid will be added to the sample list and an error message will be displayed indicating the error Further processing of the text file will stop at the occurrence of an error NOTE Sample List Possible errors and the displayed messages include e First line of text file does not contain column names The first line of the import file must list the columns to be used e Invalid name included on first line The first line of the import file contains an invalid column name lt the invalid name gt e Incorrect number of data items on a line Incorrect number of items on line lt line number gt e Invalid data type Invalid data type on line lt line number gt lt column name gt lt required data type gt Copying a spreadsheet into the Sample List To copy a spreadsheet created in another application into the Sample List 1 Click OR Select New from
500. s Explorer and the TurboMass Chromatogram or Spectrum application and arrange the windows so that both are visible 2 Select the TurboMass data files you want to view in the right side of the Explorer window 3 Select more than one file by holding down the CTRL key while you click the files 4 Drag the files into the Chromatogram or Spectrum window The Chromatogram or Spectrum window will be redisplayed showing the first function in each data file as a separate trace 45 TurboMass Software User s Guide Y Exploring Data olx File Edit View Tools Help ada S al slee xe 2 All Folders Contents of Data Ey Data C Pest03 raw E 588 raw P Standrdl raw Stan aw E Standrd2 raw E Standrd3 raw E Standrd4 raw E Standrd5 raw AmI3 raw Betalac raw E DatOraw E Di2raw E Hin raw EA haraa p E 4 object s selected A Deleting multiple data files 1 Open Windows Explorer 2 Select the TurboMass data folders you want to delete in the right side of the Explorer window 3 Select more than one folder by holding down the CTRL key while you click the folders OR Select a block of folders by clicking the first folder in the block and then holding down the SHIFT key while you click the last folder in the block 4 Press DELETE You will be prompted to confirm that you want to remove the folder and move its contents to the Recycle Bin 5 Click Yes to
501. s a data source for qualitative reports and or used as input to the automatic library search The first step will always be carried out if a qualitative method is specified in the Sample List The output of this process is a collection of peak data which can be made available to Communiqu as a data source for qualitative reports and or used as input to the automatic library search Qualitative Integration and Peak Selection Only the number of peaks specified by the Report largest n peaks parameter in the Qualitative Method will be included in the data source The steps in the processing are 1 Integrate each chromatogram The specified trace TIC or mass will be extracted from the specified acquisition 325 TurboMass Software User s Guide 326 function Peak detection and integration are carried out in the manner it is done in the TM Chromatograms environment Threshold values will be taken from the Qualitative method Integration is made with Smooth off Peak detect Join 30 Reduce 50 Raise 5 Draw vertical 90 detect shoulders off Calculate Area and Norm values for each peak These values are calculated for each chromatogram separately The peak data set associated with a specific chromatogram is supplied via the AddData function to any Qualitative Plot control plotting that chromatogram Combine the peaks from all chromatograms and sort the peaks in retention time order o Ifmore than one peak ma
502. s below blank This password will be required to gain administrative access to both TurboMass and the Security Manager Password Setup Password l Confirm Password You can either create a password here or leave both boxes blank for no password NOTE Jf the password is forgotten the software will have to be reinstalled Remember your password 9 Click OK to continue the installation TurboMass starts installing Setup Installing TurboMass VYer5 2 0 Installing C TurboMass EpcasSystem linemanager pdb ee 10 The NET Framework also starts to setup Microsoft NET Framework 1 1 Setup CY Extracting netfx msi CETTE ET 11 Click OK and the following appears 696 Appendix B TurboMass Software Installation Microsoft NET Framework 1 1 Service Pack 1 KB867460 License Agreement El View EULA for printing SUPPLEMENTAL END USER LICENSE AGREEMENT SOFTWARE UPDATE FOR MICROSOFT WINDOWS OPERATING SYSTEM SOFTWARE PLEASE READ THIS SUPPLEMENTAL END USER LICENSE AGREEMENT SUPPLEMENTAL EULA CAREFULLY BY INSTALLING OR USING THE SOFTWARE THAT ACCOMPANIES THIS SUPPLEMENTAL EULA YOU AGREE TO THE TERMS OF THIS SUPPLEMENTAL EULA IF YOU DO NOT AGREE DO NOT INSTALL OR USE THE SOFTWARE 1 Rannenl Please read the rights and restrictions described in the End User License Agreement EULA To acceptthe terms of this EULA click I accept To decline the terms of this EULA click I declin
503. s column for that row and eliminates Header from any other row Inactive rows displayed in gray cannot be selected 617 TurboMass Software User s Guide Form 3 Tab Matrix Spike Matrix Duplicate Recovery When you select Form 3 Matrix Spike Matrix Duplicate Recovery from the Select Forms dialog the Report Generation Window Form 3 Tab appears Report Generation Sample List Forms Options Help Sample List Form1 Form1TIC Form2 Form3 Status Sample ID Sample Type File Name Matrix Level Vial Quantify Method Submitter Qualitative M 1 ae une Eval 810040501 8260b_Tutorial OA_Tutor T OA TICsearch10 nit Calib nit Calib nit Calib On Init Calib MethodBlan Meth Blank B10040510 A 8260b_Tutorial 7 DA_Tutori VO TIC Spike SpikeDupt Spike B10040511 8260b_Tutorial VOA_Tuton VOA_Tutori TiCsearch10 Spike Dup SpikeDup2 Spike Dup 810040512 8260b_Tutorial VOA_Tuton VOA_Tuton TiCsearch10 MethodBlank2 Meth Blank 61004051 dediu 8260b_Tutorial OA_Tutor OA_Tutori VO TiCsearch10 Analyte 00123 Analyte B10040514 8260b_Tutorial VOA_Tutori VOA_Tutori TiCsearch10 00124 e B10040516 Wate dedi 8260 VOA_Tutori VOA_Tutori VOA TIC 50ug L alib B10040506 Wate dedi 8 VOA_Tutori VOA TIC j l rit Calib 3 6 Mediu l l l l Errors wamings for Form 3 Matrix Spike Matrix Spike Duplicate Recovery Section of the W
504. s for each compound or for all compounds within the method The facility to set different integration parameters for different compounds can be useful where peak characteristics such as peak width or shape vary between different compounds For more detailed information on integration see Processing Chromatograms on page 393 Small peaks may optionally be removed by setting one of the four available threshold parameters Relative height Absolute height Relative area and Absolute area Setting quantify method peak integration parameters 1 To use the same integration parameters for all compounds in the method select Propagate Integration Parameters from the Quantify Method Editor Edit menu A check mark will appear next to this option and the integration parameters will be copied to all compounds in the method By default integration will take place over the chromatogram range defined by the Time Window parameter in the Quantify Method 2 Ifyou want to integrate over a larger window select Integrate Window from the Quantify Method Editor Edit menu to open the Integration Window dialog and specify a multiplication factor This factor will be applied to the location window to calculate the integration window and is the same for all compounds in the method Integration Window x Factor applied to location window to Lood calculate integration window Cancel 3 To define the integration parameters click Integrate Param
505. s general warnings and all form specific errors warnings Row Colors Form uses the primary data color see Row Colors for the continuing calibration Cont Calib sample Any Tune Eval Init Calib or additional Cont Calib rows will be shown in the disregard color since they are not included in Form 8 Status Column The Status column indicates which row is currently flagged as the continuing calibration sample This may be used to distinguish between several Cont Calib rows in the sample list only one can be treated as the primary data set for Form 8 or to flag a row of another Sample Type as being the continuing calibration sample Reassign Sample Type The software allows the Method Blank assignments to be altered without going back to the Sample List Context Menu 629 TurboMass Software User s Guide A pop up menu appears when you right click on a row in the Form 8 sample list view pane Assign Mid Level Standard Assigns the selected row as the Mid Level Standard labeled as type Cont Calib sample for Form 8 Displays Cont Calib in the Status column for that row and displays the row in the primary data color 630 Environmental Reporting Error Messages and Warnings The list of samples in Environmental Reports is checked when it is opened and whenever the rows are added or the state of any row is changed All selected rows of the sample list are examined to identify errors or warnings If any errors are identi
506. s not found The options available are Blank Zero Dash Not found or n a Repeat steps 1 through 5 as required To change the settings for all fields back to default values click Default Click OK to save the changes and update the Summary window Quantify Reviewing Target Compound Data Interactive Data Review To review target compound data 1 Open the Quantify window by choosing the View Results command from the Quantify menu 2 With the Summary window by Sample displayed double click on a peak to view the chromatogram spectra and qualifier ion plots associated with that peak Quantify File Edit Display Process Window Help aa aaa S Summary StdMixFSratio StdMixFSratio DER 2 Graphs staiixtSratioy papile 3 Stalix53 Semple ID Std Mix 5 0 ppa Standard Text Mix HCB Int Std 5 0 ppm ompound 5 name Dodecane Correlation coefficient r 0 999715 r 2 0 999430 Calibration curve 26 7991 x 0 335145 Response type Internal Std Ref 7 Area IS Conc IS Area urve type Linear Origin Exclude Weighting Null Axis trans None 134 Area Height ng uL Response 0 335 ng ul 00 05 10 15 20 25 30 35 40 45 50 Z Chromatogram StdMix53 aa JF lon Ratio Data SJAJE at cs E le ees Standard Text Mix HCB Int Std 5 0 ppm Stamix53 Scan El 100 7 27 727373 Dodecane 57 4 29e7 Background Subtracted Spectrum Area StaMix53 674 7 267 Cm 673 675 66
507. sample is displayed as one row in the Sample List The Sample List Editor is part of the TurboMass top level menu You need to tell TurboMass everything that it needs to know about the samples in the list in order for it to perform a complete analysis You must describe to the system what each of the vials in the autosampler contains that is whether it contains a standard an analyte a blank or a QC sample how to acquire it it and its concentration s if it is a standard In addition you must specify the name of the file in which to store the data You may also want to add some management information such as Sample ID the submitter s name or a sample description For information on how to create a Sample List see page 205 Projects TurboMass gives you the option to organize your work into projects Projects are a very useful way of organizing all of the data files methods and results for a particular assay into one directory structure on disk When you open a TurboMass project TurboMass creates a new directory to hold all the different files associated with this project The advantage of using projects is that it becomes very simple to archive everything associated with your assay because you do not have to hunt around the disk to find the files you need and the chances of you forgetting to save an important file are greatly reduced You can save the following types of files in a TurboMass Project e Raw data files Quantify
508. se have been placed on secondary tabs Specify the chromatographic data sets which are to be subject to peak detection and integration The options are The full chromatogram From start To end OR One to four segments Windows 1 4 with specified start and end times NOTE Enter the peak integration parameters in the same manner as you have done in Chromatogram or Quantify 3 Enter a From value A blank cell indicates the chromatogram segment will start from the beginning of the data The From value must be less than the To value unless either is blank Enter a To value A blank cell indicates the chromatogram segment will end at the end of the data The To value must be greater than the From value unless either is blank Enter a Relative height threshold Rel Ht of the peak in the chromatogram default is 0 Enter an Absolute height threshold Abs Ht of the peak in the chromatogram default is 0 Enter a Relative area threshold Rel Area of the peak in the chromatogram default is 0 0 Enter an Absolute area threshold Abs Area of the peak in the chromatogram default is 0 0 Enter a mass m z or mass function Func for the segment enter TIC a selected ion or a valid mass chromatogram equation 341 TurboMass Software User s Guide 10 11 12 13 14 342 Enter the Peak to peak Noise amplitude value for integration Select the X Axis units Time min or Scan Time Selects
509. seenseeneenaeens 738 Curve Correlation Coefficient cccccecccessceesceseeeeessecseeneceseenseenes 739 interna RANE EE A sack vaau scs sev A stars N A 739 Appendix D Sample and Compound Table Output Fields 741 Contents Compound and Sample Report Output Fields cc ceecescceeseeereeeteeseeeees 743 Appendix E LIMS Import File Example cccccsscsssssssssssscssssseeees 749 Example of a Sample List Import File cc ccccccsceesceesceeseesteenteenteeeeeees 751 Appendix F Environmental Reporting Calculations ssceseeee 753 About the Calculations ssia era onaren iaer aniei a ASE 755 Volatile Organic Compound AnalySis ccccccceesseeseesecseesecnteeeteeneeees 756 Water Samp lesere a a aa a ae an Ea aa aa a 756 Soil Sediment Samples Low Level ccccesccesseeeseeeseesneeeteeeteeeseeseeensees 758 Soil Sediment Samples Medium Level ccccccsceeseenseeteeeteeeseeseensees 759 Semi Volatile Organic Compound Analysis Water Samples 06 761 Soil Sediment Samples aieea seveviag e does codsnwactter geetet saves 762 WIND TEE E EAEE E EE E E E E 763 TurboMass Software User s Guide Introduction 1 Introduction Compatability This software can be used with the TurboMass Gold or Clarus 500 Mass Spectrometer and the AutoSystem XL GC or Clarus 500 GC In this Software User s Guide we have used GC to indicate Clarus 500 GC or AutoSystem XL GC and MS or mass spectromet
