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TotalChrom Workstation User's Guide - Volume I

1. reference peak retention time void time The Void Time also corrects the retention times of reference peaks when TotalChrom calculates the expected component retention times For more information refer to Reference Components on page 8 13 Calibration Specifies the calibration setting The options are External standard Uses component amounts and response values to compute either an average calibration factor or a calibration curve Internal standard Uses amount ratios and response ratios to compute the average calibration factor or calibration curve The amount ratio is the amount of component in a standard sample divided by the amount of the designated internal standard in the same sample The response ratio is the area or height of the component peak divided by that of the internal standard peak For information on external and internal standards refer to Chapter 18 Discussion of Data Analysis Reject Outliers During Calibration Checks the response for each component from a calibration run against the current average If the response falls outside the percentage deviation from the average you specify TotalChrom rejects the results does not include them as a replicate Developing Calibration Parameters in the Method 8 5 Understanding Global Calibration Parameters 8 6 Sample Amount Options Correct Amounts For Calibration Standards Adjusts the calibrated amoun
2. sess 5 2 Working with Methods Using the Method Editor Reviewing Method Parameters Printing Method Parameters Importing Method Parameters 5 1 What is a Chromatographic Method What is a Chromatographic Method A method is a collection of parameters that determine how TotalChrom acquires and analyzes data from your chromatography equipment based on the specific requirements of your instrument and your sample Every method consists of three sets of parameters e Instrument Parameters These control data acquisition Settings include data channels oven temperatures instrument parameters and detector settings e Processing Parameters These control data analysis Settings include peak detection and integration of raw data how reports are printed and how replots are formatted e Calibration Parameters These control component information Settings include component names calibration levels and calibration data Working with Methods 5 2 Depending on your needs you can use the following tools and functions when working with methods Method Editor Allows you to access all the settings for each section of a method so that you can build a comprehensive method This chapter provides general information about the global Method Editor tasks For specific information on using the Method Editor to complete the instrument processing and calibration parameters refer to Chapters 6 7 and
3. 10 34 Using the Components Commands in Reprocess Results esesse 10 46 Displaying and Printing Information eese eren rennen enne nre 10 49 Printing a Report or Replot sese enne eene nennen nre 10 51 Printing Method Information eese eene eene nre 10 52 Using Images in Other Applications enne 10 53 Chapter 11 Building a Sequence How a Sequence Works beoe tette eee e m ee ERR ret tereti team 11 2 How TotalChrom Uses A Sequence ssesseseeseeeeeeeee nennen eene 11 2 The Information in a Sequence seesesseeeeeeeerenee eee nee enne enne nennen 11 3 Using the Sequence Editor ie e e Ert t E e 11 4 Menus and Commands in the Sequence Editor eee 11 4 The Sequence Spreadsheet eee eese nente AEE ete eterne entrent 11 5 General Procedure for Building a Sequence seen 11 9 Defining Global Parameters soret Re n Rire t detinere ilte ethan thawte 11 11 Building a Sequence by Template eese nennen rennen 11 13 Building a Sequence Vial by Vial eese enne rennen 11 17 Identifying the Sample 2 eiiis esee rin ea ente trot tod tape nda te ro ea 11 18 Specifying File Informati n ienr eee ote RP ER E ORE uid 11 22 Specifying Quantitation Values eese eene enne eene nr eneenr enne 11 24 Specifying Calibration
4. Calibration type ISOBUT ETHYLA 140 CYCLO C APenExe TcCS Wer6 1 0 Examples Solv001 raw 8848mn 788177 mv 1200 pts Use Next Prev or Retum to accept changes Click on another peak to cancel changes If the method has any existing named groups the name of the first group appears in the Name text box The Group Members list then contains a list of all components in the method with the group members selected in the list and on the plot 3 Choose New in the Edit Components dialog box to create a new named group The words New Group appear in the Name text box 4 Inthe Name text box enter a name for the new group Selecting a group name from the list of names in the Name text box actually changes the name of the group to the selected name It will not select the group To select a group use the Next and Prev buttons 5 To calibrate the group using an internal standard select a name from the ISTD list Editing Methods and Results Graphically 10 43 Working with Components 10 44 10 11 12 In the Group Members list click each component that you want to include in the group As you select each component TotalChrom highlights its associated peak in the chromatogram To calibrate the group with the current data file select Update Calibration The Level and Amount text boxes and the Calibration Type settings become enabled In th
5. ssesseeeeeeeeeeneen eene 17 17 Automating Fit Analysis Functions eese eene ener nennen nennen 17 18 Chapter 18 Discussion of Data Analysis What is Data Analysis seon edu ege ee erg Uni RR rS 18 2 D ta Analysis Parameters oo t e pe etre tede dede 18 2 How the Method Controls Data Analysis eese ener 18 2 Overview of the Steps in Data Analysis eese enne enne 18 3 Baseline Subtraction sneinen e tete i er Heide eee ee e e eene unde e dR LEE ea cedes 18 5 How TotalChrom Performs Baseline Subtraction esse 18 5 P k DeteCtlOri hee nere e oer RO ere P IECUR CR PUE Pe E Pen P E Ert 18 6 Peak Detection P rameters 25 225 nne aede arta Gite e ed Ar ee eie 18 6 The Stages 1n Peak Detection n eet aee eth tee ont 18 11 Peak Separation Criteria ccseeescsescesesesssensescsesentdocenvesocesesbassedvenesonerosbenenodensessorenes 18 14 How Timed Events Affect Peak Detection 18 15 Inte srahones as dicen EE ET ESE apse nien wp ke eh baa ahr a aah ans 18 24 Baselines Within Clusters eene nre nennen enne nns 18 24 Adjustment of Preliminary Baselines 0 0 0 0 csceeeceeecceseeeeeseceeeseceeeeeeeaeeeesaecaeeseeneeees 18 24 lu qe ER EET 18 26 Area Adjustment n nheoniitbte dete a eb ee t p Er ele 18 27 How Timed Events Affect Integration essere enne rennen 18 32 Calculation of Peak Height and Retention Times eee 18 44
6. esee 12 23 Taking Control of an Instrument eeeeseeeeeeeeen nennen enne trennen 12 24 Re establishing Communication with an Instrument eere 12 24 Breaking Communication with an Instrument esee 12 24 Instrument Ertors 2 ineo teet pedet be Ntra F 12 25 Viewing Real Time Plots ds 5 od dete dede utes 12 26 Viewing Multiple Real Time Plots eese 12 28 Rescaling a Plot ias IUE eben daten aues 12 28 Zooming In on the Real Time Plot essent 12 30 Changing the Plot On gin isis iata eR EE er Pico 12 30 Controlling a Run from the Real Time Plot Window eee 12 30 Using Monitor Mode dirt etae Peto te m Instat eee ie tu ede fene iet 12 30 Viewing Data and Instrument Information sees 12 32 Viewing Data Acquisition Information esee nennen 12 33 Viewing Detailed Instrument Information eese 12 34 Understanding Status Messages aet enne EE ee ree ipe e Tn 12 37 What the Status Messages Mean nennen eene rennen ene 12 38 Chapter 13 Working with Instruments Interactively Using Hands Or 2555s eo au Ee t re pb d eee 13 2 Setting Relays for a 900 Series Interface 13 3 Setting Zone Setpoints and Valves for a GC eene 13 5 Setting LC Parameters ideo mere aiat bip eio ER E eher 13 7 Put p ACUOIS 55e RE eheu ec eene p ote ed wa iene il ceto b Eh 13 8 Purging a Pum
7. esee eene eene enne Ea KSN E ES eaae 2 2 Startup Dialog Box dee Ho bene terne Te eMe Ete d ee ipe da rie E dedos ee Tia 2 2 File Open and File Select Dialog Boxes eese eere 2 3 Path Select Dialog BOX iii merenti eee po etd hoes oes 2 4 Program Selection Dialog BOX 5 iet reete Het tbe estere eite pti dee ms 2 5 Tokenized Eie Names enhn eim dn AR AIR n 2 6 Entering Descriptive Information About a File eese eere 2 8 Description iue dices iid e p dua edes 2 8 Using Audit Tr oan eeu ERE RERO AISES EEVA TEREA SVANES 2 10 Entering Audit Trail Information esee enne enne enne eene 2 10 Naewing the Audit Traller tee teet erede pte PR pete eee 2 11 Printing the Audit Trail eorne ra e eene enne 2 12 Using Electronic Signature nennen ente teer er RE ee nre e ce Ene Hue dep od 2 13 Starting Electronic Signatures i sire ciae de e cic b op tre edt 2 13 Entering Your Electronic Signature eese 2 14 Retaining the Requirement for Electronic Signature on a New File 2 14 Selecting an Instrument ne apu ep deae REL e ees 2 15 The Instruments That You Can Select sss 2 15 Using the Instrument Selection Panel eese 2 15 Using TotalChrom Toolbars and Status Bars sese enene 2 16 Chapter 3 Configuring TotalChrom The Configuration Editor eue Dati arden apie nie gee V e PR
8. Close New purge flow rate 0 01 to 10 00 The information on the right side of the tab reflects current pump conditions including the purge flow rate and the solvents being used gt To purge a pump 1 To change the purge flow rate and or the purge solvent being used select the solvent option you want to use and enter a value in the Flow text box The Current Method option purges the pump using the solvent composition specified in the equilibration step of the active method 2 To activate new pump conditions choose Set Pump As the flow rate and solvent percentage change the results are reflected on the right side of the dialog box 3 To start stop the pump choose Start Pump Stop Pump Working with Instruments Interactively 13 9 Setting LC Parameters Detector Actions The Detector tab of the LC Hands On dialog box varies depending on which detector you are using Autozero is available during a non spectral collecting run on the Series 200 DAD However if you autozero during data collection the data collection pauses resulting in a retention time shift of later eluting peaks gt To perform detector actions You can change the wavelength then activate it by choosing Set Detector You can use the Lamp and Autozero commands at any time LC Hands On x Pump Purge Detector Autosampler Current New Wavelength nm 260 Absorbance A au 0 0000 Tum W Lamp Off Wavelength B
9. Cancel Apply Time into run at which this event is to occur 0 000 to 160000 000 In the Time text box enter the time at which you want this event to occur From the Event list select a timed event In the Value text box enter a value if required wR wD Select Correct Actual Times Of All Baseline Events Based On Actual RT Of Nearest Reference Peak if you want your baseline timed events to shift in proportion to the shift of the retention time of the nearest reference peak 6 Choose Add to add this event to the Defined Events list You can also edit or delete the timed events once you have added them gt To edit a timed event 1 Inthe Defined Events list select an event to edit 2 Enter the new time or value in the Time or Value text boxes 3 Choose Replace gt To delete a timed event 1 In the Defined Events list select the event you want to delete 2 Choose Delete or choose Clear List if you want to delete all timed events 7 8 Selecting Optional Reports Selecting Optional Reports The Optional Reports command in the Process menu lets you generate up to six reports in addition to the report specified in the sequence These reports can be formatted according to TotalChrom report format files or according to TC Publisher methods that define the layout of the report For information on how to create a report format file or template refer to Chapter 9 gt To generate and print additional re
10. S Sample Bound User E 9704 Ray e NoMethod 0 Q 0 00 610_LINK ube NoMethod 0 0 0 00 0 00 950 Shery s Cube NoMethod 0 0 0 00 0 00 gt I File Type File Name Method Sequence Data BIE 2 To toggle the display of running files click the right mouse button to access the pop up menu The other columns in the Instrument Status window are as follows Bklg Backlogged Runs Identifies how many runs have been completed for which the data has not been transferred from the interface to TotalChrom Seq Row The current sequence row number This is the run in progress or if the instrument is ready the next run Sample Name The sample name for the sequence row Bound User The name of the user to whom the instrument is bound Elapsed Time The amount of time in minutes that the current cycle has been running Prog Program Time The length of time that the instrument program will run Acquiring and Viewing Data 12 37 Understanding Status Messages 12 38 gt To view the status of the currently selected instrument e The Status box in the Navigator reflects up to six types of information depending on the instrument configuration Series 200 LC Pump No Method ACQ No Data VF Not Ready CMD None First line The status of the active instrument Second line ACQ The status of data acquisition Third line I F The status of the active interface
11. To learn about Go to page Introduction to Instrument Parameters Selecting the Instrument Creating Instrument Notes Setting Data Channels Setting the Real Time Plot Scale Setting Control Options Creating Derivatization and Dilution Programs Series 200 Autosamplers Only 6 1 Introduction to Instrument Parameters Introduction to Instrument Parameters 6 2 Instrument parameters affect how TotalChrom acquires and analyzes data by controlling settings for the chromatographic instruments that you can access from your system These parameters include data channel oven temperature valve settings and carrier pressure solvent composition pump flow rate detector settings and others The values that you set pertain only to the selected instrument and method During data acquisition TotalChrom uses the values in the instrument section of the method to control data sampling the plotting of real time data and the creation of raw data files Set instrument parameters using the commands in the Instrument menu in the Method Editor The specific parameters that you can access depend on the instrument that you select F Method Editor C PenExe TcWS Wer6 2 0 Examples FO896bp1_mth Component List File Instrument Process Components Setup Other View Window Help Notes Data Channels Real Time Plot Scale Control Options Name command Displays a list of all instruments you can access The instrument
12. Acquiring and Viewing Data 12 33 Viewing Data and Instrument Information 12 34 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 Process Current Run Indicates whether the current run will be processed or saved but not processed Interface Information Segments Used How many runs for which data are backlogged in the interface Segments Free Approximately how many runs for which data can still be stored in the interface memory Total Runs Total number of runs completed for this instrument since the start of the initial run This does not include data in the interface that have not been uploaded to TotalChrom Viewing Detailed Instrument Information The status boxes of the Details window display information about the state of the instrument Although the Details window for all instruments contains the Current status box the items within this status box vary depending upon the instrument In addition some status boxes exist only for certain instruments Current The following items appear in the Current status box for all instrument types I F Status Status of the interface This is the same message that appears on the I F line of the Status box in the Navigator For more information refer to Understanding Status Messages on page 12 37 Elapsed Time The amount of time in minutes that
13. By worklist 2 If you want to assign an instrument for this sequence now select from the Instrument list or click the button and select from the Instrument Selection dialog box Building a Sequence 11 11 Defining Global Parameters 11 12 If your instrument contains trays select the LC autosampler tray that you want to use for this sequence If the instrument selected in the Instrument drop down list has a TurboMatrix associated with it select from the Sampling drop down list the type of injection Manual Autosampler or TurboMatrix the sequence will use Select From Template or Vial By Vial as the Build option that you want to use If you have Connect you can build a sequence by worklist Refer to your Connect documentation for information gt To enter configuration parameters 1 On the Configuration tab set the Injection Type to Single or Dual to match the instrument and type of analysis Do not confuse dual injection with dual channel The former refers to the injection of two different samples simultaneously whereas the latter refers to the use of two detectors to monitor the separation of a single sample Under Methods select One Per Row or Multiple Per Row When you select One Per Row there will be one method column labeled Method The method name that you enter will be used for acquisition analysis and component information When you select Multiple Per Row there will be three method co
14. With your cursor anywhere in the Channel A or Channel B spreadsheet choose Append from the Edit menu TotalChrom appends a new row to the bottom of the spreadsheet The new row will contain the same data as the last non program row in the spreadsheet with numeric data incremented for vial sample number raw file result file and modified file Check that the values in the appended row are correct You can use the Smart Fill command to increment values in the Number Vial and Data File columns if necessary See Editing Column Values For information about appending new cycles to a spreadsheet refer to Appending New Cycles to a Sequence on page 11 48 For information about appending cycles to a sequence from a text file refer to Appending Sequence Information from a Text File on page 11 57 Deleting Rows When you delete rows TotalChrom deletes them from both the Channel A and Channel B spreadsheets simultaneously gt To delete spreadsheet rows 1 2 Select the rows that you want to delete Press the Delete key or choose the Delete command from the Edit menu or the shortcut menu Check that the values in remaining rows are correct in the new context You can use the Smart Fill command to increment values in the Number Vial and Data File columns if necessary See Editing Column Values below Pasting Data from an External Spreadsheet Application Building a Sequence You can create sequence
15. 2 Choose OK Starting and Stopping the Pump If you are using an LC the Stop Pump command in the Run menu stops the pump The pump will start automatically when you start the instrument You can also start and stop the pump from the Hands On dialog box which is accessible through the Hands On button in the Navigator Refer to Chapter 13 Working with Instruments Interactively gt To stop the pump on an LC e Choose Stop Pump from the Run menu You can designate how long a pump can remain ready without being used in the Pump dialog box in the Method Editor If it stays idle longer than this Ready Time it will automatically stop Releasing Control of an Instrument You can choose the Release Control command in the Run menu to release an instrument from TotalChrom control If you release the instrument during a run the run is canceled In some cases you can release an instrument from control by TotalChrom to change a setting using the instrument s keyboard and then re establish control by TotalChrom Acquiring and Viewing Data 12 23 Controlling Data Acquisition 12 24 gt To release control of an instrument e In the Navigator click the Run button and choose Release Control from the pop up menu Taking Control of an Instrument The Take Control command in the Run menu allows you to take control of an instrument if its current status is Released gt To take control of an instrument e Inthe Navigat
16. 3 19 Configuring User Options Plot Options The Plot command in the Options menu controls a variety of features related to how TotalChrom displays and prints chromatograms Plot settings include e Whether or not to autoscale the chromatogram e To include or exclude header information on the printed output e Whether or not to display the reference chromatogram in the Graphic Method Editor and Reprocess Results windows and if so its size e The default plotting style you want to use You define which labels you want to appear on the plot in the processing section of the method Refer to Chapter 7 Developing Processing Parameters in the Method gt To configure plot options 1 3 20 In the Configuration Editor choose Plot from the Options menu Plot Options Reference Chromatogram Iv Show reference chromatogram ris 4 Size 4 Header on all replot pages Bunched points Reset C Data points Cancel Line segments Plotting Style Select to plot chromatograms at full scale otherwise user enters scale Deselect Autoscale Plots By Default to disable this feature Autoscaling automatically scales the chromatogram so that the tallest peak extends from the bottom of the window to the top Other peaks are scaled in proportion to the tallest peak If you deselect autoscaling a dialog box appears each time you load a new file in the Graphic Method Editor
17. conii osten ep EU Se eR UD E ERE RR RD HS B 3 Suitability REPO S ek a aeea m RD Ge bee RO P a RC ecd rr d B 4 System Suitability Reports eese eene nennen enne nennen nrenn enne B 4 System Suitability Summary Reports esee nennen B 6 Using Suit bility ante dt erobert ute teg dera ee eerte e ettet B 8 Creating Suit bihty Method iunii uterine eate ro bg B 9 Using an Existing Suitability Method esent enne B 11 Editing the Component List eese eee a nennen trennen enne B 12 Selecting Suitability Options sscan ii e nE EE E EE nein nne B 13 Selecting Result Files 5 2 5 2 EE E ET etie el A R R B 16 Printing the Suitability Method and Reports seen B 18 Automating Suitability Reports essent enne a AE en enne rennen ene B 20 Suitability Calculations n p o RR e Iro tee Re haved a B 22 Theoretical Plates by the Tangential Method ssssseeeeeeeen B 22 Theoretical Plates by the Foley Dorsey Approximation eene B 23 Talis Factor oie repete een E Ene eo B 23 Capacity Factor kj sehr ee a a TRE eret RO t e Dee ee B 23 R solution sah ikon Seshub eon n reir d peii RE AE REA ins B 24 Alpha tete emt cir eei e epe e pta PAR gts eri i B 24 Sigr al To Noi1se Rates ire ea eee rere eet ath ante beds B 25 Appendix C Interface Validation Interface Validation Module Software sss eren C 2 Insta
18. Based on your choice in Step 14 do one of the following e Ifyou selected Vertical Scaling enter a value in the Scale Factor text box e If you selected Absolute Scaling enter a value in the Offset text box e If you selected Autozero Offset or Absolute Scaling enter a value in the Full Scale text box About Scaling Types The Vertical Scaling Autozero Offset and Absolute Scaling parameters all determine the scaling of the voltage axis This section provides additional information on these parameters Vertical Scaling If you choose this option the voltage scale will be relative it will be based on the maximum and minimum points in the chromatogram With relative scaling you enter a scale factor that determines the relationship between the data limits and the voltage scale For example if the scale factor is 1 the maximum data value minus the minimum data value will set the raw scale If the scale factor is 2 the initial scale will be equal to the difference divided by 2 The plot or final scale is set by the plot offset which adjusts the initial scale by five percent to keep the chromatogram on the page The relationship between the plot scale plot offset reported high point and reported low point is shown below 7 14 Editing Replot Parameters Maximum Minimum Scale tial 7 IG Scale Factor Scale Scale 0 05 x Scale initial initial Offset Minimum 0 05 x Scale ial High Pt blot
19. Change Cancel Information to be used for this calibration 2 Choose Add to select the appropriate result file Performing a Manual Calibration 3 Selectalevel in the Level list box 4 Select Replace or Average as the Calibration Type Replace Replaces the existing replicates with the new replicates Average Averages the existing calibration replicates with the new replicates 5 Repeat Steps 2 through 4 to include more files 6 Toidentify peaks in the result file before calibration select Identify Peaks Before Calibrating Select this option if you want TotalChrom to identify peaks based on changes you have made in the method Only select this option if you know that the current version of the method will identify the peaks in the result file correctly 7 Choose OK gt To change an entry in the Filename Level Cal Type list 1 Select the entry you want to change in the Filename Level Cal Type list 2 Selecta new filename level or calibration mode 3 Choose Change 4 Choose OK gt To delete an entry from the Filename Level Cal Type list 1 Select the entry you want to delete in the Filename Level Cal Type list 2 Choose Delete 3 Choose OK Excluding and Deleting Replicates Replicate data are stored in the method The calibration table in the Components dialog box displays the average response for each level the Replicates dialog box shows the individual values that make up the average On
20. Choosing Reset clears all the changes to this dialog box and returns it to the state it was in before it opened gt Toset GC configuration options 1 In the LINK Configuration dialog box choose the Configure button next to the port selection The GC Configuration dialog box appears The settings available for each option vary depending on the instrument you are using GC Configuration x r 002 at koontzsa pGIB Type AutoSystem XL GC with Autosampler Name Instument2 m Options r Detectors PPEinsaled NO DeAfnone EPC DetB NONE meer Gasleak alam M Mode Mode nri Aux tmp zone NONE Dut nc Dut nc E r Inlets 3 r Carrier Pneumatics Injector A NONE z Pressure units Psic v Injector B NONE jf L Eee Oen ey mede Ia ERES Oen mode Ia Car NONE E Car B NONE Wawes 3 r Auxiliary Pneumatics af NONE x 2 NONE x Aux 1 NONE z PPE L Aux 2 NONE 7 EPETF 3 NONE 4 NONE x Aux 3 NONE z PPE Aux 4 NONE z PREIE 5 B Query Inst for Config Copy Inst Config Cancel Enter the name you wish to give to this instrument 2 To rename the instrument to something other than its default name enter the new name in the Name text box Configuration 3 11 Configuring Instruments 3 12 You can configure GCs three different ways e Choose Query Inst For Config to l
21. The GC oven is off Pre Run The GC is executing the pre run events Run The GC run is in progress Ready The GC is ready 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 Cool For a LINK Controlled LC Equil The pump is equilibrating Hold The pump is in a Hold state During the solvent gradient program the current step number appears Not Ready The pump is not ready Off The pump is off Pmin The pump has shut down because it did not exceed the Pinin value set in the method Pimax The pump has shut down because it exceeded the Pinax value set in the method Ready The pump has finished equilibrating Startup The pump is starting and has not yet exceeded the Pinin value set in the method Understanding Status Messages Autosampler Messages Line 6 This line displays the status of an autosampler For a LINK Controlled GC Autosampler Clean The autosampler is performing a cleaning cycle Priority The autosampler is running a priority vial Ready The autosampler is ready RUN The GC run is in progress Sampling The autosampler is performing its sampling procedure For a LINK Controlled LC Autosampler Acquiring and Viewing Data Adjust The autosampler is adjusting the position of the needle in the valve Decode The autosampler is decoding th
22. The Method Edit command in the Actions menu lets you switch to the Method Editor without going through the Navigator gt To switch to the Method Editor 1 Choose Method Edit in the Actions menu If you have changed the current sequence file the Save As dialog box appears You can save the changes to the current file or create a new sequence file Edit Method x Row number Channel Method Channel amp Instrument C Channel B Processing Calibration teen Row number containing the method to edit 1 to 1 Enter the number of the sequence row that contains the name of the method s that you want to edit Choose Channel A or Channel B Choose whether you want to edit the Instrument Processing or Calibration method for the specified row and channel If your spreadsheet has a single method column any option you select will open the same file Choose OK The Sequence Editor window closes and the Method Editor opens and displays the method you identified Edit the method parameters as necessary Refer to Chapters 6 7 and 8 for information about developing instrument processing and calibration parameters in the method Choose Save on the File menu to save the revised method To return to the Sequence Editor window choose Sequence Editor from the Other menu in the Method Editor 11 51 Building a Sequence from a Text File Building a Sequence from a Text File 11 52 You
23. This information determines how TotalChrom draws the baseline beneath the peaks The baseline codes in a report indicate the baseline used for each peak 3 Make any changes to the values for the Exponential Skim Criteria All peaks must meet all following three criteria to be skimmed If any of the peaks does not meet these criteria TotalChrom uses a vertical dropline to separate the peaks Peak Height Ratio The ratio of the baseline corrected height of the parent peak to the baseline corrected height of the child peak The actual value of this ratio must be greater than the value set here for the child peak to be skimmed off the parent To disable exponential skimming throughout the run you can set this parameter to its maximum value Adjusted Height Ratio The ratio of the height of the parent peak above its start point to the height of the child peak above the same point The actual Editing Methods and Results Graphically 10 31 Setting Processing Parameters value of this ratio must be greater than the value set here for the child peak to be skimmed off the parent Valley Height Ratio The ratio of the baseline corrected height of the child peak to the height of the valley between the parent and child peaks above the baseline The actual value of this ratio must be less than the value set here for the child peak to be skimmed off the parent 4 Choose OK TotalChrom reprocesses the data file and changes the chromatog
24. e To change the time enter a new number in the Time text box e To change the value either select one from the list or enter a value in the text box 3 Choose Replace gt To delete a timed event 1 Under Defined Events select the event that you want to delete 2 Choose Delete gt To delete all timed events e Choose Clear List Developing Instrument Parameters in the Method 6 37 Creating Derivatization and Dilution Programs Series 200 Autosamplers Only Creating Derivatization and Dilution Programs Series 200 Autosamplers Only 6 38 If you are using the Series 200 Autosampler you can access the following additional features from the Autosampler dialog box Derivatization transfers and mixes specific volumes of derivatizing reagents from source vials to sample vials You can transfer mix and react specific volumes of up to five reagents with liquid in every sample specified in a sequence Dilution performs dilutions by adding diluent to sample vials You can also perform up to four optional additions on every vial in a sequence You can only perform dilution operations if your Autosampler has the dilution sample tray installed TotalChrom saves the derivatizing and dilution programs that you set up as part of the method you are working with When you run a sequence that specifies this method TotalChrom applies the program to each sample and vial identified in the sequence Setting up a Derivatizat
25. t ood edet eee 11 52 Loading a Text File into a Sequence esee eene 11 57 Appending Sequence Information from a Text File sese 11 57 Merging Sequence Information from a Text File eene 11 58 Table of Contents v Using a Text File from the Command Line sess 11 58 Using Index Files er Pt e HR EB Rp E EH epe 11 59 Printing Sequence Information eese trennen e ener eene nennen 11 60 Chapter 12 Acquiring and Viewing Data vi Setting Up Data A quisiti n siira e ener E EE e an e nre 12 2 Choosing a Setup Type ie terit Oun e Ea E A EEEE EEEE R EES 12 2 Using Q ick Start no enia es a a AE E a nee beam E E e a 12 4 Using a Method iie RE e Ue tee D et e P E EE e E 12 6 Using a Se quence ueos eub asus A RU Nave a th naa nee eia nad AES 12 8 Using Quick Meth d 5 ni e ht eh UD Re ei e gite re 12 15 Building Vial List ate eene nee ree eene tute 12 16 Controlling Data Acquisition sess oido ith tei egre E PO RC Peak 12 19 Starting Data Acquisition iiie uer et noe ci ot pcm pt tns 12 20 Stopping Rn eec eet em eee ir o etr He dO ay 12 21 Cancelng a RUD tif ee RSEN ote o E Ri 12 21 Pausing and Resuming Data Acquisition essere 12 22 Cl anmng th Setup ca ge ae m rM RE ERU eC OPERE 12 23 Starting and Stopping the Pump sees eene rennen enne 12 23 Releasing Control of an Instrument
26. Choose OK TotalChrom recalculates the information and displays the modified calculated chromatogram Saving the New Chromatogram If you have created a new chromatogram by using the New Calculation Plot command the default title of that chromatogram reflects the two file names and operation To save the chromatogram as a new raw data file you use the Save As command gt To save anew calculation chromatogram under a new name 1 Select the chromatogram that you want to rename 2 Choose Save As from the File menu Enter any information in the Description tab of the Documentation dialog box The Save As dialog box opens next showing the temporary file name and directory in the File Name text box 3 Enter a new file name changing directories if necessary 4 Choose Save to save the file Displaying Chromatograms 14 31 14 32 2 2 CFR Part 11 2 3 3 D Preview command 14 8 14 9 6 600 Series LINK Interface See also LINK backlogged data indicators A 8 communication methods A 5 configuring 3 9 3 14 memory A 7 overview A 4 software modules A 4 viewing detailed status of 12 32 7 785 detector wavelength calibration 13 19 9 900 Series Interface acquiring data with 12 20 analog signals converting with A 3 backlogged data indicators A 8 channel options setting 6 8 configuring 3 4 3 8 data compression A 10 default specifications C 17 instruments interaction with A 3 memory A 7 overview A 2 relay se
27. If you do not select this option TotalChrom will automatically print a report and plot at the end of a run 12 To run a program after TotalChrom downloads the method to the interface select Run A User Program After Setup Enter or select the name including the path of the program you want to run 13 If after a run finishes you want the channel reset with a particular method or other options set Post Sequence Options as described in the following procedure 14 Choose OK in the Setup Instrument dialog box to initialize the instrument gt To set Post Sequence Options 1 Click on the Post Sequence Options tab in the Setup Instrument dialog box Setup Instrument C PenExe T cwS Wer6 2 NE amples C PenE xeXT cw SNVerB 2 NE xamples lt Chan gt _ lt Inst gt _ lt User gt _ 2 Select a Post Sequence Action e Selecting Clear Setup will leave the instrument uninitialized at the end of the sequence No other options in the Post Sequence Options tab will be available This is the only action available for a bracketed sequence e Selecting Use Last Active Method From The Sequence will leave the instrument set up with the last used method No other options in the Post Sequence Options tab will be available Acquiring and Viewing Data 12 13 Setting Up Data Acquisition 12 14 e Selecting Set Up With Specified Parameters will enable other options in the Post Sequence Options tab e Selecting Use Options from Configu
28. If you open another file after you select Overlay that file will appear both in its own window and in the overlay window gt To overlay chromatograms e Open the chromatogram files that you want to overlay and choose Overlay from the Window menu Chromatograms Overlay View ojx Fie Operation Options Window View Help 18 xl slalo L1G s aeaa m ele a n Toast allt ae le lie al dfe PIE eT 15 2 0 25 0 5 4 0 45 0 0 05 Start 0 000 End 5 000 Offset 35 275 Scale 803 509 7 Viewing Chromatograms Three Dimensionally The 3 D Preview command on the Options menu lets you create a three dimensional effect in an overlay window by rotating and elevating chromatograms Viewing overlaid chromatograms three dimensionally makes them visually more distinct and can enable you to better evaluate the differences between two or more similar plots Controlling the Appearance of Chromatogram Windows The 3 D Preview command is available only for an overlay window gt To change the rotation and elevation of chromatograms in overlay mode 1 Choose Overlay on the Window menu 2 Choose 3 D Preview on the Options menu e The chromatogram that is displayed in the 3 D Preview dialog box is an example and does not duplicate the overlaid chromatograms However the overlay will reflect your three dimensional changes after you close the 3 D Preview dialog box 3D Preview 3 Move the slider und
29. Information from a Text File on page 11 57 You can append a single row to a sequence by selecting the Append command from the Edit menu See Appending a Row on page 11 37 Editing Global Parameters To change the basic structure of an existing sequence use the Global Parameters command on the Change menu When you change global parameters the integrity of a sequence can be affected Make sure that the values in the sequence are compatible with any new instrument configurations you assign when you change global parameters Because global parameters define the fundamental characteristics of a sequence changing them for an existing sequence can have a serious impact For example certain vial number entries that are valid for a Series 900 Interface will be invalid if you change the instrument type to an AutoSystem GC with a built in autosampler Building a Sequence 11 49 Changing Environments From Within the Sequence Editor Changing Environments From Within the Sequence Editor The commands in the Actions menu allow you to switch directly to other functions in TotalChrom without having to go through the Navigator You can e Switch to Setup to acquire data using the sequence e Reprocess data from the sequence file using the Batch Reprocessing function e Switch to the Method Editor to revise parameters associated with this sequence Switching to Setup The Set Up command in the Actions menu allows you to switch to the Set
30. Named Groups A named group consists of two or more single peak components You must first identify a peak as a component before you can include it in a named group The group area and height are the sum of the individual peak areas and heights TotalChrom calculates the components as a group independent of its members calibrations TotalChrom reports the results as if the group is a single component You can calibrate the components in a named group individually and report the results for individual components Members of a named group can appear anywhere in the chromatogram and a single peak component can be a member of more than one named group Components Developing Calibration Parameters in the Method 8 11 Understanding Component Parameters 8 12 Timed Groups A timed group consists of a group of peaks whose retention times fall within a group time window that you define The time window consists of a start time and an end time so a timed group is comprised of a series of contiguous peaks Each peak is detected and integrated individually The group area and height are the sum of the individual peak areas and heights The group is calibrated independently of its members calibrations if they are identified as components Peaks need not be identified to be included in a timed group Identification Calibration User Values LIMS Component Type C Peak C Named group Timed group Nam
31. Peak width s 27 00 Peak width pts 54 Old sampling rate pts s 2 000000 Old bunching factor pts 2 2 Sampling rate Bunching factor E teen Enter the bunching factor 1 to 99 The dialog box has the following information and options Peak Width s The width of the peak in seconds that you just selected Peak Width pts The width of the peak in data points that you just selected Old Sampling Rate pts s The sampling rate currently set in the instrument section of the method Old Bunching Factor pts The bunching factor currently set in the processing section of the method Sampling Rate The recommended new sampling rate This option is only available in the Graphic Method Editor Bunching Factor The recommended new bunching factor Note that you can enter values other than the one that TotalChrom recommends but you can only enter a sampling rate or a bunching factor not both If the recommended sampling rate is higher than that used to collect the current data file then you might not be able to achieve optimal results for all peaks in the current file 3 Doone ofthe following e Leave Bunching Factor selected and then enter a new value e Select Sampling Rate and enter a new value Editing Methods and Results Graphically 10 29 Setting Processing Parameters If your power line frequency is 60 Hz you must enter a sampling rate as follows e for single and dua
32. To change the temperature of a Peltier tray enter a different value in the New text box then choose Set Temp to activate the setting To enable disable Peltier tray temperature control choose Turn Peltier On Turn Peltier Off Modifying a Downloaded Method Modifying a Downloaded Method The Modify Downloaded Method command in the TotalChrom Navigator lets you change method parameters in any method that has been downloaded as part of the setup The Downloaded Method command is available from the Modify button and from the Instrument menu once you set up and bind an instrument Modify Clicking the Modify button or choosing the Modify command from the Instrument menu displays a pop up menu with two commands Downloaded Method and Active Sequence See page 13 16 for information on modifying an active sequence If you have multiple instruments set up and bound Modify Downloaded Method works like other functions in TotalChrom the button applies to the instrument currently selected in the Navigator Choosing the command from the menu lets you select which instrument you want to use afterward When a single 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 choose the Downloaded Method command When multiple methods have been downloaded TotalChrom lists them for you to select from when you choose the command One will be identified as
33. To load a different method use the Open command on the File menu The procedures in this chapter assume that you selected the Autoscale Plots By Default option in the Configuration Editor If you deselected this option when you configured your system the Rescale Plot dialog box appears whenever you open a new data file For information on how to use this dialog box see Changing the Plot Display on page 10 14 Editing Methods and Results Graphically 10 5 Using the Graphic Method Editor Understanding the Graphic Method Editor Window By default the Graphic Method Editor shows a working chromatogram in the main work area of the window and a reference chromatogram above it 4s Graphic Method Editor C PenExe TcCS Ver6 1 0 Examples solvent mth Eile Process Calibration Display Other View Help tal SIR j ze ae x uj epe st MEK ISOBUT ETHYLA CYCLO ETHYLB C PenExe TcC5 Were 1 0 Examples Solv001 raw 5 849 min 568 879 mV 1200 pts I You can toggle the display of the reference chromatogram by choosing Reference Chromatogram from the Display menu To hide the reference chromatogram as the default setting deselect Show Reference Chromatogram in the Plot Options dialog box of the Configuration Editor before you open the Graphic Method Editor window File Menu Lets you load and print other methods and data files specify a report format file enter and review docum