510. select the desired column headings in the Peak List window 308 Format DB List Quantify i Cancel Update Justification Append sett Hemaye Remove All Fields list type I Brief list Normal list Full list Appending new fields to the Peak List window Select the field you want to append from the Fields list 2 Click Append Repeat steps 1 and 2 as required 4 Click OK to update the Peak List window Inserting new fields in the Peak List window 4 5 Select the field you want to insert from the Fields list Select the field before which you want to insert the new field in the Format list Click Insert Repeat steps 1 to 3 as required Click OK to update the Peak List window Removing a field from the Peak List window 1 2 Select the field you want to remove from the Format list Click Remove 309 TurboMass Software User s Guide To remove all the fields in the Peak List window click Remove All 3 Repeat steps 1 and 2 as required 4 Click OK to update the Peak List window Formatting the display of a field in the Peak List window 6 Select the field whose display settings you want to change in either the Fields or Format list Click Justification to open the List Field Justification dialog List Field Justification Caneel Field Name Height hai r Field Size Justification Width E Left SF C Centre
511. select your Qualitative Method l E TurboMass TUTORIALQUANT TutorialQuant SPL fl pen Temp General Status GC Status sll 4 Start the Analysis Before starting an analysis save any changes made to the Sample List by selecting Save or Save As from the Sample List File menu To begin acquiring data or perform post run reporting 1 Choose Start from the TurboMass top level Rum menu OR Choose gt to open the Start Sample List Run dialog box The Start Sample List Run dialog appears 345 TurboMass Software User s Guide 346 Start Sample List Run x Project Autos TUTORALOUANT PRD 5 IV Auto Quantify Samples ap I Qualitative Calculations es Wd IV Generate Communiqu Reports I Preview Reports gt Run From Sample fi To Sample 3 m Quantify Qualify and Generate Reports After Each Run At End of Sample List m Process I Pre Run I Post Run Cancel 2 Enter values or check boxes in this dialog The order in this dialog indicated the order of execution For Example you Acquire Sample Data then Auto Process Samples Auto Quantify Samples perform Qualitative Calculations and Generate Communiqu Reports Project The name of the current project appears in this text box To acquire data to a different project choose OK or Cancel exit this dialog box open another project and restart data acquisition Acquire Sample Data
512. size iq Noise threshold E Cancel Enter values for Window Size and Noise Threshold Window Size is the half width in number of scans at the baseline of the TIC peak of interest For the first run set Noise Threshold to zero to show all peaks and choose OK If the noise level in the refined spectrum is unacceptable repeat the Refine operation with a higher Noise threshold setting Values in the 0 10 range are recommended OR e Refine the current spectrum using the current Refine parameters by choosing from the Library toolbar Library Auto Refine gt To automatically use the refine parameters in all searches select Auto Refine from the library Process menu A check mark appears next to the item if it is selected To turn this option off select it from the menu again It is especially useful with automatic library searching from Chromatogram Using the Library Compare Process The Compare process allows you to compare the search spectrum to a particular library entry This can be useful if you have an idea of what the compound is or what type of compound it is particularly if the compound in question does not appear in the top 20 hit list Comparing the search spectrum to a library entry 1 Select Compare from the Library Process menu Library NIST Entry No Cancel File 2 Enter the number of the entry to which you want to compare the search spectrum You can access a different library by clicking File and c
513. splay the Account Policy dialog Account Policy Password Restrictions a z Permit Blank Password Cancel C AtLeast f Characters IV Maintain individual user settings within TurboMass I Disable TurboMass Security 2 Specify account policy by editing the following parameters Permit Blank Password At Least X Characters Maintain individual user settings within TurboMass Disable TurboMass Security Creates or modifies a user account to have no password Specifies the minimum number of characters that passwords must contain This parameter applies to new user accounts or to modified user accounts Allows TurboMass to maintain its settings parameter values window positions on a per user basis If this option is not selected any changes made within TurboMass affect all users Disables the Security application If Security is disabled no login prompt is displayed and all users are logged on with the Administrator 669 TurboMass Software User s Guide username and with full administrative privileges In order to disable Security you must have administrative privileges and you must exit TurboMass Creating a User Account There are two ways to create a user account e Enter the new user information into a new user account e Copy an exiting user account edit the policy options and save the account under a new user name Creating a user account 1 Select New Us
514. splay the Edit Text String dialog The font and color of the user text can be changed in the Colors and Fonts option on the TurboMass Tools menu Any changes made to fonts or colors will only apply to text added after the changes If you want to change existing text you must delete and reinsert it Other formatting options available for user text are as follows Justification Text can be aligned to the left right or center of the text area Border If selected draws a box around the user text Vertical If selected displays text vertically rather than horizontally Autosize If selected causes the text area to be initially defined just large enough to hold the user text If not selected two boxes will appear on the display You must select one of them and drag until text area is the required size Attach to If selected text can only be positioned within a box defined by Axis the intensity and time scan axes If not selected text can be positioned anywhere on the display 445 TurboMass Software User s Guide 446 Processing Spectra The following procedures describe how to manipulate processed spectra data Saving and Recalling Processed Spectra The spectra resulting from any spectral processing can be saved with the raw data Saving a processed spectrum 1 Select the processed spectrum in the Spectrum window and select Save Spectrum from the Spectrum File menu The Spectrum Save dialog will be displayed giving a br
515. splaying messages Shows general warnings and all form specific errors warnings As for Form 1 the Form 1 TIC display shows all rows other than Tune Eval and calibration rows in the primary data color see Row Colors which indicates that a separate report will be generated for each row Context Menu A pop up menu appears when you right click on the Form 1 TIC row with the following item 609 TurboMass Software User s Guide 610 Assign Tentatively Identified Compounds This opens the Tentatively Identified Compounds dialog which allows you to match peaks with compound names About Tentatively Identified Compounds This dialog displays when you choose the Assign Tentatively Identified Compounds command from the Forms menu or the context menu on the Form 1 TIC tab In this dialog you review the hits for the set of unidentified peaks from each sample run excluding tune evaluation and calibration samples and assign a compound name to each peak In addition to the specific compound names supplied from the NIST library search you have access to a set of generic terms such as unknown alkane unknown aromatic created previously by an administrator A typical session of assigning TICs might involve selecting names to be applied to each of 10 to 20 peaks from 20 or more samples This list of TICs must be previously generated in the Sample List window using a qualitative method If the NIST library search has done a good j
516. splays the Help topics for this window This dialog displays when New Task is chosen from the Edit menu in the Submitter Task Data window Parameter Name Load compound list from Quantify Method Description An edit box in which you can enter a name of up to 50 characters for the new task Each task name must be unique for that submitter independent of case A drop down list from which you can select the Quantify Method to be used as the source of the compound list Browse OK Cancel Environmental Reporting Click this button to open a file selector dialog from which you can select a Quantify method from any project Each task name must be unique for that submitter independent of case If the entered name is valid the dialog closes and a new task node is added to the tree under the current submitter If the entered name already exists an error message will be displayed Closes the dialog without creating a new task or compound list Export Submitter Task Data Dialog This Export dialog displays when you select Export from the File menu in the Submitter Task Data window Here you select the Submitters and Tasks with their corresponding Custom Compound List and Report Methods that you want to Export as a CCL file The default directory is the MethDB directory of your current project Parameter Select Submitter Task data to be exported Select All Unselect All OK Cancel Description D
517. ss VYer5 2 0 Destination Location Destination Location The folder where Setup will install files Setup will install Turbomass in the following folder C TurboMass Ta install to this folder click Next InstallShield 7 Accept the default directory by clicking Next 694 Appendix B TurboMass Software Installation If TurboMass software had previously been installed the install wizard next prompts to delete any existing security information Click Yes to continue and delet any previous password information Clicking No will save any previous password Question 2 jJ Would you like to delete the existing TurboMass security information The Installation Options Summary dialog opens This dialog allows you to review your setup choices before the installation process begins Setup Installing TurboMass VYer5 2 0 Installation Options Summary Click Back to change your selections or Next to begin copying files Install directory C TurboMass Installation type Complete Installation The following components will be installed Help files Installation options Cor port will be pre configured Cancel Click Next to continue the installation The Administrator Account Setup dialog appears 695 TurboMass Software User s Guide Administrator Account Setup E User Name Administrator TurboMass requires a password for the Administrator account To set a blank password leave both of the boxe
518. sseessecseeceneceseceecseeeseeeeeeeenseeenes 221 Formatting Sample Lists ccccccccsscessecesseeseeeseeesecnseceseceseeneeseeeseeeenneeses 229 Starting the Analysis ccessdencesize dude chedeaeriod ive glad E EEE ETE 240 Quantify the Datais wicscass ian ahe neta deck oad 242 Report Preview Window cccccccesccesscesecesseeeeeeeeeeeseeeseecseecseecaecnaeenseenseenas 243 Quantify csscccesesicedsccssnicassossecssescsdcersvesecsscsvacceesuesedeesdoascoseadcedaossvessocendceuceesess 247 ImtrOduUcttOnissis35sscdsyacevencchaasian oid bases atk nE o e LS ARA ATTANG 249 How Does TurboMass Quantify and Report a List of Samples 250 A Step by Step Guide to Quantification ccccccccecsseesteesteceteceteeeteeseees 256 Creating a Sample List cccceccesscessceseceeeeeseeeeeeeecseeensecnecnseenseenes 256 Projects atte tact hi Ges Wea ta oti leita Vivncet ele evasee donee aa tao tates eentous 256 Creating a Quantify Method cccccecccesccseecesseeseeeseeesseeneeneeeeeneenes 257 Updating of Analyte RTs from Internal Reference eee 268 OA OG Calculations aa i a a e a i 284 Recoveries onestea en e a E e E Thode E vets 285 Matrix Spike Matrix Spike Duplicate Recovery ccseseseeeereeeees 285 Selecting which fields will be displayed in the Quantification Method Report cccccceccceesseeseeesseeseeeseeesecseesseens 290 Starting the Analysis s 02 secssccseatsaccssteessteeseabnesevdaszeepunncaceevasstaabeano
519. ssign Analyte Assigns the selected row as the Analyte to be treated as the sample from which the MS MSD sample are prepared for Form 3 Displays Analyte in the Status column for that row and displays the row in the Analyte color Assign Matrix Spike Assigns the selected row as the Matrix Spike sample Sample for Form 3 Displays Spike in the Status column for that row and displays the row in the Spike color Assign Matrix Spike Assigns the selected row as the Matrix Spike Duplicate Duplicate sample for Form 3 Displays Spike Dup in the Status column for that row and displays the row in the Spike Dup col 619 TurboMass Software User s Guide Form 4 Tab Method Blank Summary When you select Form 4 Method Blank Summary from the Select Forms dialog the Report Generation Window Form 4 Tab appears B Report Generation Sample List Forms Options Help Sample List Form1 Form1 TIC Form2 Fom3 Form 4 DEK Status Sample ID Sample Type File Name B10040501 Matrix Level Vial Quantify Method Qualitative Method Submitter Task Water dediu B260b_Tutorial TiCsearcht 6 VOA_Tutori VOA_Tutori VO B10040504 Water fediu 8 al TiCsearch DA_Tuton VOA_Tuton VO B10040505 Water jediu al TiCsearch10 VOA_Tutori VOA_Tutori V B10040506 Water fediu b al TiCsearchiC OA_Tutori VOA_Tuton 81004050 Water dediu Jb al TiCsearch10 VOA_Tutori VOA_Tutori VO ASTD 200n Ini B10040