34. TotalChrom hides all search windows from the working chromatogram Editing Methods and Results Graphically 10 47 Working with Components Because timed groups do not use search windows the Show Windows command does not display the window for timed groups Instead timed groups have a group marker based on time that defines which peaks are part of the group You can view timed group windows by entering starting and ending times in the Edit Component dialog box as described in Creating and Editing Named and Timed Groups For more information on how TotalChrom uses search windows to identify peaks refer to Chapter 8 Updating Calibration Information The Calibrate command in the Calibration menu lets you use the results from the current data file to update the calibration information for a specified level in the current method This applies to every component in the method To update calibration for individual components use the Update Calibration check box in the Edit Components dialog box gt To update calibration information 1 Choose Calibrate from the Calibration menu to open the Calibrate dialog box Calibrate x Calibration level Mode cinci Cancel Select calibration level to update 2 Inthe Calibration Level list select the appropriate calibration level for the current data file from the list of levels defined in the current method 3 Select either Average or Replace under Mode Averag
35. Working with Components 10 46 3 In the Name field enter a name for the new group component Selecting a group name from the list of names in the Name text box actually changes the name of the group to the selected name It will not select the group To select a group use the Next and Prev buttons 4 10 11 12 To use a time reference peak select a name from the Reference list To calibrate the group using an internal standard select a name from the ISTD list Enter or edit the Group Start Time The group window marker changes dynamically as you adjust the time Enter or edit the Group End Time To calibrate the component select Update Calibration The Level and Amount text boxes and the Calibration Type settings become enabled In the Level text box enter the name of a calibration level or select a level from the list In the Amount text box enter the sum of the standard amounts for each of the member components of the group Select Average or Replace under Calibration Type Average Adds an entry to the calibration replicate list for the component in the current method Replace Deletes all calibration replicates for the current component in the current method and replaces them with one replicate for the current data file For a new component Average and Replace act in the same way because there is no current calibration information Choose Next or Prev to implement the change and mov
36. You can create new views and you can rename and delete any view except General gt To create a new view tab 1 Position the cursor on the tab to the left of where you want the new tab to appear Building a Sequence 11 29 Editing the Sequence Spreadsheet 2 Choose New View from the Format menu Create a new view x New view name 3 Entera name for the view then choose OK to display the Hide Unhide Columns dialog box 4 Select the column names that you want to include in the view and move them to the other list by clicking the appropriate arrow button 5 Choose OK gt Torename a view tab 1 Select the tab that you want to rename 2 Choose Rename View from the Format menu Old view name Sample Description New view name Carce Enter new name of view 3 Entera new name then choose OK gt To delete a view tab 1 Select the tab that you want to delete 2 Choose Delete View from the Format menu Changing the Appearance of a Spreadsheet You can customize the appearance of a spreadsheet by e Changing column widths e Synchronizing column widths for both channels e Changing the font used in the spreadsheet 11 30 Editing the Sequence Spreadsheet Changing Column Widths Building a Sequence You can format your spreadsheet by increasing or decreasing the width of columns with the mouse You can also use the Column Width command to change the width of columns gt T
37. and 8 Chapter 9 Chapter 10 Report F ormat Build Report Format Graphic Edit Build Graphic Edit Chapter 10 Chapter 11 Chapter 14 4 9 Sequence Build Sequence Chromatograms Navigator Tasks and Other Application Tasks To open an application Use this button or For more that lets you command information see Reprocess data from Chapter 15 multiple runs A Reprocess Batch Summarize component Chapter 16 data A Summary Reprocess Summary View and manipulate IRIS TurboScan spectral data with the documents optional LC spectral analysis application Spectra button Start the Review and Chapter 20 Approve application or Display the TC Publisher B TC Publisher Help file Report Console to enable you to generate reports Publish Display Reports There are other applications that you access from the Apps menu Some of these applications are documented in this manual use the table of contents and index to locate this material Other applications such as Results Review are documented in separate manuals There are various administrative functions that you access from the Admin menu These are documented in the Application Manager s Guide 4 10 Chapter 5 Building a Method This chapter explains what a method is shows how to use the Method Editor and provides the general steps to build a method that meets your analytical needs To learn about Go to page What is a Chromatographic Method
38. any reagent or liquid to the sample vial If the sample vials contain different volumes enter the smallest volume of the vial series 4 If you are using air mix mode select from the Air Mix Volume list the volume of air you want delivered through the flush syringe for each mixing cycle 5 Enter the number of reagents that you want to use for the derivatization The same number of rows are enabled in the Entry Table 6 Select a speed from the Mix Speed In list For liquid mixing this setting controls how fast the syringe draws up a sample from the vial for mixing For air mixing this setting controls how fast the syringe draws up air 7 Selecta speed from the Mix Speed Out list For liquid mixing this setting controls how fast the syringe dispenses the sample back into the vial for mixing For air mixing this setting controls how fast the syringe injects air into the sample vial Developing Instrument Parameters in the Method 6 39 Creating Derivatization and Dilution Programs Series 200 Autosamplers Only 6 40 8 In the Reagent Vial column enter the vial position of the reagent that you want to use in the derivatization 9 Inthe Volume column enter the volume of the reagent that you want the Autosampler to transfer to each target vial 10 In the Mix Cycles column enter the number of mixing cycles you want This value represents the number of times you want the Autosampler to mix the sample and the reagent after
39. nm 280 Autozero Get Values Absorbance B au 0 0000 Tum detector Deuterium D2 lamp on or off 1 To change the wavelength to be monitored for Channel A and or B enter new values in the New text boxes next to Wavelength A and or Wavelength B then choose Set Detector The Absorbance fields for Channels A and B show you the detector output at the current wavelength 2 To turn the D2 deuterium or W tungsten detector lamp off on choose the corresponding command 3 To set the detector signal back to zero choose Autozero 13 10 Setting LC Parameters gt To perform 785 detector actions LC Hands On e To set the detector signal back to zero choose Autozero Autosampler Actions The following is the Autosampler tab of the LC Hands On dialog box You can use the Flush Autosampler command at any time For an autosampler equipped with a Peltier tray you can change the temperature then activate it by choosing Set Temp You can enable disable the Peltier tray at any time with the Turn Peltier On Turn Peltier Off command Working with Instruments Interactively 13 11 Setting LC Parameters 13 12 gt To perform autosampler actions 1 2 To have the autosampler perform a flush cycle choose Flush Autosampler To have the autosampler reset the sampling needle to the correct position when a sample is introduced into the sampling valve choose Adjust Needle
40. that you select for each method determines which commands and dialog box options are available Notes command Lets you describe the instrument type and model the column type and length and other settings You can enter your own text or use predefined templates that match different instrument types This information has no effect on data analysis it only appears in the header of printed reports Data Channels command Controls how TotalChrom acquires analog and digital data by letting you set the channel and sampling rate for data collection Real Time Plot Scale command Lets you define plot offset and scaling values as well as graphic display characteristics for the real time plot Control Options command Opens a submenu that lets you set a wide range of parameters for the current instrument including autosampler valves carrier oven inlets solvent pump detector and instrument timed event options The following sections describe the dialog boxes and procedures for each command The options parameters defaults and ranges in the dialog boxes for the instrument section of the method all depend on the specific instrument that you choose for the method Some of the parameters described in the following tasks and figures might be unavailable on your system Selecting the Instrument Selecting the Instrument The Name command in the Instrument menu displays a list of all instruments you can access The instrument th
41. the chromatogram Reprocess Reprocesses the raw data file using the new baseline events Return Closes the baseline timed events display 2 From the Events list select the baseline timed event that you want to add For technical information about these events refer to the sections How Timed Events Affect Peak Detection and How Timed Events Affect Integration in Chapter 18 3 If the event requires a value choose one from the Value list 4 Onthe chromatogram click where you want the event to occur Editing Methods and Results Graphically 10 23 Setting Processing Parameters When using user forced peak events UF the event occurs at the point where you click the mouse pointer It does not automatically create the event on the baseline For additional information refer to Retention Time and User Forced Peak Events in Chapter 18 We strongly recommend using the Manual Reintegration procedure to add UF events to a method The event appears at the specified point on the plot If you make a mistake you can delete the event and try again Alternatively you can set the exact time at which you want the event to occur in the Baseline Timed Events tab Process Menu in the Method Editor 5 Choose Reprocess or Return to implement the change gt To delete a baseline timed event 1 Choose Baseline Events from the Process menu to open the baseline timed events display 2 Choose Delete Events to open t
42. 0 000 End 2 998 Offset 37 036 Scale 915 552 7 Scaling the Time From Origin The Scale Time From Origin command on the Chromatogram pop up menu rescales the X axis of the target chromatogram relative to a reference chromatogram You align the peaks by holding the origin start time constant and compressing or expanding the X axis of the target chromatogram in order that the selected peak aligns with the peak in the reference chromatogram gt To align peaks by scaling time from origin 1 Set an end time in both chromatograms 2 Right click in the target chromatogram and choose Scale Time From Origin The X axis in the target chromatogram is scaled such that the peak in the target chromatogram aligns with the peak in the reference chromatogram Scaling the Time using Two Time Points The Scale Time command rescales the X axis of a chromatogram you want to scale and shifts it relative to a reference chromatogram You select two points on each chromatogram that you want to appear at the same positions on the X axis The start and end times of the target chromatogram will be adjusted such that the marked points align with the marked points on the reference chromatogram 14 22 Aligning Peaks in Two Chromatograms gt To align peaks by scaling time 1 Set a start and end time in both chromatograms Chromatograms Halo_004_ 1aw File Operation Options Window View Help slale Le waea m e a Mi Halo_003 1aw For Hel
43. 000 to 160000 000 Introduction to Processing Parameters There are five tabs in the Process dialog box Integration Select this tab to set integration and peak detection parameters Peak detection parameters include bunching factor noise threshold and area threshold Integration parameters include peak separation criteria and exponential skim criteria Baseline Timed Events Select this tab to set baseline timed events that determine how TotalChrom processes data Optional Reports Select this tab to specify up to six different types of reports that will be printed in addition to the main report that you specify in the sequence Replot Select this tab to set the characteristics of the chromatogram TotalChrom produces after analyzing a raw data file Replot parameters include scaling factors offsets plot title and X Y axis labeling information User Programs Select this tab to specify the file names of the programs you want to run during or after data analysis 2 Select the tab for each processing function that you want to complete or edit 3 Make any changes to the values in the dialog box and then do any of the following e To save your work and close the dialog box choose OK e To save your work without closing the dialog box choose Apply e To close the dialog box and discard your changes since the last time you chose Apply choose Cancel The following sections describe how to complete ea
44. 0000 Setting Component Defaults gt To calibrate using calibration curve parameters 1 Select the Calibration tab of the Component Defaults dialog box 2 Select Use Curve as the Calibration Type r Calibration Type C Use calibration factor C Avg calibration factor 3 Under Response select Area or Height The last column of the table changes to Area or Height depending on the option you choose 4 From the Curve Fit Type list select a curve type When you set defaults you must enter an appropriate number of levels for the curve type you have selected However you do not have to change amounts from 0 0000 Based on the calibration curve type the minimum number of levels required are e Point To Point 1 e Ist Order Polynomial 2 or if you include the origin e 2nd Order Polynomial 3 or 2 if you include the origin e 3rd Order Polynomial 4 or 3 if you include the origin 5 From the Scaling list select a factor you want to use For definitions of the choices refer to Selecting Fit Parameters on page 8 16 6 From the Weighting list select a factor you want to use For definitions of the choices refer to Selecting Fit Parameters on page 8 16 7 Under Origin Treatment select Include or Force as the origin option if required Leave both options deselected to omit the origin from the calibration 8 Edit the Level Amount and Area Height values as necessary For more info
45. 27 4 When you are finished developing the sequence choose Save from the File menu The Documentation dialog box opens 11 10 Defining Global Parameters 5 Complete the Description tab in the Documentation dialog box and choose OK For a discussion about entering descriptive information about a file refer to Chapter 2 TotalChrom Basics The TotalChrom File Save As dialog box opens 6 Entera name for the sequence in the File Name text box and choose Save The dialog box closes and the new sequence name appears in the title bar 7 When you are finished working in the Sequence Editor choose Exit from the File menu Alternatively you can choose from the Actions menu to go directly to another application Defining Global Parameters Whenever you create a new sequence you enter information in the Global Parameters dialog box You also use this dialog box to change global parameters for an existing sequence There are two tabs in the Global Parameters dialog box Build Parameters and Configuration Each is described in a separate procedure gt To enter build parameters for a new sequence 1 When you choose Create New Sequence from the Startup dialog box or New from the File menu the Global Parameters dialog box opens x Build Parameters Configuration l Logon name amolime Instrument Clarus 500 TurboMatix v Fx Sampling rubus e Build From template C Vial by vial
46. 650 5 Setthe Rate Setpoint and Hold values for the other ramp levels 6 Youcan 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 change the hold time duration of a level select the point that represents the time and drag it horizontally 7 If you selected capillary mode during instrument configuration set the length and diameter of the column under Column and select whether or not you want vacuum compensation for the column Select On if the detector is at vacuum Select Off if the detector is at atmospheric pressure 8 If the instrument is configured with auxiliary pneumatics enter the Aux Pneumatics Setpoints for any auxiliary zones 9 Under Split Control select a split control mode and then do one of the following e f you select Ratio enter a split ratio in the Ratio text box Developing Instrument Parameters in the Method 6 17 Setting Control Options e Ifyou select Flow enter a split flow in the Flow text box Not Configured for PPC If the instrument has neither carrier nor auxiliary zone configured as a PPC Zone you can enter on
47. 76 error messages insufficient calibration information 17 4 Invalid Type In Text File 11 57 IVM reported by C 18 log file for 12 25 No Field Identifiers Were Specified 11 57 Overflow 12 24 Unknown Field Identifier 11 57 Wrapped 12 24 Error Messages command 12 25 events See timed events examples actual peak start point finding 18 11 area thresholds 18 15 baseline adjusted at start of cluster 18 26 baseline penetrated by chromatogram valley 18 24 bunched data points too few 18 7 calibration level names 18 47 correcting component amounts 18 53 distance between peaks exceeds noise threshold 18 8 external standard calibration curve 18 49 internal standard calibration curve 18 51 internal standard calibration multiple levels 18 52 method parameters for testing unipolar interface C 10 peak after SM event is run 18 23 peak before SM event is run 18 23 peak detection timed event effect of 18 17 peak shoulders detecting 18 13 peak top confirming potential 18 12 relationship of area threshold to peak detection 18 9 relationship of noise threshold to peak detection 18 8 18 10 single validation run text file C 17 Suitability report B 4 B 7 summary report 16 12 synchronized program 7 18 text file format 11 57 timed events effect of I and I 18 21 effect of N and N 18 18 retention time and user forced peak 18 22 unrepresented components 18 48 validation report C 15 Expand All Plots command 14 11 14 12 Expand Reference Chr
48. 8 respectively Graphic Method Editor Allows you to change a method and view the effect on a stored chromatogram instantaneously Graphic method editing lets you optimize the method for an individual run For information about the Graphic Method Editor refer to Chapter 10 Editing Methods and Results Graphically Quick Method Allows you to collect data before developing a comprehensive method For information about creating Quick Methods refer to Chapter 12 Acquiring and Viewing Data Using the Method Editor Using the Method Editor Use the Method Editor for all method operations This section describes the windows and menus in the Method Editor and also explains the general procedure for creating a method Method Editor Windows There are two windows in the Method Editor Method Summary Window Shows the instrument processing and calibration parameter settings for the open method The information that is displayed in the Method Summary window changes depending on the type of instrument you are using Component List Window Shows the list of components in the method the component calibration information and the calibration curve for the selected component Method Summary Window There are three sections in the Method Summary window Data Acquisition and Instrument Control Shows the instrument name run time information type of injection and control options such as the sampling rate and the o
49. Acquisition Viewing Real Time Plots Viewing Data and Instrument Information Understanding Status Messages 12 1 Setting Up Data Acquisition Setting Up Data Acquisition 12 2 Acquiring data in brief consists of e Receiving analog or digital signals from one or more chromatographic detectors through an interface e Converting these signals to digital data if necessary e Displaying the data as a real time plot if desired e Storing the data for analysis Once you set up and initialize an instrument you control data acquisition by using the commands in the Navigator Run menu You can view the data in real time as it is generated and view detailed information about the instruments and interfaces TotalChrom acquires data based on the instructions contained in a method file mth which you download from the computer to the interface memory using the Setup function The Quick Start setup type uses a basic default method file whereas the Method and Sequence types use more sophisticated pre defined method files You need to set these method parameters before you can acquire data This section explains e How to choose a setup type e How to set parameters appropriate for each different type and e How to build a Quick Method or Vial List if necessary for your setup Choosing a Setup Type You can set up an instrument in three different ways depending on the analytical task you need to perform These three options
50. Advanced Parameters Peak Separation Criteria r Exponential Skim Criteria Width ratio o 200 Peak height ratio 5 000 pomo ioo Valley to peak ratio Adjusted height ratio Valley height ratio 3 im Defaults mea an Number of points to average for peak detection 1 to 98 2 Inthe Bunching Factor text box enter the number of successive raw data points you want to average to establish a single bunched data point Entering Peak Detection and Integration Parameters 3 Inthe Noise Threshold text box enter a value that helps determine the difference between baseline noise and the start of a peak 4 Inthe Area Threshold text box enter a value that helps discriminate between noise spikes and peaks As a general rule set the area threshold to approximately five times the noise threshold However the optimal ratio depends on the actual peak size and signal to noise ratio 5 Under Peak Separation Criteria enter a value for Width Ratio and Valley To Peak Ratio 6 To restore the peak separation criteria to the system defaults choose Defaults 7 Under Exponential Skim Criteria enter a Peak Height Ratio Adjusted Height Ratio and Valley Height Ratio For additional information refer to Chapter 10 Changing Peak Separation and Exponential Skim Criteria Developing Processing Parameters in the Method 7 5 Entering Baseline Timed Event
51. Area C Ayg calibration factor Height Calibrate by reference Use curve Heplicates BUTYL CELLOSOLVE Curve fit type 2a Order M Origin Treatment CELLOSOLVE ACETATE ETHYL BENZENE Scaling None s I include oXYLENE Weighting Nore zj Me Purity fi 00 0000 Level Amt Area Vs 10 000000 3 234297 e 06 20 000000 8 434277 e306 30 000000 7 631546e 06 40 000000 3 353078e 06 50 000000 3 18865 Next Previous 1 drum Edit Component You can use a different calibration type for each component in a method The calibration types are Use Calibration Factor Calculates component amounts based on the constant calibration factor you enter for the individual component Note that this is different from the calibration factor you enter in the Global Information dialog box which is used for all unidentified peaks The calibration factor is divided into the peak response to obtain an amount during quantitation Average Calibration Factor Averages the response to amount values or response ratio to amount ratio for internal standard calibration at each calibration standard level It applies to multi level calibrations but does not construct a calibration curve from the data Calibrate By Reference Quantitates the component using the calibration type of a designated reference component TotalChrom calculates the amounts as if the peak were the same as the calibration reference component The designated calibrati
52. C OFF 8 CON OFF 2 CON OFF Coe Relay 1 Off When the Interface Hands On dialog box appears the status message for the interface will change from Ready to NRDY Not Ready in the Status box in the Navigator It will change back to Ready when you close the dialog box 2 Select the relays you want to turn on by clicking the ON buttons 3 Choose Set Relays to implement the settings 4 Choose Close if you do not need to read rack and or vial numbers You must choose Set Relays before choosing Close in order to change settings Working with Instruments Interactively 13 3 Setting Relays for a 900 Series Interface gt To read rack and or vial numbers from an autosampler e Choose Read RVP to have TotalChrom read the rack and vial numbers This command tests the connection to the autosampler only The rack and or vial numbers that appear in the dialog box are not stored 13 4 Setting Zone Setpoints and Valves for a GC Setting Zone Setpoints and Valves for a GC If you are controlling a gas chromatograph you can set the oven temperature autozero the detector and turn valves or relays on and off The instrument type and its current run status determine which Hands On parameters are accessible gt To set controls for a gas chromatograph 1 Select the GC in the Instrument panel then click the Hands On button in the Navigator al s OR Choose Hands On from the Instrument menu then select th
53. Configuration Information 3 26 Chapter 4 Using the Navigator The Navigator window that appears when you start TotalChrom lets you perform most TotalChrom functions in a graphic easy to use environment Large recognizable buttons duplicate many menu commands and functions are depicted in a logical flow chart style To learn about Go to page Starting TotalChrom The Navigator Window Navigator Buttons and Commands Navigator Tasks and Other Application Tasks 4 1 Starting TotalChrom Starting TotalChrom Start TotalChrom and open the Navigator window by double clicking the Navigator icon in the TotalChrom program group gt To start TotalChrom and open the Navigator window 1 Click the Start button choose Programs and open the TotalChrom folder 2 Double click the TCNav icon TCNav The TotalChrom Logon dialog box appears unless your application manager has configured your system to bypass it TotalChrom Logon x Enter user name 3 Enteror select your user name then enter your password You can change your password with the Change Password command in the Admin menu 4 Choose OK The Navigator window opens after the program initializes 4 2 The Navigator Window The Navigator Window Using The Navigator The Navigator window contains a graphical representation of the major functions in TotalChrom This window has a panel that shows instruments configured for your sy
54. Each component amount in the method is multiplied by this factor to correct for any difference between the actual and expected amounts e When sample amount is used to convert unknown samples to concentration units it acts as a divisor 3 Inthe ISTD Amount text box enter the amount of internal standard that is being added to the sample or calibration standard The units must be the same as those used for the ISTD component amounts in the calibration section of the method If you want to use the same ISTD amount s specified in the calibration section of the method use the default value of 1 0 4 Inthe Sample Volume text box enter the actual volume injected This value affects quantitation only it does not control the amount of sample injected 5 In the Dilution Factor text box enter the amount that represents the dilution factor used in the sample before injection Use 1 as the dilution factor if the sample is not diluted or if you do not want to make this correction Raw amounts are multiplied by this value to get adjusted amounts 6 Inthe Multiplier text box enter a value by which to multiply raw component amounts to get adjusted amounts 7 Inthe Divisor text box enter a value by which to divide raw component amounts to get adjusted amounts 8 Inthe Addend text box enter a value to add to raw component amounts to get adjusted amounts 9 In the Norm Factor text box enter the value that you want to use for the
55. Format Using the Report Format Editor eessen eere T nennen enne T e rennen enne 9 2 Menus and Command venden E etse ter etes fe taeda 9 2 General Procedure for Creating a Report Format seen 9 3 Creating Title Header and Footer Text ssssssssseseseeseer ener 9 5 Editing Report Columns aee UR ip ie a t e CREE Ee ERES 9 6 Adding and Deleting Columns eese enne eene nennen nennen enne 9 6 Replacing Editing Column Information eese enne 9 8 Moving Columns 2 edo eee onm eeu in 9 9 Creating a Custom Expression eeseeeeseeeeeeeeneenen sei trennt tne ne enne trennen enne 9 10 Creating Additional Custom Expressions ccsccscssscsseeeeeseeeteseceeeseceeeeeceaecaeeaeeaeeseens 9 12 Editing Report Format Options sceescsssssscssecseeseceeeseceseeecsecseesecseesecsaeeeeaesaeeseesesseenaeeees 9 13 Printing Report Format Files esee ene e nne nne nennen nnne 9 17 Chapter 10 Editing Methods and Results Graphically Optimizing Data Analyses With Graphic Editing Applications eee 10 2 Graphic Method Editing Versus Reprocessing Results eene 10 3 Using the Graphic Method Editor essent rennennnnne 10 4 Understanding the Graphic Method Editor Window eee 10 6 Loading Files in the Graphic Method Editor eee 10 8 Saving Files i
56. Fourth line CMD The run command currently in effect Fifth line The LINK controlled instrument status such as the pump status for an LC Sixth line The status of the LINK controlled autosampler Lines five and six will not appear for a 900 Series Interface Line six will not appear if there is no LINK controlled autosampler What the Status Messages Mean This information changes continuously as you acquire and analyze data report the results modify methods and sequences and perform other actions that affect the instrument or interface The color of the text that appears in the Status box changes based on the status of the run and the instrument 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 TotalChrom 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 The following are explanations of the status messages that appear in the Status box Understanding Status Messages Global Status Line 1 Active The interface is collecting data from a current run or it is in monitor mode Detached Not currently communicating with the instrument possibly due to communication errors Initializing TotalChrom is retrieving initial status information for the instrument In Reconfig This ins
57. It is set as a percentage of the vial height measured from the bottom of the vial In the Inject Delay Time text box enter the number of minutes that you want between the pump s run start signal and when the sample injection occurs If you are using a Series 200 Autosampler refer to Creating Derivatization and Dilution Programs on page 6 38 for information on the Derivatization and Dilution options When using Serial Dilution with a Peltier Tray when you Setup the autosampler it goes Not Ready and starts to cool the Peltier Tray to 4 C 13 14 15 16 In the Flush Volume text box enter the amount of flush solution that you want pumped through the sampling system for each flush cycle From the Flush Speed list select the speed at which you want the pump to flush the system In the Flush Cycles text box enter the number of flush cycles that you want to have between injections when the method changes in a sequence This value also specifies the number of flushes the autosampler performs when you choose Flush Autosampler in the Hands On dialog box In the Pre Injection Cycles text box enter the number of flush cycles that you want before each sample injection or before each vial to vial transfer in sample processing modes Setting Control Options 17 In the Post Injection Cycles text box enter the number of flush cycles that you want after each sample injection or before each vial to vial transfer in sample
58. Print Report from the Report menu The Print Options dialog box appears Print Options x 2 Dooneor more of the following e To print the report select Report e To print the complete plot that is defined by the replot parameters in the method select Annotated Replot e To print a copy of the current plot as it is scaled on the screen select Current View 3 If you are printing the current view choose Portrait or Landscape Portrait Orients the image on the page so that the time axis is parallel to the width of the page Landscape Orients the image on the page so that the time axis is parallel to the length of the page 4 Choose OK 5 Make any changes to the option in the second Print dialog box and choose OK Editing Methods and Results Graphically 10 53 Displaying and Printing Information Printing Method Information The Print Method command in the File menu offers the same printing options as the Method Editor you can print the instrument processing and calibration parameters gt To print a copy of the parameters in the method 1 Choose Print Method from the File menu to open the Print Options dialog box os 3 Cancel IV Processing parameters IV Calibration parameters I Level lists Replicate lists Audit trail Print data acquisition and instrument control parameters 2 Select the method parameters that you want to print and choose OK The Print
59. Processing method Result file Calibration method Modified Report format file Baseline teen First row to be changed 1 to 1 To change the default rows edit the values for Starting Row and or Ending Row If you did not select specific rows the default values include the entire sequence To change the default paths edit the entry for Path To Change If you selected a single cell the existing path is displayed Otherwise an asterisk is displayed to represent all cells in the range of rows Enter or select a new path for the file s Select the check box for each file type whose path you want to change Any method and data columns that are included in your selection are checked by default If you selected Same Name in the Global Parameters dialog box a single checkbox labeled Data is available for both raw and result files Choose OK Creating Notes About Your Samples Building a Sequence You may enter information about each non program cycle in the spreadsheet by using the Sample Note command gt To create a sample note 1 Double click a Note cell to open the Sample Note dialog box OR Click anywhere in the row for which you want to add a note and then choose Sample Note from the Change menu or the shortcut menu You can enter different notes for each channel 11 45 Editing the Sequence Spreadsheet 11 46 Sample note forrow 2 Sample Name Sample note descriptive
60. Real Time Plot dialog box in the method Under Time Axis define the part of the run you want to view by entering a starting and ending time in the Plot From and Plot To text boxes respectively In the Number Of Pages text box enter how many screen widths pages you want the full plot to be displayed across The amount of the plot displayed on each screen page is therefore equal to the full plot time divided by the number of pages When the plot has filled a screen page the window is cleared and the next page begins to be plotted To redisplay data from a previous screen page you can rescale the plot 12 29 Viewing Real Time Plots Zooming In on the Real Time Plot The Zoom In and Zoom Out commands in the Options menu of the Real Time Plot window let you enlarge and reduce the y axis of the real time plot as the data points are being collected If you are using a dual channel instrument you can change the views independently for each channel The Zoom In command halves the full scale value thereby enlarging the plotted peaks You can enlarge the view up to a full scale value of 0 01 mV The Zoom Out command doubles the full scale value thereby reducing the size of the plotted peaks The Zoom commands do not change the plot offset value or the time axis scale Changing the Plot Origin The Autozero command in the Options menu of the Real Time Plot window changes the offset value for Channel A and or Channel B so that th
61. Report Format Options Editing Report Format Options The Options command in the Report Format Editor opens a dialog box that contains a variety of options that relate to the information you want to include in the report gt To edit report format options Building a Report Format 1 2 Choose Options to display the Report Format Options dialog box Report Format Options x m System Header C None or Small m C Large Instrument control parameters r Report Body Options VV Print main report body Identified components Identified named groups T Identified timed groups I Unidentified peaks I Missing components Missing named groups Missing timed groups Area reject 0 00 r Compressed Mode C Always use condensed font Use normal font when possible r Miscellaneous Options Expand named groups Expand timed groups IV Print missing component report Print baseline timed event table Create ASCII delimited file Create AIA metafile Create SQL LIMS file Formfeed between reports Print replot with report Replot Size in 3 00 Cancel Minimal system information plus file names and collection parameters Select the size of the System Header you want to include in the report The system header contains summary information about the data analysis it is not merely a label like the user entered report header The following table shows whi
62. SR x 60 where RT is the run time and SR is the sampling rate 6 If your instrument supports the uploading of run logs you can select Store Run Log to upload the run log at the end of each run When you select this option TotalChrom prints the run log as part of the report 7 Doany ofthe following e To save your work and close the dialog box choose OK e To save your work without closing the dialog box choose Apply Developing Instrument Parameters in the Method 6 7 Setting Data Channels 6 8 e To close the dialog box and discard your changes since the last time you chose Apply choose Cancel gt To set channel options for a 900 Series Interface 1 Choose Data Channels from the Instrument menu to open the Data Acquisition dialog box with the Data Channels tab selected Data Channels Real Time Plot m Data Channel Voltage Range o C Dual C 1 Vol C 2Volts 2 1Volt C 10Volts Set Data Rate C By peak width at base s 20 00 By sampling rate pts s 1 000 r Data Storage T Store allidate trom ron Data Points 1800 fa Storeriniag Delay time min 0 00 Run time min 30 00 mE Apply Collect data from channel A only 2 Under Data Channel select channel A B or Dual 3 Select the required Voltage Range The required Voltage Range depends on the magnitude of the output signal from the chromatograph detector 4 Under Set Data Rate do one of the followin
63. Scale Offset Low Pt Plot Offset If the data maximum is 100 mV the minimum is 5 mV and the scale factor is 2 then the initial scale will be 47 5 mV The plot scale will be 49 875 mV rounded to 49 9 mV in the plot header The plot offset will be 2 625 mV rounded to 3 mV The high point reported on the plot header will be 52 5 mV The low point reported on the plot header will be 2 625 mV rounded to 2 63 mV Auto Zero Plot Offset If you choose this option enter the absolute plot scale The lowest point will be calculated from the minimum data value as follows Scale User entered Scale Offset Minimum 0 05 x Scale High Pt plot Scale Offset Low Pty lot 7 Offset If you enter 100 mV as the scale and the minimum data value is 5 mV the plot scale will be 100 mV and the plot offset will be 2 625 mV rounded to 3 mV in the header The high point will be reported as 102 625 mV rounded to 102 63 mV The low point will be reported as 2 625 mV rounded to 2 63 mV Developing Processing Parameters in the Method 7 15 Running User Programs Absolute Scaling If you choose this option you then enter an absolute plot scale and offset TotalChrom makes no adjustments to the bottom of the plot Scale User entered Scale Offset User entered Offset High P iot Scale Offset Low Plot Offset Running User Programs 7 16 The User Programs command in the Process menu lets you run up to five oth
64. Use curve Heplicates level 1 000000 4 2012008 05 Next Previous Edit Component Cee m Use the calibration factor defined below to calculate amounts 3 Entera calibration factor value in the Cal Factor text box 4 Under Response select whether to use Area or Height If you select Average Calibration Factor as the calibration type TotalChrom averages the slope at each calibration point on the curve and uses this average as a single calibration factor TotalChrom does not perform a linear regression on the data Because this calculation requires that the intercept of the curve pass through the origin the Origin options are not available when you add new components or edit existing components The slope at each calibration point referred to above is either a response to amount ratio for external standards or response ratio to amount ratio for internal standards for each replicate 8 34 Adding and Editing Components gt To calibrate using an average calibration factor 1 Select the Calibration tab of the Components dialog box 2 Select Avg Calibration Factor as the Calibration Type r Calibration Type C Use calibration factor Calibrate by reference C Use curve 3 Under Response select whether to use Area or Height The last column of the table changes to Area or Height depending on the option you choose 4 Edit the Level Amt and Area or Height values as nece
65. appearance of 14 7 background color of 14 4 calculating new 14 28 changing rotation and elevation of 14 9 closing 14 2 color of lines within 14 4 comparing 14 20 14 24 coordinates of 14 14 copying 14 6 default display parameters for 10 17 definition 14 1 displaying 10 21 displaying axis labels in 14 14 displaying based on result files 14 14 displaying hidden lines in 14 10 editing 14 31 expanding 10 19 14 11 14 12 hiding and showing title bars 14 14 hiding or displaying 10 21 manipulating 10 21 overlaying 14 7 14 8 printing 14 6 reducing 10 20 reference 10 6 14 20 rescaling the values in 14 13 restoring original 14 21 14 25 reverting to previous expansion level 10 19 saving 14 31 shifting time scales of 14 21 sizing automatically 14 7 target 14 20 truncated cause of 18 5 viewing three dimensionally 14 8 working with 7 13 10 6 Chromatograms menus and commands 14 3 overview 14 2 pop up menu 14 4 Chromatograms command 14 2 chromatographic method definition 5 2 iii Clear command 14 4 15 13 Clear Setup command 12 23 cluster definition 18 14 clusters peak 18 24 color chromatogram of background 14 4 of label 14 17 oflines 14 4 of text 14 18 Colors command 3 18 colors setting for screens and plots 3 18 Column Width command 11 31 columns report see report format and summary report format editor columns sequence spreadsheet duplicating values in 11 43 hiding and displaying 11 29 inserting repeating value in
66. are available in the Setup Instrument dialog that appears when you select an instrument and click the Setup button The choices in the Setup Instrument dialog box will differ depending on the type you select Quick Start If you do not have an appropriate method available you can use TotalChrom s Quick Start feature which lets you specify the essential instrument conditions and data handling parameters during the setup process Since a Quick Start method contains only the very basic parameters the result from a Quick Start analysis will be a simple default report showing peak retention times and area height normalized percentage Setting Up Data Acquisition values The methods you create using Quick Start will not contain the information that is required for component identification or calibration This option is helpful when you are first starting to use the system if you are performing a survey run on a type of sample that you have not analyzed before or when you are developing instrument settings for an analysis Method If you already have an appropriate method and have only a small number of samples to analyze you can use the Method setup option This provides all of the flexibility available in a TotalChrom method to process data For example you can customize report formats and include component names and amounts that are calculated using internal or external standard calibration For detailed information on building met