520. ssion either click the Windows close box or select Exit from the TurboMass File menu If data acquisition is in progress when you attempt to exit TurboMass a dialog box informs you that the data will be lost and asks if you still want to exit If you click Yes the acquisition stops and the software shuts down If you click Cancel the acquisition continues 25 TurboMass Software User s Guide 26 General Guidelines for TurboMass Operation e Always use unique data file names within a Sample List e Always use unique names for Sample Lists before submitting them to a queue filled with other Sample Lists e Do not stop the Sample List while General Status says Setting Up e Make sure the GC run is sufficiently long that the autosampler tower has stopped moving before the run is completed e Ifthe GC autosampler tower has been manually moved make sure it is returned to the home full counter clockwise position before the next injection Getting Started The TurboMass Top Level Window The TurboMass top level window includes features that allow you easily navigate through the software work with files and perform tasks e The menu bar includes options that allow you to access a variety of features Menus include File Edit Samples Run View Quantify Configure GC Tools and Help e The GC panel on the left side of the screen includes a run time indicated to display how long the acquisition method has been
521. stomize the Spectrum toolbar select Customize toolbar from the Spectrum Display menu Spectrum Customize Toolbar x Available Buttons Toolbar Buttons Decrement dd gt a PJ increment SHemovey iea JDefaut range The additional buttons that can be added to the default Spectrum toolbar are Save spectrum Combine spectra Tile windows Cascade windows Stack windows Adding buttons to the toolbar 1 Select the button you want to add to Available Buttons list 2 Inthe Toolbar Buttons list select the toolbar button before which you want to insert the new button 3 Click Add to add the new toolbar button Repeat Steps 1 3 as often as required 4 Separators can be inserted between toolbar buttons to divide them into logical groups To add a separator repeat steps 1 3 and then select Separator in Available Buttons 5 Click Close to exit and save changes 429 TurboMass Software User s Guide 430 Removing buttons from the toolbar 1 Inthe Toolbar Buttons list select the button you want to remove 2 Click Remove to remove the button Steps and 2 can be repeated as often as required 3 Click Close to exit and save changes Changing the order in which toolbar buttons are displayed 1 Inthe Toolbar Buttons list select the button you want to move 2 Click Move Up or Move Down to move the toolbar button Steps 1 and 2 can be repeated as often as required 3 Click Close to
522. t Delay Start minutes End minutes If just one conventional solvent delay is used only the top End box should be filled in with all the other values set to 0 Solvent delays may not overlap and must be entered in order of increasing retention time Saving and Restoring an MS Method Saving an MS Method l Select Save As from the MS Method File menu to display the Save File As dialog 2 Enter a new File Name under which you want the MS Method to be saved or select an existing file from the list displayed Save as E Save in ACQUDB z E File name Save as type Experiment File exp x Cancel 4 3 Click Save Function List Editor If the selected file already exists you will be asked to confirm that you want to overwrite the existing information Click Save to continue or Cancel and specify a different name Restoring a saved MS Method 1 Select Open from the MS Method File menu to display the Open dialog open Lookin QQacnuUDBB ss l e KE Files of type Experiment File exp x Cancel 4 2 Select the File Name of the MS Method that you would like to use either by entering its name or by selecting it from the displayed list and click Open OR Right click on the desired MS Method in the Sample List and click Open Setting Up an MS Scan Function The MS scan function editor is used to set up centroid continuum and MCA functions 1 Click
523. t peak is the last in the file then current file will be marked Complete and the next file will be selected in the file list and the first peak from that file will be selected in the peak list Click this button to select the next compound name from the compound list If this is one of the NIST plot hits then its spectrum will be displayed in the bottom spectrum control Click this button to display the Generic TIC Names dialog 613 TurboMass Software User s Guide 614 Accept PEAK plot SPECTRUM top SPECTRUM middle LIBRARY SPECTRUM bottom OK Cancel A command button that assigns the currently selected name in the right hand list to the selected peak That name will then appear in the center list in the Assigned Name column A plot of the currently selected chromatographic peak Plot properties can be changed for this and all other plots by selecting Properties from the right click context menu Behavior is similar to the TurboMass Chromatogram window The apex spectrum from the currently selected peak Plot properties can be changed by selecting Properties from the right click context menu Behavior is similar to the TurboMass Chromatogram window The background subtracted spectrum from the currently selected peak Background subtraction is performed automatically using the Chromatogram Combine function The three peak apex spectra are averaged and the spectrum of the scan just before the be
524. t the right you want to assign to the group To grant the selected right to a new group click Assign to open the Group Right Assignment dialog select the group in the Non Members list and click Add to move the new group to the Members list Right Administer user accounts and groups Members Non Members NewGroup mA CVE Hemas Security moves the selected group to the Members list Repeat step 3 for each group to be granted a new access right 675 TurboMass Software User s Guide 4 To remove a group from the Members list select the group you want to remove and click Remove to move the selected group to the Non Members list The Administrators group cannot be removed from the Members list of any group because administrators must have full access rights Assigning an access privilege to an individual user 1 Follow the procedure Creating a Group on page 672 to create a special group for the user and make the user a member of the new group 2 Assign the access privilege to that group using the procedure Assigning group rights on page 674 Managing the Audit Log The audit log maintains an audit trail of the TurboMass use by tracking each occurrence of each auditable event specified in the Audit Policy You can set up the Security Audit policy from the Audit Policy dialog You can monitor the audit log from the Audit Log Viewer Setting up an audit policy 1 From the Security Manager window click OR
525. tectors select the Detector Mode and Output settings that match any additional detectors installed on your GC for Channel A and or B Under Carrier Pneumatics select the Pressure units and other options Select a setting for Carrier A PVel Denotes programmable linear velocity operation This option is only available for CAP and PSSx injectors in Cap Control Mode You enter the average values for capillary column linear velocity in the method as well as values for column dimensions 147 TurboMass Software User s Guide 148 and vacuum compensation CFlow Denotes operation at a constant flow rate Enter pressure values in the method The pressure is varied by the GC to maintain a constant mass flow rate through the column as the oven temperature changes This mode does not require you to enter column dimensions in the method PFlow Denotes programmable flow operation Enter flow values in the method Press Indicates direct pressure programmable control in the pressure units you select IFlow Denotes constant flow operation Enter flow values in the method If appropriate repeat the process for Carrier B Under Auxiliary Pneumatics select PPC for any auxiliary zone that has a PPC controller installed Select the settings to control pressure or flow of the auxiliary zone s Click OK A check mark in the LINK Configuration dialog indicates that the GC has been configured Saving the configur
526. ted Clicking this button applies check marks to all Submitters and Tasks Clicking this button removes any check marks from all Submitters and Tasks OK Cancel Environmental Reporting Clicking OK imports the selected Submitter Task data If a name conflict occurs i e the same Task name already exists for that same Submitter a dialog displays with the message Data already exist for Task lt taskname gt Enter new task name The dialog will include a New name edit box and OK Cancel and Cancel All buttons The OK button will be disabled until you enter a new name for the Task Upon clicking OK the new Task will be created and the data imported Clicking this button closes the dialog without exporting any data 649 TurboMass Software User s Guide Report Method Tab An independent mapping of Forms to Communiqu Report Methods can be defined for each Submitter and Task This mapping is global across all Projects NOTE It is up to you to ensure the appropriate report methods are in the Project this occurs automatically when a new project is created via the Project Wizard If specific report methods have not been selected for a given Submitter Task then the Default or the most recently selected set will be assigned to that Submitter Task see below The Report Methods dialog uses the Form descriptions that appear on the EPA Forms The separate VOA SV and Matrix columns of the dialog describe when the
527. ted enables calibration of the peaks in the top raw display file graph This feature allows selection of one peak at a time with the display being recalibrated after the selection of each peak bringing the other masses in the spectrum into line Setting Automatic Calibration Check Parameters 1 Select AutoCal Check Parameters from the Calibration Edit menu to open the Automatic Calibration Check dialog 125 TurboMass Software User s Guide Automatic Calibration Check x m Check Missed Reference Peaks Maximum Std Deviation 2 Cancel fo 30 lV Apply Span Correction Check Acquisition Calibration Ranges 2 Specify the AutoCal Check parameters and click OK Missed Reference Peaks Maximum Std Deviation Apply Span Correction Check Acquisition Calibration Ranges Setting Mass Measures Allows you to enter a number of consecutive peaks from the reference file that the system is allowed to miss before a warning is issued to the user Performs the same function as Missed Reference Peaks if the residuals for a particular calibration exceed the number entered Applies an extra correction to the mass scale that is dependent on the mass range being scanned This correction ensures that mass assignment will be correct even if the mass scale that you are working with is different from the one that the instrument was originally calibrated over It is not recommended that this option be us
528. ted with the Clarus GC MS Overview of system management procedures Reinstalling TurboMass software Presents methods for performing quantify calculations Defines output table field options and formats An example of a LIMS file Sample List for import Equations showing the reporting calculations 21 TurboMass Software User s Guide Conventions used in this Guide This guide designed for Windows users assumes that you will be using a mouse or similar device to perform TurboMass operations Many shortcut keys are listed on the TurboMass menus and the documentation for your operating system can provide information about equivalent keyboard procedures This section discusses capitalization terminology and the way that references are used in this guide 22 All menus commands and dialog option names appear with initial capital letters whether or not they are completely capitalized in the user interface The names of keyboard items such as the ENTER key are capitalized This will help you to distinguish these items from narrative or procedural text Throughout the TurboMass documentation the following terms are used to refer to program elements and the actions that you perform to carry out tasks Click The term click refers to moving the mouse pointer over a button or icon on the screen and depressing the left mouse button Select The term select refers to highlighting an object or item or moving the cursor
529. ted row as the Tune Evaluation sample for Form 5 Displays Tune Eval in the Status column for that row and displays the row in the primary data color Enabled when the Form 5 tab is selected NOTE It is valid for the same row to be identified as a Tune Eval for Form 5 and a Cont Calib for Form 7 Assigns the selected row as the Continuing Calibration sample for Form 7 Displays Cont Calib in the Status column for that row and displays the row in the primary data color Enabled when the Form 7 tab is selected NOTE It is valid for the same row to be identified as a Tune Eval for Form 5 and a Cont Calib for Form 7 and Form 8 599 TurboMass Software User s Guide Menu Command Item Assign Mid Level Standard Select Forms Options Customize Display Help Help Topics Sample List Context Menu Description Assigns the selected row as the Continuing Calibration Mid Level Calibration sample for Form 8 Displays Cont Calib in the Status column for that row and displays the row in the primary data color Enabled when the Form 8 tab is selected NOTE It is valid for the same row to be identified as a Tune Eval for Form 5 and a Cont Calib for Form 8 and Form 7 Displays the Select Forms dialog If you select a new sample list within the Select Forms dialog the existing sample list will be replaced and any reassignments will be lost Opens the Customize Field Display dialog to enable you to select t
530. ted to be in one of these databases or lists the speed and accuracy of the search can be improved by restricting results to members of those databases or lists NOTE If no libraries are selected no library search will be performed This is the default method for only picking Qualitative Peaks 343 TurboMass Software User s Guide Qualitative Method Editor Untitled oiaiele 2 0i F Fine F Hoooc MIR 20 Click Save or Save As from the File menu then name and save the method This method name will now be available in the Sample List under the Qualitative Method column 3 Put the Qualitative Method in the Sample List After creating and saving a Qualitative Method enter it in your Sample List 1 Display your Sample List H oMass TUTORIALQUANT TutorialQuant SPL alele a 2 gt mle Waa tamm e ee ell ss ERED 344 Qualitative Method 2 Move the slider on the bottom of the Sample List window to the right until you can view the Qualitative Method column E TurboMass TUTORIALQUANT TutorialQuant SPL File Edit Samples Run View Quantify Configure GC Tools Help 0 x l alem a a gt mmf an waa tam 2 E ele Conditions Quantify Method Calibration Standard Standard Tiaa Standard Jor General Status GC Status Ready No Instrument 0 0 Shutdown Enabled 3 Double click in the cell and
531. temperature program 163 TurboMass Software User s Guide 164 7 You can also change the values directly on the curve by dragging the points associated with each ramp level When you release the points after dragging the new values appear in the table e To change the rate of a level select the point that represents the temperature and drag it horizontally e To change the temperature value of a level select the point that represents the temperature and drag it vertically e To change the hold time duration of a level select the point that represents the time and drag it horizontally 8 Under Cryo select the type of sub ambient cooling that you want to use or set Coolant to Off 9 Ifyou are using sub ambient cooling enter the values for the cryogenic Cut in temperature and the oven Timeout in the respective fields 10 Under Oven enter the maximum oven temperature allowed This value protects the installed column 11 In the Equil time field enter the number of minutes that you want the oven to equilibrate at the initial temperature before it becomes READY For temperature programming ramping set the Equil Time to at least 2 min 12 Under Heated zone setpoints if you have non programmable inlets enter the temperature for Injector A and Injector B If you have programmable inlet type POC or PSS configured in either inlet program mode or oven tracking mode POCI PSSI POCO or PSSO select either On or Off f
532. tered Context Menu This pop up menu appears when you right click on a row in the Form 5 sample list view pane Assign Tune Evaluation Sample Assigns the selected row as the Tune Evaluation sample for Form 5 Displays Tune Eval in the Status column for that row and displays the row in the primary data color 623 TurboMass Software User s Guide Form 6 Tab Initial Calibration Data The Form 6 tab Initial Calibration Data has a unique layout among the Forms It consists of three adjustable size panes the calibration sample table the compound data table and the message window Report Generation Sample List Forms Options Help Sample List Form1 Form1 TIC Fom2 Form3 Form 4 Form5 Fom6 Sample ID File Name Time Date VOA STD 5ng mi B10040504 11 11 20 04 Oct 2005 VOA STD 20ng ml B10040505 11 44 54 04 Oct 2005 VOA STD 5 ng mi B10040506 1218 34 04 Oct 2005 VOA STD 100ng m B10040507 125220 04 Oct 2005 VOA STD 200ng m B10040509 13 59 37 04 Oct 2005 Level3 Level 4 Level5 Avg RAF Curve Fit e 0 411 0 412 0 417 0 411 Toluene d8 1 316 1 307 1 313 1 313 Bromoflurorobenzene 0 352 0 355 0 363 0 353 Dichlorodifluoromethane 0 374 0 351 0 327 0 361 Chloromethane Vinyl Chloride 0 512 0 486 0 482 0 500 Bromomethane 0 337 0 331 0 357 0 346 Chloroethane 0 316 0 313 0 314 0 322 Trichlorofluoromethane 0 568 0 546 0 553 0 565 1 1 Dichloroethene 0 397 0 386 0 392 0 398
533. the User Peak Value is left at zero or set to 1 the concentration values will not be changed 13 Optionally set the Reporting Threshold value in concentration units to filter quantitative results in reports This value is passed to Communiqu via the data source IMPORTANT The Reporting Threshold value will be used as the Reporting Limit for the purpose of setting flags on Form 1 and determining what Compounds to show for Compound on the general environmental Quantitative Report 263 TurboMass Software User s Guide PKIEnvQuant template if no Custom Compound List which includes Reporting Limits is defined 14 Optionally set the Standard Concentration Factor Std Conc Factor Set this parameter on a per compound basis and it is used by Quantify to adjust the concentration values in standard samples in the sample list including Init Calib and Cont Calib prior to calibration of the compound Because TurboMass only provides for 20 unique concentration values A thru T in the sample list an alternative mechanism is required for analyses such as environmental work where multi level calibration of a large number of compounds can lead to the need for hundreds of distinct standard concentration values The Standard Concentration Factor is the factor by which the designated concentration in the sample list A thru T must be multiplied in order to result in the actual concentration in the standard sample Since only one Sta
534. the Configuration Editor User menu you can change the fonts used to print out the GC method summary and you can set up quick paths 151 TurboMass Software User s Guide 152 Changing Fonts The Font dialog lets you choose the typeface style and size of text that will appear in the Method Editor Summary Selecting a Font l 2 3 OR Click the fonts tool Font x Eont Font Style Size arial Regular r 2 m a Cancel Courier T Courier New Fixedsys Fr Lucida Console FP Lucida Sans Unicode T Marlet Modem Bold Italic Sample all AaBbYyZz MS Sans Serif MS Serif Roman Italic Bold Apply ie T q el To open the Font dialog select Fonts from the User menu Select font to change The Method Editor Summary is automatically selected in the Select font to change drop down list Select a Font Font Style and Size of text Click OK Specifying Quick Paths Specifying a quick path lets you quickly choose a frequently used path in any file selection dialog in the GC editors This provides for example immediate access to your mass spectrometry project file instead of scrolling and clicking through the Windows file selection method GC Control Adding a path to the Quick Paths list 1 Inthe Configuration Editor select Quick Paths from the User menu Quick Paths C TurboMass T urb 2 Click Add The TurboMass Path Select dia
535. the Error Log click Print 3 To clear the Error Log click Clear 187 TurboMass Software User s Guide Working with the GC Interactively There are two commands that let your work with the GC interactively Hands On and Modify Active Hands On lets you change some settings after GC setup Modify Active lets you change a downloaded method Using Hands On The Hands On command in the GC menu lets you control certain settings after you have set up the GC You can set the GC oven temperature autozero the detector and turn valves or relays on and off You can access Hands On either during or outside of a run The actual parameters available depend on whether or not a run is in progress The Hands On command is not available until you have initialized the GC with a method Setting controls for the GC 1 Select Hands On from the GC menu and click Close The GC Hands On dialog is displayed showing the oven temperature and the current valve settings GC Hands On Ea Oven Temperature Close Current C 75 Setpoint C 75 Set Temp Heas l Set Vaives NOT Autozero ko Pte Sate ARS oto Teta bg aita Jolt ap 8d sks Ute i i 4 NONE i I Disable Scroting New oven temperature value 60 to 450 188 NOTE GC Control 2 Inthe Setpoint field enter the setpoint oven temperature for the GC and click Set Temp 3 Click Autozero if desired 4 Select the valves you want to switch
536. the File menu to display a Sample List with one default row 2 Add rows and columns to the Sample List so that it has the same number of rows and columns as the worksheet in the other Windows application If the number of rows and columns displayed in the Sample List is not the same as in the other Windows application data may be lost 3 Select the relevant area in the other Windows application and copy it 4 To modify currently displayed rows in the Sample List Editor position the cursor on the cell at the top left corner of the paste area and click Paste 227 TurboMass Software User s Guide Printing a Sample List 1 Click OR Select Print from the File menu to display the Print dialog 2 Select the printer print range number of copies and click OK 228 Sample List Formatting Sample Lists Column widths can be changed in the same way as any Windows spreadsheet There are many different columns of information that can be displayed in the Sample List Selecting columns for display 1 Click OR Select Customize Display from the Field option on the Samples menu to open the Customize Field Display dialog Customize Field Display MWFile Name FILE_NWAME VIMS File MS_FILE Inlet File INLET_FILE a Task TASK vVlUser USER V Submitter SUBMITTER Conditions CONDITIONS Sample Type TYPE IID ID Conc A CONC 2 Select the appropriate checkbox
537. the GC This value does not control the injection volume that value is in the GC Method but it is used in calculations GC column Enter information about the GC column used for the analysis It is enabled if a GC is configured on the system Injector Select from the drop down list injection port A or B into which the sample will be injected this controls the Clarus GC autosampler Moisture Enter the moisture content determined for a soil sample This field is enabled only if the Matrix is Soil pH Enter the pH of the sample Sample Prep Information Date received Date the sample was received in the lab The date is displayed in the short format defined in the Windows Regional settings Clicking the down arrow command button displays a calendar control to enable you to select the Date received Dated extracted Date the sample was extracted for analysis The date will be displayed in the short format defined in the Windows Regional settings Clicking the down arrow command button displays a calendar control to enable you to select the Date extracted Sample wt Sample vol The weight or volume depending on sample matrix taken for analysis This field is enabled if the Analysis type is Volatiles or Semi volatiles If the Matrix setting is Soil the caption is Sample wt and the units displayed are grams g If the Matrix setting is Water the caption is Sample vol the units displayed are milliters mL Dil
538. the GC Status area The status area displays the general status the GC status and the oven status The status information changes constantly as you acquire data modify GC methods and perform other actions that affect the GC The GC status must be either No Method or Run Done to successfully set up Otherwise GC communication lockups may occur The General and GC Status messages are color coded as follows Green Indicates that the instrument is ready to start a run acquire data Blue Indicates that the interface is active a run is in progress or the interface is uploading data to TurboMass Red Shows that the instrument is not ready to collect data because it is not connected it has no method or it has been paused General Status Active The interface is collecting data from a current GC run Backlog Data from one or more completed runs still reside in the interface Detached Not currently communicating with the interface possibly due to communication errors Not The instrument is not turned on or it is not connected to the Connected 185 TurboMass Software User s Guide 186 Init Error Initializing In Reconfig No Method Post Run Pre Run Ready Run Done Run Log Setting Up System Reconfig GC Status Equil Hold computer An error occurred during initialization TurboMass is retrieving initial status information for the interface The interface is reconfiguring itsel
539. the Sample List s to be used as input The selection of Tentatively Identified Compounds from the initial qualitative processing will also be made within this window This window displays a comprehensive view for generating reports using the EPA Forms 1 through 8 that apply to GC MS analyses The process of generating the Forms will involve the reprocessing a Sample List by the TurboMass software as with other Communiqu reports but there are several unique aspects in this case 1 The Sample List is queued for reprocessing from this window rather than from the Sample List window 2 The Start Sample List Run dialog does not appear The reprocessing always uses the following options gt Auto Quantify Samples On Quantify Samples only gt Generate Communiqu Reports On gt Quantify Qualify and Generate Reports After Each Run or summary reports at the end of the sample list 3 Which sample rows are processed will be indicated by the user on the Sample List tab Individual rows can be turned on or off for processing 4 The Report Method supplied to the Report Manager and hence the template s provided to Communiqu will not be that in the Report Method column of the Sample List but will instead depend on the Forms selected by the user and the Submitter and Task associated with the sample The Report Method in the Sample List can be execute in the usual manner Run Start from the Sample List Environmental Reporting