67. as reference peaks in the component list However you cannot use named or timed group components as reference peaks For information about optimizing component identification refer to Chapter 18 Discussion of Data Analysis Internal Standard Components If you select Internal Standard as the method of Calibration in the Global Information dialog box you must associate each component that is not itself an internal standard with a designated internal standard component You can define one or more components as internal standards in the component list However you cannot use named or timed group components as internal standards When you use an internal standard TotalChrom relates amount ratios to response ratios in order to compute the calibration curve or average calibration factor The amount ratio is the amount of component in the calibration standard divided by the amount of the internal standard component in the same sample The response ratio is the area or height of the component peak divided by that of the internal standard peak For more information about the internal standard method refer to Understanding Component Parameters External Standard Versus Internal Standard Calibration in Chapter 18 Discussion of Data Analysis Calibration Type Identification Calibration User Values LIMS Calibration Type r Response C Use calibration factor
68. at a time you can access a group of related result files by opening the index IDX file in which they are referenced gt To use an index file to open result files 1 In the TotalChrom File Open dialog box select IDX Files idx from the Files Of Type list then select an index file TotalChrom opens the raw data file associated with the first result file in the index file and processes it using the copy of the method embedded in the result file 2 To move through the result files in the index file you selected use the Previous File and Next File commands on the File menu Editing Methods and Results Graphically 10 11 Using Reprocess Results Understanding the Reprocess Results Window By default Reprocess Results shows a working chromatogram in the main work area of the window and a reference chromatogram above it ata Reprocess Results C PenExe TcCS Ver6 1 0 Examples Solv001 rst olx Eile Process Components Display Other Help Salda aa elll E bu 2 2 a ISOBUT ETHYLA CYCLO TOLUEN 4 159 min 690 498 mv 1200 pts You can toggle the display of the reference chromatogram by choosing Reference Chromatogram from the Display menu To hide the reference chromatogram as the default setting deselect Show Reference Chromatogram in the Plot Options dialog box of the Configuration Editor before you open the Reprocess Results window The Reprocess Results
69. boundary line which restricts you from exceeding 100 percent in the 96 axis and preceding the time for the previous step Se Time seep rine Toe meow woo on T s fom iso foo foo foo foo foo i s pea iso eso foo foo 5a fro ames pojeo foo foo fso po E fr000 Joo Joo Joo los M Release the mouse button when the solvent percentage and time period are correct 80 0 60 0 40 0 20 0 0 0 10 0 e Time ELE pe peer foo pa mo pe 1 00 100 0 TotalChrom updates the values in the table and revises the numbers for the other solvents so that the total remains at 100 percent Setting Control Options Duplicating and Deleting Program Steps You can duplicate and delete steps in the pump program by using the Duplicate and Delete choices in a pop up menu gt To duplicate a step in the pump program 1 From the group of available solvents select the solvent you want to work with The corresponding curve appears for the solvent that you select 2 With the right mouse button click the point on the gradient curve that you want to duplicate The Delete Duplicate pop up menu appears 3 Choose Duplicate TotalChrom adds another program step to the curve using the same parameters as the step you selected For example if the step you select has a time duration of 15 minutes the new step will have the same duration and will appear after the original step TotalChrom also in
70. box for that instrument Select Method as the Setup Type Setup Instrument HTSETUITITE TIS SEQUENCE C PenExe TcwS Werb 2 0Examples D SPenE xeXT cw SNVerB 2 XE xamples Chan Inst User fitit Kaaren A soma lige as LK emen In the Method text box enter or select the name of a method file In the Raw file path and Result file path text box enter or select the path where you want to store your data files The check box relating to paths is hidden not merely disabled for all users The raw and result paths are initially filled with your default paths Setting Up Data Acquisition Allowable changes to the contents of these fields via typing or folder button depend on the permissions set in System Configuration In the Base File Name text box enter a file name or set a tokenized name by clicking the button The default Base File Name is typically set in System Configuration Allowable changes to the contents of these fields via typing or folder button depend on the permissions set in System Configuration Your application manager may have set up Default base names in System Configuration Do not end a base file name with a number since it will be treated like a cycle number If you must use a number then use a legal separator for example hyphen or underscore Do not use a period 10 Acquiring and Viewing Data TotalChrom will automatically append a
71. calibration will be the average of all the replicates Cal Replace Represents a calibration run TotalChrom will replace the results of all previous calibration data for the components at the specified calibration level TotalChrom erases stored calibration replicates Cal Bracket Overlapped A type of bracketed calibration in which the final set of calibrations for one group of samples also acts as the first set for the next group Cal Bracket NonOverlapped A type of bracketed calibration in which each group of samples uses its own set of calibrations Standards are duplicated between sample groups Cal Grand Avg Averages all occurrences of each calibration level in the sequence and uses that average to process and report all samples Program Lets you run a user program in the sequence Refer to Including a User Program in a Sequence on page 11 46 Serial Dilution Used with the LC Series 200 Autosampler Serial Dilution function For more information refer to Appendix D Serial Dilution Blank Spike Std Check Ctrl Sample Precision Suitability Other names for Sample that indicate an unknown sample to be analyzed Your application manager might define other additional names for Sample CInup Shutdn Causes the instrument portion of the method to be run However no injection is made and no raw data file is created If there are multiple method columns you can only assign the name of a method i
72. can continue xi Logon name manager Audit Trail Event Time f 2 13 2004 3 21 55 PM File EAPenEseNT CWS Ver6 3 0 Examples default mth Changes Created by File SaveAs from C PenExeST clw S Wer6 3 0 Examples defaul Changed instrument type from S00 Series Intelligent Interface to PE Aute Changed run time from 30 000000 to 20 000000 Changed total time from 30 000000 to 20 000000 Changed sample rate from 1 000000 to 12 500000 b Reason Comment off Cancel IV Retain audit trail information Vv d Keep the requirement For electronic signature Using Audit Trail gt To enter information in the Audit Trail dialog box 1 Select a reason for the change s from the Reason list There is a global list plus a supplementary list for each job type A composite list appears for a each user based on their job type Enter any information about the change s you made to the file in the Comment text box If you 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 If you are saving the existing file as a new file Save As select Retain Electronic Signature if you want to have this feature enabled in the new file Choose OK The information you enter in the Audit Trail dialog box is saved with the file that y
73. close the main window not the individual plot window and return you to the Navigator Rescaling a Plot The Rescale command in the Options menu of the Real Time Plot window lets you change the scaling parameters of the plot while data are being collected The initial parameters come from the instrument section of the method Changing the parameters in the Rescale dialog box does not change the parameters in the method 12 28 Viewing Real Time Plots gt To change the scaling parameters in the real time plot Acquiring and Viewing Data l Choose Rescale from the Options menu The Rescale dialog box opens If you are using a single channel instrument only the parameters for that channel are available m Channel A Voltage Axis Offset mv o 000 Full Scale mV feo 000 Time Axis jl Plot From min 10 00 Trim p 00 Plot To min 120 00 Plat hie mm p 00 Number of Pages fi Number ot Pages fi Cancel Accept these plot parameter settings Under Voltage Axis enter new values for Offset and Scale if you want to change the Y axis scale of the real time plot e Offset value Specifies the voltage corresponding to the bottom of the plot window The default when you open the window is the value you set in the Real Time Plot dialog box in the method e Full Scale value Specifies the vertical size of the real time plot The default when you open the window is the value you set in the
74. command B 12 Edit or Add Component command 8 9 Edit Text command 14 17 14 18 electronic signature 2 13 Electronic Signature 141 end peak timed event 18 40 Entire Chromatogram command 10 19 equations vi adjusted amounts 18 77 adjusted internal standard amount 18 54 18 69 adjusting expected retention times 8 14 amount ratios converting to raw amounts 18 76 amount scaling 18 57 average calibration factors 18 59 calibration factor 18 66 capacity factor B 23 collected data points 6 7 confidence limits test 18 63 correcting component amounts 18 53 correlation coefficient 18 64 exponential skim 18 31 external standard calibration factors 18 59 first order linear curve 18 72 gain error C 20 generating new raw data point 14 29 initial component amount 18 75 internal standard calibration factors 18 60 k value 8 5 least squares approximation from regression calculation 18 58 linearity errors C 20 normalization for 900 Series interface A 3 offset and multiplier 14 30 outlier test 18 66 point to point curve fit initial amount 18 72 regression calculation 18 58 relative retention B 25 relative retention value 8 5 resolution B 24 sampling rates for 900 Series interface A 3 search window total size of 8 13 second order quadratic curve fit 18 72 signal to noise ratio B 25 system efficiency B 22 B 23 tailing factor B 23 third order cubic curve fit 18 73 volume adjusted amounts converting to raw amounts 18
75. complete the Sequence Template dialog box for Channel B When you complete the sequence template TotalChrom builds the sequence To edit the sequence refer to Editing the Sequence Spreadsheet on page 11 27 11 16 Building a Sequence Vial by Vial Building a Sequence Vial by Vial Building a Sequence You can build a sequence by individually defining each sample to be analyzed This is referred to as building the sequence vial by vial Because only one sample is added at a time you can include sample specific information The Append New Cycles dialog box opens when you build a new sequence and select Vial By Vial as the Build option in the Global Parameters dialog box You also use this dialog box when you add cycles to an existing sequence with the Append New Cycles command 9 By worklist There are four tabs in the Append New Cycles dialog box Each is described in a separate procedure Identification For sample data and the instrument method Files For processing and data parameters Quantitation For sample values Calibration For auto calibration parameters available only for calibration cycles Append New Cycles 11 17 Building a Sequence Vial by Vial 11 18 The Append New Cycles dialog box contains the following command buttons Add Applies data to the sequence and leaves the dialog box open Add Close Applies data to the sequence and closes the dialog box Cl
76. data analysis Chapter 10 Editing Methods and Results Graphically Explains how to create an optimal method or modify an existing method by manipulating the chromatographic display in the Graphic Method Editor It also explains how to optimize the results for a single analysis by using the Reprocess Results function Chapter 11 Building a Sequence Describes how to develop a sequence using the Sequence Editor A sequence controls data acquisition and analysis Chapter 12 Acquiring and Viewing Data Explains how to set up your instruments and interfaces to acquire data from chromatographic instruments It also describes how to control a run view the real time plot as data is being collected and how to view detailed information about the instruments and interfaces Chapter 13 Working with Instruments Interactively Explains how to use the Hands On and Modify functions in TotalChrom to work interactively with instruments before during or after a run Chapter 14 Displaying Chromatograms Describes how to use the Chromatograms function to examine raw data files graphically how to compare two or more data files and how to perform mathematical operations on two files Chapter 15 Reprocessing Files In Batch Describes how to use the Batch Reprocessing function to reprocess the data from multiple files Introduction and Overview 1 9 Using this Guide Chapter 16 Summarizing and Reporting Component Data Describes how to use the Summa
77. default component information 1 Choose Defaults from the Components menu to open the Component Defaults dialog box Component Defaults There are three tabs in the Component Defaults dialog box Identification Select this tab to establish parameters for component identification The options on this tab change depending on the component type you select Calibration Select this tab to set the calibration defaults you want to use User Values LIMS Select this tab to specify default constants to use in calculations You also use this tab to set the default for tagging components for SOL LIMS if you have Connect Developing Calibration Parameters in the Method 8 2 Setting Component Defaults 8 22 2 Make any changes to the values in the Component Defaults dialog box and then do any of the following e To save your changes and close the dialog box choose OK e To save your changes without closing the dialog box choose Apply e To discard your changes since the last time you chose Apply and close the dialog box choose Cancel The following sections describe how to complete each tab of the Component Defaults dialog box Entering Component Identification Defaults You can specify that TotalChrom identifies new components as peak named group or timed group components This section describes the procedures for setting defaults for each type Generally you set up component identification def
78. detector program enter the amount of time that you want the step to last 5 In the Wavelength columns for Channels A and B enter the wavelength that you want to use The valid range is from 195 nm to 365 nm in 1 or 5 nm increments If you enter a value set in the configuration program that is not a multiple of 5 TotalChrom rounds upward to create a correct value 6 Inthe Bandwidth columns for Channels A and B enter the total wavelength range around the nominal selected wavelength Developing Instrument Parameters in the Method 6 31 Setting Control Options 6 32 Under Spectral Acquisition select the Mode that you want to use The options are Off Collects no spectral data Apex Collects a spectrum at the apex of each detected peak Auto Collects a spectrum at the upslope apex and downslope of each detected peak Time Collects a spectrum at regular time intervals and at the apex of each peak detected If you selected Time as the Mode option select the interval at which you want to collect spectra from the Sampling Period s list The available rates depend on the data sampling rate that you set in the Data Channels dialog box For higher sampling rates more time intervals are available This frequency of spectral acquisition occurs between the Start and End Times In the Start Time text box enter the time into the run at which you want to begin collecting spectra The Start and End Time opt
79. digit minute and two digit second 6 Build and save a Quick Method and if necessary a Vial List as explained in Using Quick Method on page 12 15 and Building a Vial List on page 12 16 7 Select Suppress Processing if you do not want to process the data immediately after it is collected This automatically suppresses the data analysis process including the printing of reports and plots and the creation of a result file You may want to select Suppress Processing if you plan to use your computer for another task and do not want to be interrupted by data processing at the end of each run Since data processing is a compute intensive task it can cause your computer to be unresponsive for several seconds as the various data analysis functions are carried out You can use Batch Reprocessing later to obtain results from the analyses 8 Select Suppress Reports Plots if you do not want to print a report and plot Otherwise a report and plot will automatically print at the end of a run 9 Choose OK in the Setup Instrument dialog box to initialize the instrument Acquiring and Viewing Data 12 5 Setting Up Data Acquisition Using a Method gt To use the Method setup type to acquire data 1 12 6 If you are setting up an LC and the interface status is Released choose Take Control from the Run menu Select an instrument in the instrument selection panel and click the Setup button to open the Setup Instrument dialog
80. do not use this option repeatedly in a sequence it is not included in the Append New Cycles dialog box Replace Replaces all retention time replicates at all levels with the actual values from the current cycle This is equivalent to choosing the Reset RT button in the Graphic Method Editor 5 If necessary repeat this procedure for the second channel Editing the Sequence Spreadsheet When you edit a sequence spreadsheet you change existing data By using commands from the Edit Change Build and Format menus you can Format spreadsheet views Change the appearance of the spreadsheet by altering the width of columns and by changing the font Edit the data in individual spreadsheet cells or in selected groups of cells Edit spreadsheet rows by moving copying inserting appending and deleting them Edit the values in individual columns or in selected groups of columns Create notes about your samples Edit the global parameters of a spreadsheet to change its basic structure Append new cycles to the spreadsheet Editing Basics You can use several methods to assist you when editing a spreadsheet Building a Sequence To edit the value in an individual cell select the cell and type directly into it To open a shortcut menu of commonly used commands click the right mouse button in a selected element 11 27 Editing the Sequence Spreadsheet 11 28 e To specify changes that you want to make to spreadsheet
81. eene ne trennen tree 16 25 Chapter 17 Performing a Fit Analysis viii Whiat 18 Fit Analysis 4 5 eut tese eere qe HERR XE EXER AGENTE RE E S EE O EEEE E 17 2 The Fit Analysis Window eene tee dede Ple pereo te da eee aedes eed p enin 17 3 Fit Analysis Status Bar and Menus esee eene 17 4 Vaewing the Calibration Curve 4 acer ete et p eren nee e et erecti deett 17 5 Changing the Calibration Curve Display eese eren 17 6 Setting Limits for the Calibration Curve essent 17 6 Changing Calibration Curve Labels eene nee 17 7 Changing Fit Par metets cei ote esp ee esegue ten e ap 17 8 Charising the Scaling Factor erede ap o ee bone e RH basses 17 8 Fitting and Weighting the Calibration Curve eene 17 9 Displaying Curve Information eese nennen rennen nennen nenne 17 11 Solving For New Amounts and Responses csssssscseeeeceseeeceseceeesceneeseceaeeeeaeeateseeneeats 17 11 Using the Data List Spreadsheet eese enne nennen nennen 17 12 Editing Calibration Data in the Data List eese rene 17 14 Editing Rows in the Data List enne nennen nnne 17 14 Entering Repeating Values uet rer s 17 15 Closing th Data List Dialog 4 2 4 eene eee ht dete etes 17 15 Printing and Plotting Calibration Data essent enne eene 17 16 Saving Calibration Data to the Clipboard
82. either inlet program mode or oven tracking mode POCI PSSI POCO or PSSO select either ON or OFF for Injectors A and B POCO and PSSO track the oven program temperature 5 C 12 If the option is available enter an Auxiliary zone temperature Setting GC Carrier Parameters You can use the Carrier tab of the Instrument Control dialog box to set carrier parameters such as the inlet pressure or flow rate for carrier gas The options that are available in the Carrier dialog box depend on whether the instrument has a carrier or auxiliary zone configured as a PPC Programmable Pneumatic Control zone Configured for PPC If the instrument has either carrier or any auxiliary zones as a PPC zones 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 Developing Instrument Parameters in the Method 6 15 Setting Control Options Rate column Represents the rate at which 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 column Gives the pressure flow ve
83. elements use the Change Values command e To edit the values in spreadsheet columns use the Fill Renumber Files and Path commands The Sample Fill In command ensures that sample information for replicate injections is the same The Fill Down command copies the contents of a selected cell to all cells in the same column below it The Renumber Files command renumbers the base data file name in multiple columns The Path command changes the path that is associated with method and or data files The Smart Fill command increments sample numbers vial values and the cycle numbers that are associated with data file names in a single column When one or more cells in the Data Raw Data File or Result File column are selected you can use the Edit Token String command in the Change or context menu to create a file name based on tokens or to edit the existing tokenized file name See Chapter 2 for details on using the Token Editor dialog Formatting Spreadsheet Views You select which columns to display by clicking the view tabs at the bottom of each spreadsheet You can display a different view for each channel but the available views and their contents are the same for both channels As installed the General view includes most of the available columns and the remaining views are groupings of logically related columns You can change the contents of views with the Hide Unhide command and you can create rename and delete views w