540. the generic names supplied or Having decided that none of the generic names is applicable either click the New Name button and enter a new generic name for selection or Right clink on the current peak s retention time and select Hide Show This will place an X under the Del eted column and the peak will not be reported Edit the qualifier codes applied to the peak if required The TurboMass software will automatically change the codes if a generic name is selected see the Behavior table Click Next Peak or select another peak or click Next Sample to review peaks from the next file Click OK after reviewing the files and changing the TIC assignments as required to save all assignments and close the dialog Or you can click Cancel to abandon the procedure without saving changes to the data 615 TurboMass Software User s Guide 616 Status E Report Generation Sample List Forms Options Help Sample ID BFB Form 2 Tab SMC Surrogate Compound Recovery When you select Form 2 SMC Surrogate Compound Recovery from the Select Forms dialog the Report Generation Window Form 2 Tab appears with the files displayed in the summary data color Level Vial Quantify Method Sul britter Analysis Aediu 8260b_Tutorial VOA_Tutori VOA OA Tutor VOA STD 5ng 0A STD 20ng 0A STD 50ng DA STD 100n TiCsearch10 DA STD 200n Tutorial B10040509 g Y Hi B10040510 8260b_Tutorial V
541. the installation of NIST 2002 v2 0 0 8 Click OK When prompted for the setup type leave the default Typical checked and click Next gt 711 TurboMass Software User s Guide Setup Type 9 The next window displays the default install directories leave the default options checked and click Next gt Choose NIST 02 MS Software Destination Locations If the following folders do not exist the system will prompt to create them 712 Appendix B TurboMass Software Installation Confirm New Folder Confirm New Folder 10 Click Yes to Confirm each new folder The install process will next prompt to search the hard drive for any existing installed libraries Select Drives to Search 5 A REMOVEABLE 713 TurboMass Software User s Guide 11 Click Search 12 The next screen will prompt to connect any libraries found on the drive to the MS search program If any libraries are displayed in the list highlight the libraries that should be included in library searches check Copy or Link and click Next gt to continue Find and connect User libraries to MS Search Program i x To connect your user MS libraries to the MS Search Program select libraries from the list below then select Copy or Link To locate user MS libraries on your computer click Search for User Libraries button Click Next to continue Selected User libs action 3 Copy C Link O librar
542. the primary data color see Row Colors for the continuing calibration Cont Calib sample All other rows will be shown in the disregard color and are not used for the report Status Column The Status column indicates which row is currently flagged as the continuing calibration sample This may be used to distinguish between several Cont Calib rows in the sample list only one can be used for Form 7 or to flag a row of another Sample Type as being the continuing calibration sample Reassign Sample Type The software allows the continuing calibration file assignments to be altered Context Menu This pop up menu appears when you right click on a row in the Form 7 sample list view pane Assign Continuing Calibration Assigns the selected row as the Continuing Calibration Cont Calib sample for Form 7 Displays Cont Calib in the Status column for that row and displays the row in the primary data color Environmental Reporting Form 8 Tab Internal Standard Area and RT Summary When you select Form 8 Internal Standard Area and RT Summary from the Select Forms dialog the Report Generation Window Form 8 Tab appears Section of the Window Description Sample List view This is essentially a read only display The view cannot be sorted and no data item in any cell can be directly edited Column widths can be changed in the standard way by dragging the header divider Message pane This is a read only display window Show
543. the raw chromatogram If they are sufficiently similar as determined by the MCQ Index parameter then the mass chromatogram is preserved otherwise it is removed Essentially mass chromatograms that contain spikes or are noisy will be dissimilar after smoothing and standardization to the raw mass chromatogram and are hence rejected 479 TurboMass Software User s Guide Setting the CODA processing parameters 1 Select CODA Options from the Strip Options menu to open the CODA dialog MCQ Index o 750 Cancel Smoothing window 5 points Default 2 Set the following parameters and click OK MCQ Index Specifies how similar the smoothed standardized mass chromatogram must be to the raw mass chromatogram before it is preserved The parameter is in the range 0 1 inclusive a value of 0 will preserve all mass chromatograms and result in the raw file being copied to the output A value of 1 will result in all mass chromatograms being rejected and an empty file Values around the default value of 0 75 are most useful with the range 0 65 0 85 recommended Smoothing Specifies the amount of smoothing given to raw mass window chromatograms The default value of 5 is usually adequate This window is a number of data points around the central point Stopping a Process When you stop a process before completion the output data file will contain all the information written up to the point at which the process was sto
544. the sample results as well as the graphs select Display Table Set the Orientation to Portrait or Landscape for each part of the Quantify Report Click OK to exit and save the changes Selecting which fields are displayed in the Quantify Summary Reports gt Select Output Compound Format or Output Sample Format from the Quantify Edit menu For more information about formatting Summary Reports see Selecting which fields will be displayed in the Summary window and Summary Reports on page 238 Selecting the Chromatogram display range for the Quantify Sample Report The Quantify Sample Report uses the Chromatogram display parameters l To set the Chromatogram display parameters select Chromatogram from the Quantify Display menu The Quantify Chromatogram Display dialog is displayed I Add to existing chromatograms _ Cancel Display Range Integration 7 Select Show Internal Reference if you want the internal reference peak shown with the current peak Select Add to existing chromatograms to display each new chromatogram to those already on display Set the Display Range to Integration to use the integration range or to Acquisition to use the acquisition range Quantify If the Display Range is set to Keep Current TurboMass will use the acquisition range Printing Quantify windows 1 Select Print from the Quantify File menu 2 Select to print All Windows or Current Window and click OK to print the
545. these three concentration levels can be defined as Conc A Conc B and Conc C As the standard is serial diluted change the values assigned to Conc A B and C in the Sample List to reflect the new concentrations Set the Peak Location parameters to determine how a peak within a peak list is identified as matching a method compound A peak can be classified as a match according to its Retention Time or Relative Retention Time whether it falls within the specified Time Window and whether it satisfies the Peak Selection criterion Retention If selected a peak within a peak list is identified as a match if it Time elutes at the Retention Time specified and within the Time Window specified Quantify Relative If selected a peak within a peak list is identified as a match if it Retention elutes at the time at which the compound is expected to elute Time relative to the compound specified in the Internal Ref text field 8 Set the Retention Time or Relative Retention Time and Time Window parameters in one of the following ways Using the mouse a b c d e Arrange the TurboMass display so that you can see both the Quantify Method Editor and the Chromatogram window showing the chromatogram you want to use Select the Compound for which you want to set parameters in the Method Editor Right click at one end of the chromatogram region of interest and drag the mouse horizontally to the other end As you drag the mous
546. thin the data system Groups provide a convenient way of managing the capabilities of users it is often easier to remember which privileges a particular group has rather than those of an individual The Administrators group cannot be deleted and always has full access rights Group Rights See Access Rights Privileges Appendix A TurboMass Security Logon Name The logon name is the name by which a user is known to Security Each logon name has an associated password and user account To log in to Security a user must provide a valid logon name and password Password A specific word used to log on when Security is enabled that verifies the user s identity Passwords are case sensitive Right Privilege See Access Rights Privileges Security Manager The TurboMass application that administers the TurboMass security system The Security Manager cannot be run at the same time as TurboMass User A TurboMass user who usually has more limited access privileges than an Administrator User Account A record maintained by Security that contains information about a particular user Username The name by which a user is known to TurboMass A user logs on to TurboMass by providing a valid username and password A user s group rights determine his individual rights 663 TurboMass Software User s Guide 664 Security Model The Security Model is based on user accounts Users are members of groups and groups have access p
547. tion Curves A calibration curve is formed for each of the compounds in the method Samples that are to be used when forming a calibration are assigned the Standard type in the Sample List The Sample List also specifies the concentration of each of the calibration standards The peak which represents each compound must be located within a sample s peak list A response value for each of the located peaks can then be calculated For located peaks information such as compound name and peak response is saved in the peak list For each compound one calibration point is obtained from each of the Standard peak lists Calibration points are plotted as response against concentration A polynomial is fitted to these points to form the compound s calibration curve The calibration curves are saved to a file with the same name as the Quantify Method The Quantify Method specifies how to locate peaks calculate responses and fit curves Quantify Calculation of Compound Concentrations R4 b Peck bi Dek myk 2 Conpaunis kocak Peck tr beat Rata Locale Peck tr ACap ants A Compans AiCarpounts Gane Ra Cial Peck Caabe Rok Rpores Rpones Pegperees pry Gab ear Apy Gab ear Ay cton Cues anes Cures npani cores Apk TurboMass calculates the concentration of each of the Method compounds for the samples in the Sample List The peak which represents each compound must be located within a sample s peak list A response
548. tion of the files in the Sample List Post Run Specify the name of the process that will be run after the acquisition of the files in the Sample List For example to switch the instrument out of the operate mode and turn off various gases NOTE Jfyou want to run a process after each sample in the Sample List has been acquired format the Sample List to display Process and enter the name of the process to be run for each of the samples If you want the process to automatically operate on the data file that has just been acquired select Options from the Sample List Tools menu then deselect the Use Acquired File as Default parameter on the System tab 3 When all are entered click OK 347 TurboMass Software User s Guide 348 Data Acquisition 1 2 Data Acquisition Starting an Acquisition There are two ways of starting an acquisition a single sample acquisition from the Tune page or a multiple sample one from the TurboMass top level screen Single Sample Starting a single sample acquisition 1 Click Acquire on the Tune page 2 Set the required parameters 3 Click Start to begin data acquisition Note that this method of starting an acquisition does not have a solvent delay time or specify a GC method It is best for recording background and calibration gas spectra Start Acquisition x Data File Name ATSE ai Text Data Format Continuum X m Masses m z Start Mass 500 End Mass 504 me
549. to start processing the data file The status bar at the bottom of the Combine Datafile Functions dialog displays the progress of the current process Selecting a Data File and Subrange to Process The Input section of the Combine Datafile Functions dialog identifies the data file that will be processed Changing the current input file Click Input from the Combine Datafile Functions dialog This opens the Input Datafile dialog from which a new file and directory can be selected Input Datafile x i Mass Range Start amu J Cancel File End amu 260 l r Retention Time Defaut Start min 0 20 Endimin faas File w50 Function 1 2 Set the parameters and click OK 3 Clicking Default sets both Mass Range and Retention Time to the full range of the current file By default the entire selected file will be processed and all functions will be combined into a single function To specify subranges see below Selecting a new input file automatically defaults the name of the output file Processing a mass or retention time subrange of the input file has the advantages of reducing both processing time and the size of the resulting output file Strip and Combine Functions Selecting a different file and function Click File to open the Combine Functions Data Browser Selecting a new file automatically defaults Mass Range and Retention Time to full range Enter values f
550. to this field is saved if you click Previous Modify or Next If instead you click another compound or another button a dialog displays with the message Save changes to this compound and includes Yes and No buttons Clicking Yes saves the modified value with the compound Clicking No leaves the compound s reporting limit unchanged A command button that sets the reporting limit for water samples for all selected compounds in the list to the value in the Reporting limits Water edit box Reporting limits Soil Set All Previous Modify Next Environmental Reporting An edit box that displays the reporting limit value 0 000 to 999 999 999 for soil samples associated with the currently selected compound which may be checked or unchecked A change made to this field is saved if you click Previous Modify or Next If instead you click another compound or another button a dialog displays with the message Save changes to this compound and includes Yes and No buttons Clicking Yes saves the modified value with the compound Clicking No leaves the compound s reporting limit unchanged Click this button to set the reporting limit for soil samples for all selected compounds in the list to the value in the Reporting limits Soil edit box Click this button to set the reporting limit values of the currently selected compound to the values in the Reporting limits edit boxes Water and Soil and then selects the
551. tores the instrument to an uncalibrated state 2 Inthe confirmation dialog click OK to delete all instrument calibration OR Click Cancel to abort the operation Displaying a Calibration Graph 1 Select From File from the Calibration Calibrate menu to open the Display Calibration Graphs dialog Display Calibration Graphs x m Select Calibration Type Static Scanning Select Calibration File Combine scans in data file fast From fi To fi Browse Raw Data Gk Cancel 2 Select the desired Calibration Type Static Scanning or Scan Speed Compensation 3 Click OK 130 Mass Calibration Displaying a Verification Graph You can display the verification graphs for a particular calibration type Normally an acquisition would be performed and a calibration made Use this process to reprocess the data using the calibration file to verify the accuracy of the calibration l 2 3 Select Verification From File from the Calibration Process menu to open the Display Verification Graphs dialog Select the desired Calibration Type Static Scanning or Scan Speed Compensated Click OK Making a Calibration from a Data File 1 Select From File from the Calibration Calibrate menu to open the Display Calibration Graphs dialog Display Calibration Graphs x m Select Calibration Type C Static m Select Calibration Fie Combine scans in data file
552. tr fet e a aa os dave tiu racial ste lieavtaa tates 156 Developing a GC Method cccccsccsseceseceseceseceeeeeeeeeeneeeseeeseeeseeentees 156 Setting Control Options cccccccseesseesteceteceeceeceeeeseeeeseeeseeeseeeeeeeeees 159 Setting GC Carrier Parameters cccccecsseessecsseeseeseceseceseenseenseennes 165 Entering Descriptive Information for GC Files eeeeeeeeeeeereeeees 173 Printing GC Method Parameters 0 ccccccsseesseeseeseenteesecneeeeenaeens 178 Controlling the GC cececcecccessceseeeeeeeeeeseeeeeesaecsaecaecesecnseeeseeseeeeeeeseeeeeaes 179 Equilibrating the GC oirir liir aeiia ea AA a 179 Stopping and Restarting the GC ccccesceseceseceseceseeeeeeeeeeeeeeeeeeenaes 179 Releasing and Taking Control of the GC eee eeeeeeeeteceeeneeeneeeees 180 The Details Window siririn ea E e i E E 181 Viewing a Real Time Plot of GC Detector Data 0 0 eeeeeeeeeee 181 Viewing Data Acquisition Information ceceeeeeeeceeteceeeeeeeeeeeees 182 Viewing Detailed Instrument Information 0 eeeceeeeseeteeneeereeeee 182 Understanding GC Status Messages ccccccsccsseessecstecsteesteeeeeeeceaeens 185 Viewing Error Messages ascaris tornei anei iaaa a E GE SE 187 Contents Working with the GC Interactively 0 ccccceccceesceseeeseeeseeeseenseceeeneenseenes 188 Using Hands ON silepte aetra aai e aE eeesta lee 188 Modifying the Active Method cccecccesccesscesseeeeceseeeeseeeseeeeeeneeentees 1
553. trum nl Refine window in scans n2 Refine noise level Combine Cm n1 n2 n3 n4 n5 n6 x n7 Cm Combined spectrum nl n2 Average range start and end values n3 n4 First subtract range start and end values n5 n6 Second subtract range start and end values n7 Subtract range multiplication factor Smooth Sm s1 n1x n2 Sm Smoothed data sl Smooth type Mn mean Md median Sg Savitsky Golay nlx Number of smooths not for median n2 Smooth window TurboMass requires that you enter an estimate of the width of the raw data peak at half height in Daltons and uses this to calculate the width of the smoothing window See Spectrum for the rule used for this calculation Getting Started Subtract Sb nl n2 Sb Spectrum which has been baseline subtracted nl Order of polynomial which has been fitted to baseline n2 Percentage of data points which lie below baseline Center Cn s1 nl n2 s2 Cn Centered data sl Centering method Top highest point on peak Med Median of peak Cen centroid of peak nl Peak width at half height n2 Topmost percentage of peak used to calculate centroid s2 Method used for calculating peak intensities height Ht or Area Ar Using Explorer to work with Multiple Data Files It is also possible to use Windows Explorer to open several TurboMass data files at once and display them in Chromatogram or Spectrum Opening multiple data files 1 Open the Window
554. ture 3 Click OK Audit Trail Dialog If you previously enabled auditing for a file the Audit Trail dialog appears every time you save the file or select Save As to save it under a new name This dialog cannot be opened manually by any menu command or button Entering information in the Audit Trail dialog 1 Select a reason for the change s in the Reason field 175 TurboMass Software User s Guide 176 Logon name Administrator A Current Date Time 4 2 01 4 11 20 PM File DNData lee22001 PRO NACQUDB oven Odeg1 min mth Created by File SaveAs from D Data lee22001 PRO ACQUDBoven Ode Set description to test Changed autosampler from 0 to 1 Changes Comment a Retain audit trail information User Logon Name at start of Turbochrom 2 Enter any information about the change s you made to the file in the Comment field 3 Ifyou are saving the existing file as a new file Save As select Retain Audit Trail Information if you want to copy the Audit Trail information from the existing file to the new file and have auditing enabled in the new file 4 Click OK The information you enter in the Audit Trail dialog is saved with the file that you are auditing The Audit Trail The Audit Trail tab in the Documentation dialog displays a history of changes made to the audited file It appears when you select Display Audit Trail from the File menu You cannot edit the information in this
555. tus is shown on the TurboMass top level display GC Status If GC control is configured the GC run time is shown on the GC panel along with the oven temperature General Status and GC Status General Status refers to the PC communications with the GC while GC Status refers to the state of the GC usually with respect to the current run Both are described in GC Control on page 139 The scan status sample number and scan number are shown in the Status bar at the bottom of the window MS Status If a GC is not configured the MS run time is shown on the MS panel and the scan status sample number and scan number are shown on the Status bar at the bottom of the window The MS status displays several states Operate Green High voltages are on data acquisition is possible Red High voltages are off data acquisition is not possible Pressures High vacuum pump is up to speed High vacuum pump is not up to speed 355 TurboMass Software User s Guide Red Operate is off filament is off possible open filament Chromatogram Real time Update To view the chromatogram that is currently being acquired in real time gt Inthe Chromatogram window click OR Select Real Time Update from the Display menu The chromatogram display will be updated as the acquisition proceeds Spectrum Real time Update To view the spectrum that is currently being acquired in real time 1 Open the data file from the Chromatogram window
556. tware User s Guide Samples Field Align Align text to the right in the current Right column Samples Sample List Invokes the Sample List Wizard Wizard The following icons are shown in the TurboMass GC and MS panels Opens the GC Method Editor 210 Sample List Creating and Editing Sample Lists NOTE The Sample List is saved with the RAW data file when data is acquired If you change the Sample ID field in the sample list and try to print environmental reports the Sample ID reverts back to the original setting when the files were acquired You may want to change the Sample ID field if you modify the sample list to acquire new samples Creating a new Sample List To create a new Sample List 1 Click OR Select New from the File menu to display a Sample List with one default row displayed OR Create a Sample List using the Sample List Wizard See the Sample List Wizard on page 2 Add the desired number of rows to the Sample List by either clicking Add Row to display the Add Samples dialog editing the Number to add and clicking OK Number to add _ m Cancel OR Selecting the desired number of rows in the Sample List and clicking Insert 211 TurboMass Software User s Guide 212 Opening an existing Sample List 1 Click OR Select Open from the File menu to display the Open file dialog Open 71x Look in 9 Sampledb f amp c z Default spl Fiename
557. u Pasting information into a chromatogram window from the Windows Clipboard 1 Click OR Select Paste from the Chromatogram Edit menu to paste the default Clipboard object to chromatogram Select Paste Special to choose which object to paste into Chromatogram These objects would typically be metafiles bitmaps or text 421 TurboMass Software User s Guide 2 Drag the outline of the image to the required position with the mouse You can paste the contents of the Clipboard whether a bitmap a metafile or text into a chromatogram window If the data are in textual or metafile form you can re scale it using the mouse and there will be no distortion of the image However if you paste a bitmap re scaling is done by stretching the image which will cause some distortion To avoid this scale the image to the required size before you copy it to the Clipboard Removing pasted input from the display 1 Select the item you want to remove 2 Press the DELETE key 422 Spectrum 1 4 Spectrum Getting Started You can open the Spectrum window in several ways Displaying the first scan of the current data file To display the first scan of the current data file do one of the following Double click at the required retention time in the Chromatogram window Right click and drag the mouse across the appropriate range of interest in the Chromatogram window to initiate a Combine Spectrum process Select Spectrum from t
558. uantify calibration curves 5 Calculation of compound concentrations 6 Printing reports of results How Does TurboMass Quantify and Report a List of Samples After data for all of the samples have been acquired TurboMass must perform several tasks to get from a list of samples to a printed report of their concentrations While you do have considerable flexibility in the control of these processes quantification is still a straightforward operation consisting of the following basic steps Quantify Integration of Chromatograms Sample lit Sample 1 Sample 2 Sample n Quantitation Method All Compounds Integrate Integrate Integrate Chromatograms Chromatograms Chromatograms Peak List Peak Lis Peak List Sample 1 Sample 2 ample n Chromatogram integration is made up of two processes smoothing and peak detection You specify how these processes are to be applied in the Quantify method The results of the peak detection are stored in a peak list that has the same name as that of the sample data file being processed The Sample List indicates which sample data files are to be integrated Each compound in the Quantify method specifies a chromatogram trace that is to be used to Quantify that compound The chromatogram for each of the method compounds is integrated and the resulting peaks are saved to a single peak list 251 TurboMass Software User s Guide 252 Generation of Calibra
559. ue JP Red 255 Sat ZJ Green 0 CalolSold Lum i20 Blue OK Cancel Help Add to Custom Colors Define Custom alors gt gt 3 Click Add to Custom Colors to display the new color in one of the Custom colors fields 4 Click OK 33 TurboMass Software User s Guide 34 TurboMass System Global Parameters TurboMass includes an option that allows you to specify preferences that apply to a number of windows These options are called TurboMass System Global Parameters Rather than setting these parameters in every window you can set the values at the top level and the system will automatically apply the settings to all relevant windows To modify the System Global Parameters select Options from the TurboMass Tools menu to display the Options dialog System Processes Mass Defect Display Type Scan Number Ei Axes Labelling m z he I Use Acquired File as Default Display Type Axes Labeling Use Acquired File as Default Select either Scan Number or Retention Time This will determine the values entered to select spectra in Spectrum and Library Select Da e u e or m z to determine axis labeling for spectral displays Da represents Daltons previously called amu u represents atomic mass units e represents the elementary charge Select this parameter to always show the last acquired raw file when the Spectrum or Chromatogram windows are opened Getting Start