84. file name substitution for the following variables RAW Full path and file name of the last raw data file RST Full path and file name of the last result file MET Full path and file name of the instrument method SEQ Full path and file name of the sequence file IDX Full path and file name of the index file AIA Full path and file name of the AIA metafile 11 47 Editing the Sequence Spreadsheet 11 48 If you must include the name of an explicit file rather than one of the tokens listed above you must enclose the name in quotation marks If TotalChrom is running in a networked environment and the command line must include the name of an explicit file use the UNC name instead of a mapped share name 4 Choose OK An X appears in the Note column to indicate that user program information exists for this row and the program name is displayed in the Name column Including a Serial Dilution Program in a Sequence You can include an LC Series 200 Autosampler Serial Dilution program in a TotalChrom sequence by selecting the Serial Dilution cycle type and specifying a Serial Dilution file gt To include a Serial Dilution program in a sequence 1 In the Type cell of the row for which you want to include a serial dilution program select Serial Dilution from the List The Serial Dilution dialog box opens and TotalChrom disables all columns for the Serial Dilution row except Type Name and Note S
85. for any attached interface or instrument You can also use the QuickStart option through the Setup function to create a control acquisition method you can use to collect data quickly You can use these chromatograms to optimize the new method The TotalChrom Navigator is described in Chapter 4 Using the Navigator The QuickStart option the Status function and the Setup function are described in Chapter 12 Acquiring and Viewing Data Analyzing Data TotalChrom stores raw data in a raw data file on your disk At the end of a data acquisition run it analyzes the data according to the data acquisition method you used it detects peaks and establishes baselines it determines peak beginnings and endings and it determines the separation of adjacent peaks Finally it generates a report and plot and stores the results in a separate file If you are using the TotalChrom default method or default sequence or if you have used the QuickStart option to create a method or sequence TotalChrom will use the default parameters store your raw and result data and generate an area percent report with a single page plot at the end of the run The QuickStart option is described in Chapter 12 Acquiring and Viewing Data Introduction and Overview 1 3 TotalChrom Functions Creating Data Acquisition Methods You create and modify control and acquisition methods by using the Method Editor in TotalChrom A method consists of three sections
86. for that channel from Configuration When PPC is enabled for the selected channel the Carrier Control drop down list is enabled The contents of the list depends on the Inlet type and the Capillary Mode settings from Configuration 6 16 Setting Control Options 2 From the available program tabs under the table e g Carrier A Carrier B Aux 1 or Oven choose 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 appears 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 In the Initial Setpoint field of the table set the flow pressure velocity for the start of the run If the program you are editing is a constant flow pressure velocity program then you can only enter an initial Setpoint value in the table 4 Inthe 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 for most instruments enter 999 For the HP5890 enter
87. in the Graphic Method Editor raw data files and method files You can also specify a report format file to use for printed output After you load a raw data file that file name appears in the status bar and the name of the method used to process the data appears in the title bar You can either e Change the method used to process the current raw data file by opening a new method file e Use the same method to evaluate different raw data files e Save the method or result data as a new file leaving the current files intact To maintain the current view and retain the same scaling parameters choose Preserve View from the File menu before loading a raw data file gt To load a raw data file 1 Choose New Data File from the File menu to open the TotalChrom File Open dialog box Locate and select the raw data file that you want to open You can select an index file instead as described under Using the Graphic Method Editor starting on page 10 4 Select the Load Data File Method check box to load the method that is associated with the new data file If you do not select this TotalChrom uses the method that is currently loaded in the Graphic Method Editor Choose Open TotalChrom performs peak detection integration and component identification TotalChrom then displays the chromatogram for the file you selected gt To load a different method file 1 Choose Open from the File menu to open the TotalChr
88. need to determine how much data to collect to achieve the most accurate quantitation The Sampling Rate Bunching Factor command in the Process menu helps optimize peak detection by e Measuring the peak width to determine the right sampling rate for future analyses e Setting the best bunching factor to reprocess files that already exist Because the sampling rate is the rate at which TotalChrom collects data you cannot change it for an existing file If you enter a new value for sampling rate in Graphic Method Editor TotalChrom does not reprocess the raw data for the current session However TotalChrom saves the new value in the method and uses it in future analyses You cannot enter a new sampling rate in Reprocess Results because you are modifying a stored data file not the method gt To seta new sampling rate or bunching factor 1 Choose Sampling Rate Bunching Factor from the Process menu The status bar message prompts you to outline the narrowest peak to use for the calculation 2 Drag to outline the narrowest peak in the chromatogram This is the same action you would perform to expand the working chromatogram to show just that peak You do not need to select the entire peak because TotalChrom only uses the starting and ending times of the region that you select Setting Processing Parameters When you release the mouse button the Sampling Rate Bunching Factor dialog box appears Sampling Rate Bunching Factor x
89. of the following e Inthe Navigator click on the Graphic Edit button or choose Graphic Edit from the Build menu hs Graphic E dit e Inthe Method Editor choose Graphic Editor from the Other menu The Graphic Method Editor window opens The TotalChrom File Open dialog box appears in the foreground prompting you to select a raw data file 2 Locate and select the name of the raw data file that you want to edit and choose Open TotalChrom performs peak detection integration and component identification on the raw data using the method named in the file header Then TotalChrom displays the chromatogram In addition to opening raw files by selecting them one at a time you can access a group of related raw files by opening the index IDX file in which they are referenced 10 4 Using the Graphic Method Editor gt To use an index file to open raw files 1 In the TotalChrom File Open dialog box select IDX Files idx from the Files Of Type list then select an index file The first raw file in the index file is loaded analyzed and a chromatogram is displayed using the method that is associated with the raw file 2 To move through the raw files in the index file you selected use the Previous Data File and Next Data File commands on the File menu The method that is loaded with the first raw file does not change as you move through the raw files even if subsequent files were analyzed with a different method 3
90. of the values in the Time column for all the steps that you create The Detector Time field displays the data acquisition time of the analysis 2 InStep 0 of the table click in the Time Flow and solvent fields and then enter amounts for the equilibration step 3 Enter the Time Flow rate solvent composition and Curve type for each additional program step The Time field activates the other fields in each row and the curve changes as you enter each set of values Depending on the specific pump that you are using TotalChrom completes the solvent percentage either for solvent B or for solvent D so that the total solvent composition is 100 percent Also if you change the value of solvent B or the value of solvent D the value of solvent A adjusts so that the total remains 100 percent 6 26 Setting Control Options For the Model 250 LC Pump the resolution at which you can enter time and flow values changes across the allowed range You can enter times between 0 and 9 9 minutes to the nearest 0 1 minute but times between 10 and 999 minutes must be to the nearest minute Flow rates between 0 and 0 99 mL min can be to the nearest 0 01 mL min but flows between 1 0 and 10 0 mL min can only be to the nearest 0 1 mL min TotalChrom will beep if your entry causes a switch from one resolution range to another 4 Toreduce the amount of equilibration time after the first run select Enable Solvent Saver and then enter the new amount of equ
91. on the chromatogram and click the right button one or more times until the plot appears at the level of expansion you want To immediately return the plot to the default view choose Entire Chromatogram from the Display menu When you select a portion of the working chromatogram to expand it TotalChrom does not normally expand the reference chromatogram The Expand Reference Chromatogram command enables you to expand both chromatograms simultaneously Editing Methods and Results Graphically 10 19 Changing Display Options 10 20 gt To expand both reference and working chromatograms simultaneously l 2 Choose Expand Reference Chromatogram from the Display menu In the reference chromatogram select the part of the plot you want to enlarge TotalChrom redraws both plots to show the part of the run you selected The following figure shows both chromatograms expanded atu Graphic Method Editor C PenExe TcCS Ver6 1 0 Examples solvent mth File Process Calibration Display Other View Help lial SIR j eje x uj ee st ISOBUT C PenExe TcCS Wer6 1 0 Examples Solv001 raw 5 021 min 763 853 mV 237 pts For Help press F1 gt To reduce just the reference chromatogram Click the right mouse button inside the reference chromatogram TotalChrom restores the reference chromatogram to the previous scaling the working chromatogram maintains its current level of expansion gt To reduce both r
92. on your screen 5 In the Execute After list box select the point during data analysis at which you want to run the program 6 Select Synchronize With Data Analysis to pause data analysis until the user program causes it to resume In the following example data analysis pauses after quantitation while the user program MY APPLIC EXE runs Analysis resumes with report generation when the program stops Integration Baseline Timed Events Optional Reports Replot User Programs r Program Name and Options ETEV ome C d m Delete d Delete All Command line Jamswwapcee eal Execute after unis 1 te m Data processing is to be paused and will be restarted by the program Chapter 8 Developing Calibration Parameters in the Method This chapter explains how to use the Method Editor to set calibration parameters in a method For general information about using the Method Editor refer to Chapter 5 Building a Method To learn about Go to page Introduction to Calibration Parameters Understanding Global Calibration Parameters Editing Global Calibration Information Understanding Component Parameters Setting Component Defaults Adding and Editing Components Loading and Merging Components From Files Deleting Components Changing Parameters for Multiple Components Simultaneously Performing a Manual Calibration Deleting all Calibration R
93. range of components that you want to change 10 Choose OK TotalChrom updates the component list to reflect the changes you specified Developing Calibration Parameters in the Method 8 45 Performing a Manual Calibration Performing a Manual Calibration 8 46 The Calibrate command in the Components menu lets you use response values from one or more result files to update the calibration information in a method file The procedure consists of e Selecting one or more result files e Selecting a calibration level for each result file e Selecting the calibration type for each combination of result files and calibration levels e Performing the calibration To perform a manual calibration you must have a component list and calibration levels associated with each component in the list You also need to verify that the calibration parameters for each component are correct before you perform a manual calibration When you manually calibrate a method you create calibration replicates A replicate is a repetitive analysis of the same calibration standard for a particular calibration level Since it is a unique analysis you can use replicates to average calibrations gt To perform a manual calibration 1 Choose Calibrate from the Components menu to open the Manual Calibration dialog box Selected files Add Calibration Parameters des E Type Average Replace Identify peaks before calibrating Delete
94. replicates from the method Load command Lets you load a new component list from another file Merge command Lets you add components from another file Developing Calibration Parameters in the Method 8 3 Understanding Global Calibration Parameters Understanding Global Calibration Parameters The settings in the Global Information dialog box apply to the method as a whole including how TotalChrom calibrates peaks that are unidentified in the run Global Information LIMS Results Volume units JY m Unidentified Peak Quantitation Quantitation units n Calibration factor fi 000000e 06 Sample Volume ul fico Always use calibration factor Use nearest component kaman o 000 Use nearest reference Calibration Extemal standard M RRT Calculation Intemal standard Use first peak in run as RAT reference F C Use this component as RAT reference Reject outliers during calibration PEAK Y Allowed deviation 3 000 Sample Amount Options I Correct amounts for calibration standards I Convert unknown samples to concentration units Cancel Apply The units for volume entries for display purposes only Every new method contains a set of default parameters which appear in the Global Information and Component Defaults dialog boxes You only need to change the defaults if you are creating a component list This section exp
95. select an often used path You set up these paths in the Configuration application see Quick Paths in Chapter 3 for information 2 4 Using Common Dialog Boxes Program Selection Dialog Box TotalChrom Basics The Program Selection dialog box opens when you click the folder icon next to an edit box that requires a user program filename Some TotalChrom applications let you specify a user program to run in conjunction with data analysis Your application manager sets up your access to these programs If you have access to user programs you will have a choice of entering a program name in the edit box or clicking the folder icon to open the Program Selection dialog box Program Selection x e Ifa list of programs appears in the Program Selection dialog box select the program from the list These are the only programs to which you have access e If no list appears click the Browse button and select a program 2 5 Using Common Dialog Boxes Tokenized File Names The system manager is able to define default raw result and modified base file names in the Default Base Names dialog box for each user based on the use of tokens to represent key data values This is accomplished through the Default Paths Base Names button on the Users tab of the System Configuration screen This procedure is described in the Application Manager s Guide For example the token Inst is replaced by the instrument name User by
96. sequence gt To pause a sequence e Click the Run button in the Navigator and choose Pause Sequence from the pop up menu to halt data acquisition at the end of the current run if one is in progress gt To resume a paused sequence 1 Click the Run button and choose Resume Sequence The Resume Sequence dialog box appears showing the name of the sequence file in use 2 Select Start Next Run When Ready to start the run as soon as the instrument is ready Normally you will want to select this option only if you are using an instrument configured with a LINK controlled autosampler 3 In the Starting Row text box you may enter the row with which you want to resume data acquisition Controlling Data Acquisition If the sequence includes bracketed calibrations you will not be able to alter the starting row and ending row entries In order to obtain valid results a sequence of this type must be run in its entirety without modification You can pause a bracketed calibration sequence but it can only be resumed from the point at which it was paused 4 Inthe Ending Row text box you may enter the row with which you want to end data acquisition 5 Choose OK to resume the sequence Clearing the Setup You can stop a sequence and clear the setup from the interface or LINK by choosing Clear Setup in the Run menu gt Toclear the setup 1 Click the Run button and choose Clear Setup A confirmation dialog box appears
97. start time for Plot 1 that is greater later than the original start time the preceding data will not be included in the calculation In the End Time text boxes for each file enter the time at which you want the chromatogram to end This defines the ending point for the new raw data file If you enter an ending time for Plot 1 that is less than the original ending time TotalChrom does not use the data after the new ending time in the calculation Select a Baseline Adjustment option This is a correction factor that is applied to each data point to ensure that minimum values are not negative values because TotalChrom cannot process values below zero Baseline Adjustment affects only the new data Automatically Calculate Causes TotalChrom to calculate the baseline offset in order that no negative data point values are generated Set Lets you enter the amount by which to offset the baseline If the amount you enter is not sufficient to eliminate data point values of less than 1 TotalChrom applies an additional offset in order that all values are greater than zero The allowed range is 1 0e 100 to 1 0e 100 Select one of the options under Normalization For Second Plot These define how you want to scale Plot 2 before you perform the calculation TotalChrom uses the following equation to generate each new raw data point R P operator P x M O B where R is the resultant data value Pj is the first plot data value
98. the Data Acquisition dialog box with the Data Channels tab selected Data Acquisition x Data Channels Real Time Plot r Data Channel Source CH Dual Channel A Det T CE Channel B ps m Set Data Rate C By peak width at base s jo By sampling rate pts s 125 m Data Storage I Store all data from run Data Points 15000 T Store run log Delay time min pp Run time min foo teen Collect data from channel 4 only Series 200 DAD The Data Channels dialog has a slightly different configuration for a Series 200 DAD detector but the name and function of the available controls is the same as those described in this procedure Series 200 UV VIS The Data Acquisition dialog screen for the Series 200 UV VIS uses the standard LINK instrument layout Since only a single channel is available with the Series 200 UV VIS Channel A is always selected and Channel B and the Dual radio buttons are disabled The Source setting will always be Series 200 UV VIS the only selection available 2 Under Data Channel select channel A B or Dual 3 Under Source select a data source for one or both channels from the list of choices supported by this instrument Setting Data Channels 4 Under Set Data Rate do one of the following to set the rate at which the instrument will sample its detectors e Select By Peak Width At Base and then enter the number of seconds in the text b
99. the command You can edit these defaults as necessary gt Torenumber data files 1 If you want to renumber specific rows or columns select them then choose the Renumber Files command The Renumber Files dialog box appears Starting row fi Ending row 1 Starting number In Iv Apply to other channel also Renumber all base names C Renumber specified base name only File types to renumber Iv Raw M Result teen Renumber modified raw data files 2 Tochange the default rows edit the values for Starting and or Ending Row If you did not select specific rows the default values include the entire sequence Editing the Sequence Spreadsheet 3 If you want the new numbering to apply to the other channel select the Apply To Other Channel Also check box 4 Enter the number you want for the new starting number Select an option to indicate whether you want to renumber all base names or a specific base name only 6 If you are renumbering a specific base name enter that name in the text box If you selected a subset of rows the name from the first selected row is provided as the default If you enter a base name that does not exist an error message will be displayed You must use Smart Fill to change a base name 7 Selectthe check box for each file type that you want to renumber Any data file types that are included in your selection are checked by default 8 Choose OK Using Fill Down