560. ulate Plots calibration curves for all standards calibration curves Quantify Calculates concentrations for analyte samples using compounds the current calibration curves Blank subtract When a sample defined as a blank is encountered compounds the value is saved and subtracted from subsequent samples until the next blank is encountered this new value is saved and subtracted from the next set of samples 315 TurboMass Software User s Guide 316 NOTE 3 Click OK to exit Controlling Quantify Reports Four printed reports of quantification results are available Quantify Compound Summary Report Displays quantification results for each of the Quantify compounds ordered by compound Quantify Sample Summary Report Displays quantification results for each of the Quantify compounds ordered by sample Quantify Calibration Report Gives calibration curve graph for each Quantify compound Quantify Sample Report Graphically displays all located chromatogram peaks and tables quantification results Report is grouped by sample The Chromatogram application is opened when producing the report Printing Quantify reports 1 Quantify Reports will be automatically printed at the end of a sample list analysis if Print Quantify Reports is selected when a sample list analysis is started OR Select Print Report from the Quantify File menu to open the Quantify Reports dialog Reports wig V Quantify summary
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562. ument Data Thresholding parameters that allow you to control how the system preprocesses data before they are sent to the host computer Instrument Data Thresholding allows you to specify the type of data you want to acquire and save to disk and which type of data you want to discard Limiting the amount of data stored on disk can be particularly desirable when acquiring continuum data and doing long GC runs Additional options allow you to set the SIR Baseline Level the ion counting threshold spike removal and zero baseline offset Setting Data Thresholding Parameters Changing data thresholding parameters 1 Display the Tune page by clicking a in the MS section of the instrument status panel in the TurboMass top level window 2 On the Tune page select Instrument Threshold Settings from the Options menu The Instrument Threshold Settings dialog appears Profile Data Profile Data Spike Removal OK Baseline Level ig I Use Spike Removal ae Cancel Points per Dalton 16 bd Minimum Spike Intensity p Spike Percentage Ratio p r Centroid Data Minimum centroid height e Minimum points per peak p SIR Data SIR Baseline Level fe lon Counting Threshold E 3 Set your parameters Profile Data Instrument Data Thresholds While not normally used for GC MS TurboMass can collect Profile Data that shows mass peak shapes as in Tune The profile data parameters let you co
563. urrogate Bromoflurorobenzene Dichlorodifluoromethane Vinyl Chloride Bromomethane Trichlorofluoromethane 1 1 Dichloroethene Methyl Tert butyl Ether Methylene Chloride 1 1 Dichloroethane 2 2 Dichloropropane Chloroform Benzene Type CAS number Abbreviation Maximum in blank MDL Water Soil Response Factors Minimum RRF Maximum RSD Init Cal Maximum Difference Target 75 71 8 Trichloroethene Dibromomethane 1 Bromo 2 chloroethane Toluene trans 1 3 Dichloropropene 1 1 2 Trichloroethane Ethylbenzene p m Xylene o Xylene Isopropylbenzene Bromobenzene n Propylbenzene 1 3 5 trimethylbenzene sec Butylbenzene Previous Cancel Compounds A list view of all compounds defined in the Quantify Method The currently selected compound row will remain highlighted The list displays e The compound number this will be the same number displayed in the main Quantify Method Editor window Clicking on Sorts the compounds in the order in which they appear in the Quantify Method main window or reverse order if clicked again e The compound type Target Spike Surrogate or Internal Standard see also Type control Clicking on Type sorts the compounds by type in alphabetical or reverse alphabetical order or reverse alphabetical order if clicked again e The compound name as it appears in the main Quantify Method Editor window Clicking on Name sorts the compounds by name in alphabetical or
564. ution factor Dilution factor applied to the sample Undiluted is 1 221 TurboMass Software User s Guide 222 Soil extract vol The total volume of the methanol extract Enabled only if the Analysis type is Volatiles the Matrix is Soil and the Concentration level is Medium Soil aliquot vol Volume of the aliquot of the sample methanol extract Enabled only if the Analysis type is Volatiles the Matrix is Soil and the Concentration level is Medium Extraction type A text field that indicates how the sample was extracted Conc extract vol The concentrated extract volume Enabled if the Analysis type is Volatiles or Semi volatiles GPC Cleanup A drop down box that indicates whether or not the sample was subject to a GPC gel permeation chromatography cleanup procedure Enabled if the Analysis type is Semi volatiles Cleanup A text field that describes any non GPC cleanup procedure used Enabled if the Analysis type is Volatiles or Semi volatiles The following parameters are informational only used for reports Decanted A drop down list that indicates whether or not the sample was decanted Enabled only if the Analysis type is Semi volatiles and Matrix is Soil Heated purge A drop down box that indicates whether or not a heated purge was used Enabled if the Analysis type is Volatiles or Semi volatiles Surrogate lot ID A text field allowing identification of the lot number of the surrogate standard
565. value for each of the located peaks can then be calculated and saved along with the compound name and other peak information in the peak list A concentration is calculated for each of a compound s located peaks by applying the compound s calibration curve Concentration information is saved in the peak list 253 TurboMass Software User s Guide 254 Displaying Quantify Results Quantify displays the results of quantification in three windows Summary window Shows a list of results that can be ordered either by compound or by sample Graphs window Shows the calibration curve for each compound in the method with calculated statistics Peak List window Shows the information saved in the peak list for each sample The Summary window allows you to thoroughly examine the Quantify results To recall integrated chromatograms double click on a point in the summary and modify baselines as necessary Reporting Results Quantify Reports x Quantify summary by sample W Calibration curves T Quantity samples Cancel Format Four printed reports of Quantify results are available Quantify Compound Summary Report Displays quantification results for each of the Quantify compounds ordered by compound Quantify Sample Summary Report Displays quantification results for each of the Quantify compounds ordered by sample Quantify Calibration Report Gives calibration curve graph for each Quantify compound
566. ve select Active and enter the minimum and maximum molecular weights in the Min and Max fields Specifies the minimum or maximum molecular weight that an element must have for its entry to appear in the Hit List To specify a particular molecular weight enter equal Min and Max values These parameters specify the number of particular elements that must be present in the library entry molecular formula in order for the entry to appear in the Hit List Specifies the minimum number of elements that must be present in an entry in order for it to appear in the Hit List Specifies the maximum number of elements that must be present in an entry in order for it to appear in the Hit List To activate the filter specified in the Max Min fields select the Active checkbox Enter elemental formulas in the standard format as an element symbol followed immediately by its count if greater than unity and then immediately by another symbol as relevant For example suppose you want to set the Elements parameter to C6H20NCIBr2 Enter symbols in the standard upper and lower case format Note that Cl does not need a 1 after it and that there are no spaces The specific order of elements is 499 TurboMass Software User s Guide irrelevant If you have a specific formula to match enter this formula in both the Min and Max fields and do not select Include Other Elements If an element appears only in the Min field there is no uppe
567. ve when the button is in the down position Displays the Help window 557 TurboMass Software User s Guide 558 Communique Reporting 2 0 Communiqu Reporting About the Report Method Editor In this section we will show you how to use the Report Method Editor and Communiqu to modify an existing report template and create a new report template A vital aspect to the flexible reporting capabilities of the TurboMass software will be the data model This defines the data that will be made available to Communiqu for design of the template and generation of the report Most TurboMass data is available through the data model This includes 1 All existing quantitative data generated by the TurboMass Quantification process including Area and Norm values 2 The chromatograms and spectra defined by the Qualitative method and its processing 3 Values associated with the multiple ion ratio identification process ratios pass fail etc 4 Peak plots associated with multiple ion ratio processing for target compounds and internal standards 5 Calibration curve plots associated with target compounds Library search spectral plot data and text results 7 Quantification and Qualitative method parameters TurboMass creates a collection of Data Objects that appear in the Communiqu Report Creator In the Communiqu Report Creator note that collections in the Communiqu sense of the word are ind
568. vel parameter Baseline 0 lon Counting 0 AB0005 2 0 128 Sm SG 2x1 00 Cm 1 18 Scan El 100 6 6le4 576 02 Baseline Level 5 564 03 0 AB0002 2 0 128 Sm SG 2x1 00 Cm 1 18 100 576 02 Baseline Level 564 03 0 AB0001 4 0 232 Sm SG 2x1 00 Cm 1 18 100 576 02 Baseline Level 564 03 o4 T T T T T T AB0000 2 0 128 Sm SG 2x1 00 Cm 1 18 100 re 576 02 Baseline Level 564 03 0 Dale 550 555 560 565 570 575 580 585 590 595 600 605 610 615 620 625 630 635 640 645 650 Figure 3 Effect of increasing Baseline Level on Heptacosa spectrum The second example shows the effect of increasing the lon Counting Threshold on a part of the spectrum that contains only background noise The bottom trace was acquired with the lon Counting Threshold set to zero For subsequent traces the lon Counting Threshold was set to 1 2 4 6 and 25 As the lon Counting Threshold is increased the amount of noise stored is reduced the normalizing intensity value at the top right corner of the trace is also reduced Instrument Data Thresholds Baseline 0 lon Counting 25 Data Storage Compressed AB0250 2 0 128 Cm 1 18 100 m o4 Scan El 1 REDEE AB0060 2 0 128 Cm 1 18 100 AB0040 2 0 128 Cm 1 18 100 625 624 Baseline 0 lon Counting 0 AB0020 4 0 232 Cm 1 18 100 625 50 o4 63 645 72 640 93 643 54 Dai 628 630 632 634 636
569. w Report Method a Qusttve Report PO ae a z TE ieee O e M D E E Move Up aera ea Move Down nea romatagram Plat 3 Click the Append button This template appears in the Report Template field This is a display of the reports defined for the current method 582 Communiqu Reporting Z Report Method Editor New Report Method 01 x File Help 0gaBlela m Template 1 Qualitative Report Qualitative Report Frequency Generate report for every run v X Output IV Print hardcopy J Save to database I Save to file Send via email Setup i dove U Sections Mot Sections On Sections Off Modify do Jown Chromatogram Plot Delete Clear List Report name prefix When the list is empty New Method after Clear List or after all reports have been Deleted the controls on the right will be set to default values In this way the Append button is always enabled and valid Using the Move Up and Move Down command buttons reorders the Reports in the list Reports will be processed by report number i e in the order in the list Set the other options on this screen For example set the Frequency to one of the following Generate report for every run Generate report for every run of specified type Analyte Blank QC or Standard Generate report only for final row in the sample list Set the Output options and specify a Report name pr
570. ween main and isotope peaks Values of lenses are ramped over a narrower range using the values determined in stage 4 to see where the high mass peak intensity maximizes The value of multiplier ramped until the low mass peak intensity is 80 of full scale When AutoTune has finished it displays a status message indicating that AutoTune has been successfully completed Click OK to return to the Tune page The tuning parameters determined by AutoTune will be saved to the current tune parameter file Instrument Tuning Kea 2 Click to start AutoTune You will hear a click when the reference gas solenoid valve opens and AutoTune begins The first page of AutoTune is displayed Ts AUTOTUNE STATUS Stage GF READY TO START AUTOTUNE Hampina 3 Alternatively you can click Setup to display the AutoTune Setup dialog and customize your Tune parameters Se E ine low mass x and high mass calibraton r Level range Maintenance Full m Tune Masses Low Mass Da 69 High Mass Da 502 Prints a report of the m Peak Width at Half Height AutoTune results at the Sea completion of the High Mass Da 0 6 AutoTune m Target Tune J Print Report J DFTPP BFB Correction r Final Multipler Setting I User Set 10 101 TurboMass Software User s Guide 4 Click OK to accept the setup parameters The AutoTune dialog appears with the message Read