100. the current cycle has been running The following item appears in the Current status box only for a 900 Series Interface Ch A B Voltage Current signal level for that channel The following items appear in the Current status box only for a LINK controlled GC Aux Current flow pressure Carr A B Current carrier flow pressure Inj A B Current injector temperature Oven Temp Current oven temperature Program Time Length of time to run the oven program Viewing Data and Instrument Information The following items appear in the Current status box only for a LINK controlled LC Flow Current actual pump flow rate in mL min or uL min ABCD The current percentage of each solvent Pressure The current pump pressure A negative value for pump pressure indicates that the pump pressure calibration is incorrect Refer to the operator s manual for your specific pump for information on how to correct this problem AA B The current monitoring wavelength of the detector for Channels A and B Program GC only You can select to display a table or a graph of a program in the Program status box The program selections include the oven program and each configured programmable zone While you can display only one program as a table you can select several programs to include in a graph The vertical bar in the graph moves to display the current elapsed time Zones GC only The setpoint Init Set for all z
101. the program you want to run Choose OK in the Setup Instrument dialog box to initialize the instrument Using a Sequence When you set up a sequence for any instrument other than one with a LINK controlled autosampler a tab for Post Sequence Options is added to the Setup Instrument dialog box You use this tab to define what will happen when the sequence ends The two tabs are described in separate procedures gt Touse the Sequence setup type to acquire data 1 If you are setting up an LC and the interface status is Released choose Take Control from the Run menu Select an instrument in the instrument selection panel and click the Setup button to open the Setup Instrument dialog box for that instrument 3 Acquiring and Viewing Data Setting Up Data Acquisition Select Sequence as the Setup Type then enter or select the name of the sequence file Setup Instrument ie e o z 8 cs men C PenExe T cw SSVerb 2 NE amplesNSeries 200 LC Pump seq hearer Corman ire The name of the first method to be downloaded appears in the Method text box and the first and last rows in the sequence are shown in the Starting and Ending Row text boxes For a sequence setup the Raw and Result file path fields are disabled and blank If the path specified in the sequence you selected is the path that you want to use do not select the Store data in above paths or sub directories in preference to
102. those shown if the default file has been modified Building a Report Format 9 3 Using the Report Format Editor Ele Noe Bet Edt piees Hep osle alaj z veau DEFAULT REPORT Whenever you change an untitled or existing report format the word MODIFIED appears in the status bar at the bottom of the window It disappears after you save the modifications 9 4 If you wish change the default title and create a report header and footer Refer to Creating Title Header and Footer Text on page 9 5 Set up the columns you want to use for this report Refer to Editing Report Columns on page 9 6 and Creating a Custom Expression on page 9 10 When you are finished developing the report format choose Save from the File menu The Documentation dialog box opens Complete the Description tab in the Documentation dialog box and choose OK For a discussion about entering descriptive information about a file refer to Chapter 2 TotalChrom Basics The TotalChrom File Save As dialog box opens Enter a name for the report format in the File Name text box and choose Save The dialog box closes and the new report format name appears in the title bar When you are finished working in the Report Format Editor choose Exit from the File menu Creating Title Header and Footer Text Creating Title Header and Footer Text The commands in the User Notes menu enable you to create report title header and footer text in
103. three digit run or cycle number to this base file name to create the data file names If the file name already exists in the path TotalChrom will append a date time stamp to the file name the four digit year two digit month two digit day two digit hour in 24 hour style 14 2 pm two digit minute and two digit second Your application manager may have set up your system to automatically append a date time stamp to all files Enter the Starting File Number you want to be appended to the base file name for the first run If necessary TotalChrom will add leading zeros to your entry to generate the three digit cycle number For example the entry 2 will become 002 Subsequent runs will use the same file name with the appended number incremented for each run If necessary edit the Method or build a Vial List as explained in Using Quick Method on page 12 15 and Building a Vial List on page 12 16 Select Start Run When Ready to start the run as soon as the instrument is ready You use this option when you want a LINK controlled autosampler to begin its first injection of the new setup as soon as the instrument reaches the Ready state If the sample vials are not in the autosampler yet you may issue the Start Run command later Select Single Run Data Buffering if you do not want to store data from multiple runs in the interface This forces single run data buffering even when there is enough space to store multip
104. to enter methods and data file names for Channel A 2 Inthe Processing and Calibration Method text boxes enter or select the name of the method s that contains the parameters that you want to use You can enter the name of a method that does not yet exist as long as the path exists and you create the method before you run the sequence If you selected One Per Row in the Global Parameters dialog box these text boxes will not be available 3 In the Report Format File text box enter or select the name of the report format file that you want to use with this cycle 4 Inthe Raw Data File and Result File text boxes enter or select the individual base data file names that you want to use for raw and result files OR If you selected Same Name in the Global Parameters dialog box enter or select the base data file name that you want to use for both files in the Data Files text box 11 22 Building a Sequence Vial by Vial You can include the full data path here add it in the spreadsheet after you complete this dialog box or enter or change it during setup The base file name itself may contain 80 characters TotalChrom creates a result file RST for every raw data file RAW The base name s you enter here are used to name these files along with a three digit cycle number starting at 001 that TotalChrom appends to them If you run a sequence more than once TotalChrom appends a timestamp to file names when necessary to
105. to the component parameters such as search window sizes or reference peak assignments You can then review the new peak identities by selecting each peak in turn gt To assign or move a component name to a peak 1 2 Choose Edit Components from the Calibration menu In the plot window click the peak that you want to re identify From the Name list select the name of the component you want to assign to this peak Make any changes to the other component options Choose Next Prev or Return to implement the changes If you try to assign a component name to a peak that is already identified as another component an error message appears Editing Methods and Results Graphically 10 41 Working with Components 10 42 If you do not want to delete the old component you must first re assign that component to an unidentified peak You cannot designate a component as unassigned 6 Choose Return to close the Edit Components dialog box Creating and Editing Named and Timed Groups In TotalChrom you can identify a group of peaks as a single component for the purposes of calibration and reporting A named group consists of two or more single peak components that are grouped together in order to be reported as a single entity Before you can assign a component to anamed group you must first identify the peak as a component Members of a named group can appear anywhere in the chromatogram they do not have to be located cont
106. to the expected retention time Do one of the following e To use the current component as a retention reference for other components in the method select This Component Is A Retention Reference e To use another component in the current method as a reference select a retention reference from the Reference list e Select no reference in the Reference list if this component needs no retention reference If the method specifies internal standard calibration do one of the following e To use the current component as an internal standard for other components in the method select This Component Is An Internal Standard e Touse another component as an internal standard component select one from the Internal Standard list If you are performing an internal standard calibration you must select an internal standard Developing Calibration Parameters in the Method 8 31 Adding and Editing Components 9 To use this component as the reference for calculating RRT select the corresponding check box You will be prompted to confirm any change that you make The state of this check box for each component reflects what you entered for RRT reference in the Global Information dialog box or what you set here last time e If you designated this method to use the first peak as the RRT reference then this check box will not be selected for any component If you designated this method to use a specific component as the RRT re
107. used interchangeably throughout this guide To learn about Go to page Using the Chromatograms Application Controlling the Appearance of Chromatogram Windows Displaying Information in Chromatograms Adding and Editing Chromatogram Labels Aligning Peaks in Two Chromatograms Calculating a New Chromatogram 14 1 Using the Chromatograms Application Using the Chromatograms Application The Chromatograms application allows you to display and examine multiple raw and result data files at one time After you display the chromatograms you can perform the following functions to analyze and compare the results of this data 14 2 Print a copy of the chromatogram or file summary data on the selected data files Copy a chromatogram to the clipboard for use in another application Stack cascade or tile open chromatogram files Compare two or more chromatograms by overlaying them in the same window Expand or zoom selected parts of a single chromatogram and expand two or more chromatograms simultaneously Change the low and high voltage values Show or hide various features such as title bars axis labels coordinates component names and peak retention times Add time labels and create custom labels Align the chromatograms in a variety of ways to eliminate the effects of small differences in chromatographic conditions Create a new raw data file by performing a mathematical calculation on two existing files To o
108. vii global parameters in sequence defining 11 11 editing 11 49 effect of changing 11 49 global status messages 12 39 Graphic Edit command 10 4 Graphic Method Editor calibration commands 10 36 file types in 10 8 menus and commands 10 6 overview 5 2 10 2 window 10 4 Group Detail tab 20 101 Group Table 97 H Hands On command 13 2 13 3 13 5 13 7 Hands On overview 13 2 header tab 20 106 header report 9 5 10 52 16 16 Help system 1 12 HF See horizontal baseline forward timed event Hide Unhide Columns command 11 28 horizontal baseline backward timed event 18 38 horizontal baseline forward timed event 18 36 HR See horizontal baseline backward timed event I See peak end detection timed event icons data analysis 18 3 Hands On 13 2 identification of components optimizing 18 45 identifiers in text file 11 53 identifying components 8 30 IDX See index files Import command 5 9 index file loading raw files from 10 4 loading result files from 10 11 overview 15 4 reprocessing 15 4 versus sequence file 15 4 viii viewing 11 59 Insert command 17 14 instrument See also instruments disconnecting 3 15 errors 12 25 parameters adjusting after setup 13 7 definition 5 2 downloading A 6 entering 6 2 personality modules A 4 settings adjusting after setup 13 2 status messages 12 42 timed events deleting 10 35 setting 6 36 10 33 Instrument Configuration command 3 2 3 9 Instrument Event Properties 20 74 Instrument Events co
109. voltage in chromatograms Shift Time Allows you to shift the time period that you have configured in chromatograms Shift Voltage Allows you to shift the voltage range that you have configured in chromatograms Scale Time From Origin Changes the time scale such that the end times in two chromatograms match each other Scale Voltage From Changes the voltage scale such that the end voltages in Origin two chromatograms match each other Scale Time Changes the time scale of a target chromatogram to align the start and end times with a reference plot Scale Voltage Changes the voltage scale of a target chromatogram to align low and high points with a reference plot Clear Removes all starting and ending times and low and high voltage values added to a chromatogram This command applies to one chromatogram at a time 14 4 Using the Chromatograms Application Opening Chromatogram Files You can open multiple raw and result data files during the same session by using the Open command on the File menu A raw data file is always necessary to plot a chromatogram because that is where the data points are stored When you open a result file TotalChrom uses the associated raw data file to plot the chromatogram Result files enable you to display peak baselines peak retention times and component names When you open files TotalChrom displays each chromatogram in the colors that are specified in Configuration Each file will open in its
110. window contains the following menus and commands File Menu Lets you load save result files print report plot or method parameters enter and review documentation about a result file and copy and save the plot image for use in other applications Process Menu Lets you edit instrument timed events and baseline timed events optimize processing parameters such as noise and area thresholds and manually integrate peaks by redrawing the baseline Components Menu 10 12 Using Reprocess Results Lets you identify peaks manually and display search windows Display Menu Lets you control display characteristics including the plot scale and whether the report header peak report or reference chromatogram appear on the screen Other Menu Closes Reprocess Results and opens the optional LC spectral analysis application Status Bar The status bar at the window bottom shows the raw data file name the cursor X and Y coordinates the number of points in the chromatogram Help for the currently selected command and whether or not you have modified the file Loading Files in Reprocess Results You usually work with result files in Reprocess Results However you can also select another report format file for reports and replots TotalChrom uses the selected report format file to determine the format for printed output TotalChrom also uses some aspects of the format to display the Peak Report information above the chromatogram When you
111. x 1 i 1 LE z o FET w 2 a w 256 E ES E C PenExe TcwS Wer6 2 ONE xamples Solv001 raw 2 991 min 461 983 mv 1200 pts 7 For Help press F1 The report information for the current run is displayed above the chromatogram replacing the reference chromatogram if present in the format defined by the currently specified report format file The menu bar also changes to include the following menu and command Report menu Lets you alternate between viewing report contents and header information select another report format and print full reports and replots Return command Removes the report information and returns to the main application window Editing Methods and Results Graphically 10 51 Displaying and Printing Information 10 52 gt To view report header information 1 Choose Report Header from the Display or Report menu The report header appears in a scrollable window You can scroll through the window to view additional information in the header To switch to the Peak Report list from this view choose Peak Report from the Report menu Choose Return to remove the report information and return to the main application window gt To view the report information for detected peaks 1 Choose Peak Report from the Display or Report menu The report information display shows the results for all detected peaks The data columns in the window are those defined in the report format associat
112. 1 Report Window Report Tab seen enne en etre 20 105 Report Window Header Tab eese enne enne 20 106 Report Window Status Tab sees entree 20 108 Viewing Reports and Results from a Single TotalChrom Report TCR File 20 109 Viewing Multiple Samples Simultaneously eene 20 110 Multiple Eile Selection iiiiane es ri Co petat DAE e ac Ett es 20 110 File List with Multiple File Selection eene 20 111 Plot Window with Multiple Chromatograms Overlaid esses 20 112 Plot Window with Multiple Chromatograms Stacked sesssss 20 113 Plot Window Rescale Dialog eeeeeeeeeeeeeeeeeeneenen nennen 20 115 Report Window with Multiple File Selection eene 20 116 Summary View Context Menu ceesecsesecseseecsseceeesecseesecnessecsaeenesaecaeesesnesseesaees 20 117 Report Window with Multiple File Selection eene 20 118 Aligning Chromatograms eese nee is eenn n En E i enne nenn nenne trennt 20 118 Marking the Reference Plot eese eren Ea Eki nennen enne 20 118 Reference Plot Context Menu essere nennen enne nennen nre 20 120 Marking the Plot to be Aligned norice ntaa nne 20 120 Aligned Plot Context Menu ien ee Ri pem p tied Megha atin 20 121 Ahlenng the Plots Ae rehenes 20 12
113. 11 43 width 11 31 11 32 common baseline timed event 18 32 component See also components amounts calculating 8 15 8 33 calculating adjusted amounts 18 77 calculating initial 18 70 18 75 calculating with constant calibration factors 18 75 calibrating with reference calibrations 18 75 converting ratios to 18 76 converting volume adjusted 18 76 correcting 18 53 correcting calibrated 8 6 determining unknown 8 37 defaults customizing 8 20 identification defaults entering 8 22 definition 18 4 18 45 optimizing 18 45 overriding 10 49 information adding editing 8 29 changing 8 43 list in suitability method B 12 lists adding a peak component to 8 31 adding named group to 8 32 adding timed group to 8 32 creating 10 36 creating editing manually 16 9 definition 10 36 editing 16 10 loading 16 7 names form of 10 36 hiding or showing 14 14 parameters overview 8 2 8 9 quantitation definition 18 4 types overview 8 30 values user definable 8 19 Component List command 17 4 Component List window 5 3 5 4 8 9 components See also component adding 8 28 8 30 assigning names to peaks 10 49 calibrating by reference 8 15 8 35 18 56 definition 18 4 overview 18 46 18 49 changing several simultaneously 8 43 deleting 8 42 editing 8 28 8 39 10 38 identifying 8 30 loading from files 8 40 in component lists 16 9 matching peak s 8 9 merging 8 40 8 41 16 10 selecting multiple 8 32 setting identification defaults 8 22 Configur
114. 14 17 rotating 14 19 Labels command 17 7 levels adding calibration 8 37 library file LIB A 4 Limits command 17 6 LIMS options defaults setting 8 27 setting 8 38 linear least squares regression analysis C 19 Index linearity error C 20 Lines command 10 16 LINK See also 600 Series LINK Interface LINK configuration options setting 3 11 resetting 3 15 Link Position To Data command 14 17 14 19 LINK controlled autosamplers acquiring data with 12 20 restarting 12 22 setting up 12 16 LINK controlled GC setting detector parameters for 6 19 LINK controlled instruments channel options for 6 6 LINK controlled LC pump module without autosampler acquiring data with 12 21 LINK controlled LC adjusting instrument parameters 13 7 liquid chromatograph autosampler parameters setting 6 21 configuration options setting 3 13 control options setting 6 20 detector parameters setting 6 30 pump parameters changing graphically 6 27 status viewing detailed 12 32 List Window Properties 20 40 LLS See linear least squares regression analysis LM See locate maximum timed event Load From Method command 16 9 Load From Peak List command 10 36 Load From Result File command 16 9 Load Text File command 11 57 Load Method File command 8 40 loading components from files 8 40 local reprocessing controls 15 12 locate maximum timed event 18 22 low voltage changing 14 26 M See manual integration timed event Main Toolbar review and approve 20 17 Manua
115. 18 16 baseline to point 18 34 bunching factor 18 15 common baseline 18 32 end peak 18 40 exponential skim 18 42 horizontal baseline backward 18 38 horizontal baseline forward 18 36 locate maximum 18 22 manual integration 18 42 negative peak detection 18 18 noise threshold 18 15 18 16 peak detection 18 16 peak end detection 18 20 retention time 18 22 smooth peak ends 18 23 start new peak 18 41 tangential skim 18 42 user forced peak 10 24 18 22 valley to valley baselines 18 33 Timed Group command 10 45 timed group components Index adding to component list 8 32 creating and editing 10 45 defaults 8 23 definition 8 12 10 42 displaying 10 47 time into run values 14 17 14 18 title bars hiding and showing 14 14 Title command 16 15 title report 9 5 16 15 Tokenized file names 2 6 TotalChrom capabilities 1 3 1 7 starting 4 1 overview 1 2 troubleshooting instrument related errors 12 25 validation runs C 18 Type menu command 10 38 U UF See user forced peak timed event See user forced peak timed event Undo command 14 4 unidentified peak quantitation parameter 8 6 unipolar interfaces testing C 4 unsegmented memory overview A 7 user forced peak timed event 10 24 18 22 User Label Properties 71 user options configuring 3 17 3 25 user program in a method 7 16 in a sequence 11 46 Process Time programs 11 46 quiet mode 7 18 Real Time programs 11 46 running Fit Analysis as 17 18 running Suitability as B 20 running