571. will be plotted at 100 amu that is a sum of all masses between 99 5 and 100 5 amu The Map program will sum all scans in a window equal to the scan resolution to create the map display Summing scans in the data file can also improve the signal to noise ratio this will help to make peaks more visible and reduce the displayed noise Mapping part of the data file of interest 1 Select Create Map from the Map Process menu The Create Datafile Map dialog is displayed Create Datafile Map x r Static File C ATMINTRO PRO Data GAS2 Function 1 Browse r Retention Time Resolution Mass Range Start min f5 Mass amu fi 000 Start amu 45 End min 6 4 Scans fi End amu 750 Cen oean Map 2 Enter values for the Mass Range and Retention Time range that you wish to map 3 Click OK 533 TurboMass Software User s Guide 534 Manipulating the Display You can alter the display retention time and mass axis ranges using the mouse or by using a menu command The Map Display menu contains commands for changing the range of the mass axis and restoring the default display Altering the display range with the mouse gt Mass and retention time axes may both be expanded by clicking with the mouse on the spectrum The previous state of the display can be restored by clicking Altering the range of the retention time axis gt Left click at one end of the region of interest and dra
572. window since each report is displayed when it is generated and further processing of the sample list is paused until the preview window is closed S TurboMass Report Preview a4 Pato pip al By ame Print Current Print All Cancel All Reports Next Preview Print reports but don t preview them Environmental amp Chemical BU Quantitation Report C TurboMassi TUTORIALREPORTS PROData StdMix58 raw 07 Oct 03 08 42 23 PM Page 10f7 U44366C Unknown HCB Int Std SIR z 1007033pr Printed 15 Oct 03 02 52 29 PM Method StdMixs mth Vial Number 24 i stdmix4m EXP St MixSIR odb lastupdated 15 Oct 03 06 17 10 AM 1 Octanol Retention Time 5 925 min Concentration 0 8409 ppm Pass Fail Pass TSR El Sana TSR Ei Siss a 1 5405 5 3504 100 Time Time o Time 5900 8 000 5800 6 000 5800 6 000 Tapt mz 5600 Quaerit nz 6400 Guster _mz7000 Rt mz Awa S Time Range Rafo Range Ratio 595 BAD Ezg 582 6 025 wao 592 s00 1187 2 n7 817 wo saw 7ao 16971 243 663 sas To review a report within this environment 1 Use the page navigation and display tools to examine each page of the report Click the appropriate button to indicate the action settings regarding printing of the current report and previewing of future reports 243 TurboMass Software User s Guide Main Report Preview Toolbar Control 4 4 Page 2 of gt fs 244 Description The text
573. wnloaded The first time you open this window the IPM will not have been downloaded 4 From the Configuration Editor window select Configure from the Instrument menu The serial port connected to GC dialog is displayed 5 Verify the serial port in this example COM2 LINK box connection and firmware version If the mass spectrometer and your computer were configured for COM1 then COM is your serial port Appendix B TurboMass Software Installation 6 Click on the Query Port for Type button The Interface type is displayed in the box Click the Continue button The LINK Configuration dialog with the COM port and instrument name displays Select Port A from the LINK Ports and Instruments list instl is displayed in the box to the right of Port A Select the Clarus 500 GC with Autosampler in the nstrument Module list If your Clarus 500 GC has an autosampler select Clarus 500 GC with Autosampler even if you won t be using the autosampler You can change this setting from the Method Editor LINK Configuration 1 721 TurboMass Software User s Guide If you make a mistake click Restart This disconnects the GC and clears the LINK port Clicking Reset clears all the changes to this dialog and returns it to the state it was in before you opened it When the software verifies this connection a box appears under Configured and a Configure button appears LINK Configuration jal El
574. ws with blank Analysis or Matrix column Rows az If Matrix is Soil then the Conc Level column cannot be blank General Error Sample list contains Soil sample with blank Conc Level column Rows az For items 1 to 5 the display of row numbers exhibiting the error is determined in one of the two following ways 1 The first Calibration file Quantify Method etc located ignoring any referenced by the Tune Eval sample will be taken as the correct one and any row that references a different one will be flagged as in error 2 The Calibration file Quantify Method etc that is referenced most frequently in the selected rows will be taken as the correct one and any row that references a different one will be flagged as in error Environmental Reporting Contiguous groups of rows will be displayed in the form xz while isolated rows will displayed separated by commas General errors must be cleared before the report generation process can proceed Although general errors can be cleared by unchecking rows this may leave a sample list that cannot be used to generate the required forms i e Form specific errors may be generated in the process In this event you may have to leave this environment and edit the sample list or create a new one before generating reports Warnings A warning is defined as a condition that does not meet the strict rules of CLP reporting but may be valid in the context of CLP like reporting Warnings do not preve
575. x Index for first processed data file _proc002 dat Second processed data file _proc002 idx Index for second processed data file _Tcfuncl raw Data files from the first conventional GC detector _Tefunc2 raw Data files from the second conventional GC detector Getting Started Displaying Spectra There are several ways in which you can ask to display the Spectrum window The two most common ways are selecting Spectrum from the TurboMass View menu or double clicking the Chromatogram window Selecting a spectrum using the TurboMass menu gt Select Spectrum from the View menu The spectrum displayed will be the current default spectrum this will be either the last spectrum viewed or if acquisition is in progress the last spectrum acquired If the Spectrum window is already on display it becomes the current window If whole rows are selected in the Sample List editor spectra from the data files represented by these rows will be displayed Selecting a spectrum from Chromatogram gt Double click the chromatogram at the retention time of interest The spectrum displayed will be the spectrum closest in retention time to the position where the mouse was clicked If the Spectrum window is already on display the selected spectrum will either be added to the one currently on display OR Will replace the one currently on display if the Spectrum toolbar button is activated OR Will be displayed in a new document window
576. x Spike Recovery 100 where 285 TurboMass Software User s Guide SSR Spiked sample result calculated concentration from the Spike Matrix Spike or Spike Dup Matrix Spike Duplicate sample Sample result calculated concentration from the unspiked Analyte sample Spike amount added taken from the Quantify Method The relative percent difference RPD of the recoveries of each compound in the matrix spike and matrix spike duplicate shall be calculated as follows Rpp _ abs MSR MSDR MSR MSDR where MSR Matrix spike recovery calculated from the Spike and Analyte sample pair x 100 MSDR_ Matrix spike duplicate recovery calculated from the Spike Dup and Analyte sample pair Since the numerator is calculated from the absolute value of the difference between the recoveries the RPD is always expressed as a positive value AutoBuild Automatically Building a Quantification Method After a chromatogram is labeled with the desired names the names retention times spectra and largest ion can be automatically used to build a quantification method See the following procedure 1 In Chromatogram expand the time axis to the range of interest by dragging the left mouse button 2 Select Integrate from the Process menu Drag the right mouse button over a background range of the chromatogram to set the noise peak to peak amplitude 3 Click OK This will integrate the chromatogram 4 Select Lib Search P
577. ximizes within 2 scans eliminate all but the one with the largest area or the first one if there are two with equal area o If Exclude target compounds is set in the method remove peaks that maximize within 2 scans of the actual retention time of the target compound taken from the quantification results This setting is ignored if no quantification results are available If this option is not checked and quantification results exist then these results compound name concentration and concentration units will be associated with the appropriate peak in the data source However Area and Norm results will always come from the qualitative processing Sort in descending area order Eliminate all but the largest by area n peaks where n is the Largest peaks parameter from the qualitative method Re sort in retention time order Add the peak data to the data source Qualitative Method Qualitative Method Editor The main window consists of menu bar tool bar and three tabs of parameters e General e Search Parameters e Library Settings The General parameters are needed for all qualitative reports that require a peak data set Since Search Parameters and Library Settings are only required when a library search is to be performed these have been placed on secondary tabs Qualitative Method Editor Untitled 15 x File Help 3 e e S m Of General Search Parameters Library Settings Peak
578. y 7 To make the detector autozero at the start of each run select Autozero On 8 Ifthe Value field is available enter a value to specify an offset 9 Ifthe Polarity option is available select Positive or Negative 10 If the Filament option is available select On or Off 11 Under Gases specify the gas flow rates for the detector 12 If the GC configuration includes either REC Recorder or INT Integrator settings for analog output set the following options under REC or INT e Select an Attenuation value for analog output from the Attenuation drop down list e In the Offset field enter the amount by which to offset the analog output for an external recorder 14 Repeat Steps 2 through 11 for the second detector Setting Instrument Timed Events Use the Instrument Timed Events tab of the Instrument Control dialog to select one or more timed events from a predefined list and enter the time at which you want the event to take place 171 TurboMass Software User s Guide Adding or editing timed events 1 Select the Instrument Timed Events tab of the Instrument Control dialog Autosampler Oven Irlets Carer Detectors Insttument Timed Events Time min 0 00 Add Event mo T Heper Value 0 ae Defined Events p Valves Event Value Time o 2 Fi Jamada 3 ba Wits its Tete ke Teka Cancel Apply Events currently defined for this method 2 Inthe Time field enter t
579. y To Start Autotune 5 Click Start to start AutoTuning the mass spectrometer The AutoTune status dialog is displayed The status dialog displays the part of the tuning process that is currently occurring The AutoTune status bar is updated to show the progress of AutoTune AutoTune has seven stages 102 Instrument Tuning Setting Scope Parameters Various parameters can be set to control the peak display You can control the speed at which the display is refreshed Changing the Scope Setup 1 Click OR Select Scope Parameters from the Tune Options menu Scope Setup x r Time OK Scan Time s fo 05 ox Inter Scan Delay s 0 1 2 Make any required changes to the settings 3 Click OK Scan Time Controls the speed with which the Tune peak display is updated and Inter The tuning system will behave more responsively if the scan time Scan Time and inter scan time are short The following options are available by right clicking on the spectrum plot on the Tune page Grid Select Horizontal and or Vertical a check mark appears in the menu to display a horizontal grid and or vertical grid on the peak display Intensity When this parameter is set to Relative Intensity the percentage intensity of the base peak in the active tune segment window is displayed When this parameter is set to Absolute Intensity the absolute intensity of the base peak in the active tune segment window is d
580. ys appears when you save a new file If auditing has not been started for a file then the Description tab also appears when you use Save As to save an existing file with a new name e Ifauditing has been started for a file the Audit Trail dialog appears every time you save that file with either Save or Save As You enable an audit trail by selecting Start audit trail on the Description tab Once an audit trail is started the Description dialog will not appear automatically if you select Save As However you can display it at any time by selecting Description from the File menu 173 TurboMass Software User s Guide The Description tab in the Documentation dialog The Description tab opens when you save a new file and if auditing is not enabled when you select Save As to save an existing file with a new name You can also select Description from the File menu to open the Documentation dialog showing the Description tab Entering information in the Description tab 1 Enter any descriptive information about the file that you want to store with it To start a new line press CTRL M Description Description Logon Name Administrator Begin recording changes made to the file 2 Ifyou want to start tracking changes to the file select Start audit trail 174 GC Control Documentation 472 01 4 11 20 PM DEFAULT This will cause the Audit Trail dialog to appear every time you save this file in the fu

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