116. 2 Moving Alignment Markers essere eene nennen inen ene 20 124 Viewing a Static Overlay Plot sess ener 20 125 Miewing a Static Stacked Plot sente eode Ett 20 130 Interactions Between Windows eese ener nennen enne nennen ene 20 132 Table of Contents xi Summary Properties s 5 ni ERIT PEE prn HORE RR ri RR dae 20 133 Reviewing and Approving Reports sees eene ennemis 20 135 About Reviewing and Approving Reports essent 20 135 How to Sign a Single Report essent ren E enne nennen ene 20 135 How to Sign Multiple Reports eese 20 135 About the Report Review Window eseeeeeeeeeeeeennennnnnennenne nennen nennen 20 136 Report Review Window dede nd dedidit eee ides 20 137 A DOUut the S tats Bat ridet ee ebd 20 137 Report Review Toolb t 3 eps decile Sb alae aa Gales 20 138 Electronic Signature 5 2 toed va oet eer ero eoe pte eo pde le ces ERASE 20 141 Electronic Signature Dialog essere nennen nennen 20 141 Reason for Hold Dilog 3 2 23 2 eae PERDE POE EE ERR nd 20 144 Comment Review Dialog oe eer RE bietet n esr tete eben te deeds 20 145 Sion Report Dialog nae eR ais beaten enti tem o e e e tib fed 20 146 Sign Reports dialog 2 oreet enata ae e ete eee eet eee 20 146 Context menu Sign Reports dialog eene 20 147 Review and Approve Scenario esesesess
117. 34 gt Tosetinstrument timed events l In the Graphic Method Editor choose Instrument Events from the Process menu to open the Instrument Timed Events display 4s Graphic Method Editor C PenExe TcCS Ver6 1 0 Examples auto mth Delete Event Reprocess Retum Help x ss be e C PenExe TcCS Wer6 1 0 Examples Solv001 raw 1 573 min 606 773 mv 1200 pts 7A The menu bar changes to show the following commands Delete Events Lets you delete one or more instrument timed events from the method Reprocess Reprocesses the raw data file You do not need to use this command here because instrument timed events cannot affect data processing Return Closes the instrument timed events display and returns to the Graphic Method Editor The instrument timed events available for the current instrument appear in the list For some events such as relays you use the Value text box to enter the required values From the Events list select the timed event that you want to add If the event requires a value choose one in the Value list On the chromatogram click where you want this event to occur The event appears at the specified point on the plot If you make a mistake you can delete the event and click again To set a more precise time enter Setting Processing Parameters the exact time when you want the event to occur in the Instrument Timed Events dialog box in the Method Edi
118. 4 2 Inthe Ready Time text box enter the number of minutes that the pump remains in a READY state after which you want the pump to shut down A Ready Time of 999 means that the pump will continue in the READY state indefinitely 3 In the Standby Time text box enter the number of minutes that the pump remains in a READY state after which you want the pump to change to the standby flow rate A Ready Time of 999 means that the pump will continue to use the flow rate set in the grid as long as the pump remains READY 4 In the Standby Flow text box enter the pump flow rate during standby mode 5 From the Pressure Units list select either PSI or BAR as the units for inlet pressure depending on the instrument that you are using 6 Inthe Max Pressure text box enter the upper pressure limit above which the pump will shut off 7 Inthe Min Pressure text box enter the lower pressure limit below which the pump will shut off A typical value for the lower pressure limit is 100 PSI or 6 BAR 8 Under Solvents Names enter the labels you want to use in the available Solvent text boxes Creating Pump Programs To create a pump solvent gradient program or pump program you use the Pump Program tab of the Instrument Control dialog box This tab contains a table and a gradient curve which let you define the composition of the solvent s at each step in the run You can change the table parameters and the curve either by editing the va
119. 8 35 overview 8 13 regression calculations 17 9 18 58 Re Identify command 10 39 10 41 relative scaling 7 14 relative window 10 40 relay events 10 35 parameters 13 9 settings adjusting after setup 13 3 Release Control command 12 23 Rename View command 11 30 Renumber Files command 11 42 Replace command 14 5 replicate injections 11 44 Index replicate definition 18 46 replicates 8 5 8 47 8 49 replot generation step in data analysis 18 4 parameters editing 7 12 printing 10 53 suppressing 7 12 Replot command 7 12 report format see also summary report format editor TurboRGEN designing columns 9 6 custom expressions in 9 10 general procedure 9 3 headers and footers 9 5 Report Format Editor overview 9 2 selecting AIA metafile 9 16 selecting ASCII text file output 9 16 selecting options to include 9 13 selecting SQL LIMS files 9 16 title 9 5 printing content of file 9 17 selecting for output in Graphic Method Editor 10 9 10 52 in Method Editor 7 9 in Sequence Editor 11 7 Report Format Editor overview 9 2 Report Format Editor process number 9 15 report generation step in data analysis 18 4 Report Header command 10 51 10 52 Report Properties 20 89 report status 20 6 Report tab 20 105 Report window 20 44 Report Window 20 87 report auto calibration 18 61 18 67 reported retention time 18 13 Reprocess command 10 23 10 34 Reprocess Results function 10 11 loading files 10 13 opening 10 11 overview 10 2 10 13 repr
120. Bunching Factor command 10 28 Save As MetaFile command in Chromatograms 14 6 in Graphic Method Editor Reprocess Results 10 55 Scale Time command 14 4 14 22 14 23 Scale Time From Origin command 14 4 14 22 Scale Voltage command 14 4 14 26 14 27 Scale Voltage From Origin command 14 4 14 26 scaled amount values reversing 18 75 scaling alternative amount overview 18 57 factors 17 8 options 8 17 parameters 6 10 7 11 12 29 relative 7 14 SD gain error C 21 search window calculating total size 8 13 definition 8 13 10 47 10 50 displaying 10 50 hiding 10 47 overlapping a 8 13 overlapping overview 18 45 setting up 8 13 segmented memory creating A 7 Select command 12 32 sequence acquiring data with 12 8 building by template 11 13 building vial by vial 11 17 calibration parameters 11 26 calibration types 11 14 configuration settings 11 11 creating 11 9 11 10 defining each sample 11 17 editing method from 11 51 IVM C 12 modifying during a run 13 16 overview 11 2 parameters file information for 11 22 overview 11 3 quantitation values for 11 24 reprocessing 15 4 spreadsheet appearance of 11 30 changing font 11 32 changing method data paths 11 44 color codes 11 3 11 6 column width 11 31 columns hide unhide 11 28 columns list of 11 6 copying and pasting in 11 33 11 37 editing 11 27 11 32 11 35 editing multiple cells 11 34 entering file names in 11 33 format 11 5 rows 11 35 Type column 11 8 views 11 28 11 29 Seq
121. Calibration Type C Use calibration factor 9r i Calibrate by reference C Use curve The table in which you specify the calibration levels becomes active Under Response select whether to use Area or Height The last column of the table changes to Area or Height depending on the option you choose Edit the Level Amt and Area or Height values For more information on levels refer to Adding Default Calibration Levels on page 8 26 gt To calibrate using a reference component 1 2 Select the Calibration tab of the Component Defaults dialog box Select Calibrate By Reference as the Calibration Type r Calibration Type C Use calibration factor C Avg calibration factor Select a component from the open method in the Cal Reference list You do not have to select a specific component to use Calibrate By Reference as the default calibration type However you must pick one when you add new components The Cal reference factor value is the factor that is modified to act AFTER the raw adjusted amount has been calculated in the usual way In other words Cal Reference Factor acts as an additional multiplier on the raw amount The factor can only be used if the calibration reference component s calibration type is Use Calibration Factor or a first order curve FORCED THRU THE ORIGIN The permitted range will be the standard TotalChrom floating point range positive numbers only The default value will be 1
122. Chapter 5 Building a Method What is a Chromatographic Method esee eene enne nennen 5 2 Working with Methods ect gre pei nee been remove pP E soles 5 3 Using the Method Editor onsacisananaiiiunaru nsn aE ennemis 5 4 Method Editor Windows neniaro iiaee a onean nne nennen nein EE nete nein 5 4 Method Summary Window sees nennen E tene tenete trennen 5 4 Component List Window ssteeeneie ette e ie p t dr EAS 5 5 Method Editor Commands eese eene nennen entente trennen 5 6 General Procedure for Creating a Method essere 5 7 Reviewing Method Parameters eeseseseseeeeeee eene enne nennen rennen enne nre nene enne nenne 5 9 Printing Method Parameters csssesssecscesecseseecsseeccssecaeesccseescesaecseeesaseeesaecesseeseeseenaeeees 5 10 Importing Method Par inetets ior nib aD due E EO e Rd DEP PR Rn 5 11 Chapter 6 Developing Instrument Parameters in the Method Introduction to Instrument Parameters seen ener enne 6 2 Selecting the Instrument s sieniin ie ee reete cta edet te eren ote parete te A ded 6 3 Creating Instrument Notes o BI nente eet EU HER Hep erp eoe Ve E ee del da 6 4 Setting Data Channels 2 2 n araia e rele ate DO e Dr ehe ost 6 6 Setting the Reale Time Plot Scale diee tet eei eie eee ede t Pete eate 6 10 Set ng Control Options vic e aeneus n IUe on hd iiem en 6 11 Setting Control Options for GCOS kes
123. Chapter 7 The following sections explain how to set processing parameters in the Graphic Method Editor and Reprocess Results and see their effects on a completed run Except for the instrument events command which appears only in the Graphic Method Editor the processing tasks are identical for both applications Setting Baseline Timed Events Baseline timed events affect how TotalChrom detects and integrates peaks during a run Therefore you can use them to help maintain consistent results when peak and baseline noise characteristics change You can set baseline timed events in the processing section of the method in the Graphic Method Editor You can also set baseline timed events in the Reprocess Results window however the events set there apply to a single file only and not to the method as a whole In either case the procedures are identical Setting Processing Parameters gt To set baseline timed events 1 Choose Baseline Events from the Process menu to open the baseline timed events display 4s Graphic Method Editor C PenExe TcCS Wer6 1 0 Examples solvent mth olx Defe ent Reprocess Retum Help x se 21 e MIBK ISOBUT ceo TOLUEN C PenExe TcCS Wer6 1 0 Examples SolvO01 raw 3 861 min 878 711 mV 1200 pts Z For Help press F1 7 The menu bar changes to show the following commands Delete Events Lets you delete one or more baseline timed events from
124. Component Identification eese ener nre nennen trennen trennen 18 45 Overlapping Search Windows enne nennen enne 18 45 Optimizing Component Identification eese enne 18 45 ioie LaTe n Ea aA EEE tut tei ut eR D 18 46 Cahbration Levels a dn reete tete eic ds ee Ce E eR E ta IBEN ESPE Ep ASt 18 46 Calibration Curves RR 18 47 External Standard Versus Internal Standard Calibration sss 18 49 Replace Versus Average essent teee trennen trennen 18 55 Retention Time D ta iue nee nt ROO RARI Rn Rees 18 55 Computation of the Calibration Curve sese 18 56 Auto Calibration Report eere Ro pe rp ede liie He eei iUe 18 61 Quantitations 5i otn avete nine a a a rd ie 18 68 Correction of Internal Standard Amounts sse 18 69 Calculation of Initial Component Amounts eese ene 18 70 Reversal of Scaling Options iso ete p dor RE eres 18 75 Conversion of Amount Ratios to Raw Amount ccesccsseesseeseeeeeeeeeeeeeeseeeteeeteeeaes 18 76 Conversion of Volume Adjusted Amounts seen nee 18 76 Computation of Adjusted Amounts eese eene nennen eere nennen 18 77 Quantitation of Unidentified Peaks 00 0 cc cccecssccescesssecensceeseeceeeeeesseceeeeeseeceteeeesaeeees 18 78 Table of Contents ix Chapter 19 Converting Files to Other Formats Converting TotalChrom Files to ASCH Text
125. Components dialog box 2 Inthe User Label text box type a label that associates the values with the component 3 Inthe User Values text boxes type the constants that you want to use 4 Select Send Results For This Component To LIMS if you want to send the information for this component to SQL LIMS For information refer to the Connect documentation Adding and Editing Components Editing a Component The procedure for editing a component is the same as that for adding a new component except that you choose an existing component instead of entering a new name gt To edit component information 1 Do one of the following e Choose Edit Components from the Components menu e Double click on the component name to open the Components dialog box 2 Use the mouse or the Next and Previous command buttons to select the component that you want to edit from the list in the dialog box 3 Edit the component parameters as necessary For specific procedures refer to Adding a Component on page 8 30 Developing Calibration Parameters in the Method 8 39 Loading and Merging Components From Files Loading and Merging Components From Files 8 40 When you build a method you can use the component list from another method text file or result file and edit the component information as necessary for the current method To use the components from another file you choose the Load and Merge commands in the Components menu
126. Delay Time 0 00 min Sampling Rate 0 40 pts sec Process Current Run Yes Segments Used 1 Segments Free 29 Total Runs 0 Active Sampling WF State Sampling Elapsed Time 5 37 min ChA Voltage 575 mV Viewing Data Acquisition Information The information that appears in the Details window is grouped into several categories The following categories are common to all instrument types Sample Information Sample Name Name of the sample as specified in the sequence file For dual injection analyses there will be separate names for Channels A and B Sample Number Number of the sample as specified in the sequence file For dual injection analyses there will be separate numbers for Channels A and B Raw Data File Ch A Ch B or both The full name of the current raw data file for each active channel Sequence Information Sequence File Name and path of the current sequence file Starting Row The first row of the sequence that is going to be run Ending Row The last row of the sequence to be run Curr Seq Row The position of the current run in the sequence Vial The vial number associated with the current or next run If this is unknown a will appear For a dual injection run the two vial numbers if known appear 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
127. E a Aroaren _ A r Sormana ligies x _ cma 4 Inthe Raw file path and Result file path text box enter or select the path where you want to store your data files The check box relating to paths is hidden not merely disabled for all users The raw and result paths are initially filled with your default paths Allowable changes to the contents of these fields via typing or folder button depend on the permissions set in System Configuration 12 4 Setting Up Data Acquisition 5 In the Base File Name text box enter a file name or set a tokenized name by clicking the lt button The default Base File Name is typically set in System Configuration Allowable changes to the contents of these fields via typing or folder button depend on the permissions set in System Configuration Your application manager may have set up Default base names in System Configuration Do not end a base file name with a number since it will be treated like a cycle number If you must use a number then use a legal separator for example hyphen or underscore_ Do not use a period TotalChrom will automatically append a three digit run or cycle number to this base file name to create the data file names If the file name already exists in the path TotalChrom will append a date time stamp to the file name the four digit year two digit month two digit day two digit hour in 24 hour style 14 2 pm two
128. ExeXTcCS Wer6 1 0 Examples SolvO01 raw 88348mn 820215mV 1200pts Use Next Prev or Retum to accept changes Click on another peak to cancel changes NS The dialog box appears on the right side of the window and a reduced view of the plot appears on the left The menu bar changes to display the following commands Type menu Lets you select the type of component to add or edit 10 38 Working with Components Re Identify command Re identifies peaks after you change component information Return command Closes the Edit Components dialog box and restores the main Graphic Method Editor window Adding and Editing Single Peak Components The following procedures explain how to identify a previously unidentified peak by creating a new component and how to change information for an existing component If you want to change which peak a component is assigned to refer to Re Identifying Peaks on page 10 39 gt To add or edit a single peak component 1 Choose Edit Components from the Calibration menu The Edit Components dialog box appears and the plot display changes to reflect component names retention times and search windows The first peak in the plot which TotalChrom may or may not have identified as a component has a dotted rectangle around it to indicate that it is the currently selected peak Choose Next and Prev in the dialog box to select the next or previous peak Click the peak that
129. HABC2 THHHHE ABCIHHHEX Y Z 11 15 Building a Sequence by Template Use only one set of pound signs A pattern such as ABC DEF will give sample numbers of the form ABCO1DEF because only the first set of characters is replaced by a number 12 In the Starting Number text box enter the value that you want to become the first number in the sample number pattern This number will be increased by an increment of one for each new sample in the sequence 13 In the Number Of Samples text box enter the total number of samples to be analyzed in the sequence TotalChrom uses this value along with the entry from Samples Between Calibrations to determine where to insert sets of calibration cycles in the sequence 14 Enter a number in the Injections Per Sample text box to indicate how many injections to include for each sample in the sequence 15 Under Autosampler enter the Initial Vial Number for the first sample or calibration standard in the sequence TotalChrom increases the number for subsequent samples Replicates use the same vial number 16 If you are using an autosampler that can access vials randomly select the option AII Calibrations From One Vial Set to use the same set of vial numbers for all calibration sets 17 If you are using a LINK controlled GC autosampler select the Injection Site which is either the front or the rear inlet or injector 18 Choose OK 19 If the sequence is a dual injection
130. INK controlled autosampler to begin its first injection of the new setup as soon as the instrument reaches the Ready state If the sample vials are not in the autosampler yet you may issue the Start Run command later Select Single Run Data Buffering if you do not want to store data from multiple runs in the interface If Single Run Data Buffering is not selected the interface memory will be divided into segments large enough to store the data from a single run This enables the interface to acquire data from multiple runs even if the Navigator window is closed or the computer is turned off For more details refer to Appendix A How Interfaces Collect Data Select Suppress Processing if you do not want to process the data immediately after it is collected This automatically suppresses the data analysis process including the printing of reports and plots and the creation of a result file You may want to select Suppress Processing if you plan to use your computer for another task and do not want to be interrupted by data processing at the end of each run Since data processing is a compute intensive task it can cause your computer to be unresponsive for several seconds as the various data analysis functions are carried out If you suppress processing you can use Batch Reprocessing later to obtain results from the analyses Select Suppress Reports Plots if you do not want to print a report and plot Setting Up Data Acquisition
131. ISE eR HEROS 3 2 Nnnc E 3 2 M nUS ii snegsinoi bea nte me pn Diptera nei e diit 3 3 Configurme Instrumints nemico ege Eee ra ie eee detener o ted 3 4 Configuring a 900 Series Interface sese eene rennen ene 3 4 Configuring a 600 Series LINK Interface and Attached Instruments 3 9 Resetting a LINK Configuration sees ener enne 3 15 Disconnecting an Instr ment 4 eere ET gehe eta EE nent 3 15 Using Run Co nters eed t ere ep eie 3 15 Configuring User Options oin hee t t etd e pec A eee ee pcne te es 3 17 BROMUS c 3 17 Colors s etta eode tera e a t OT V ae 3 18 Plot Options 32 amada ardeo EROR b ERREUR 3 20 Quick Patlisz5 2 ico oO SIRE me BO 3 21 Reporting ec e eben p ce n cto e Cn iiie tei covet ERNETEN 3 23 Project Directory fri oce Ub Beh ster nin dette ete dete tdt 3 23 Printing Configuration Information eese eren nennen enne enne rennen enne 3 25 Chapter 4 Using the Navigator Starting TotalChrotm 52 2 atu aea eA Ead tendens 4 2 The Navigator Window ater t a e EOD Re A SC ted 4 3 Navigator Buttons and Commands eese nennen rennen enne 4 4 Navigator Tasks and Other Application Tasks eeeeeeeeneen enne 4 7 Performing Navigator Tasks eene enne ener nnne 4 7 Opening Applications from the Navigator esee enne enne 4 0
132. LIMS Cancel Apply label associated with this component 15 chars 2 Inthe User Label text box enter a label that associates the default values with a component 3 In the User Values text boxes enter the default values that you want to use 4 Select Send Results For This Component To LIMS if you want the default to be to send the information for this component to SQL LIMS For information refer to the Connect documentation Developing Calibration Parameters in the Method 8 27 Adding and Editing Components Adding and Editing Components 8 28 You add and edit components in the Components dialog box The New Component and Edit Component commands in the Components menu both open the Components dialog box The difference between the two commands is in the initial mode of the dialog box e When you choose New Component the dialog box is ready to accept your input of a new component add mode e When you choose Edit Component the dialog box is ready for you to select an existing component to edit edit mode Whichever command you use once the Components dialog box is open you can both add and edit without having to close and reopen the dialog box to change the mode e To switch from editing to adding choose the New Component command button e To switch from adding to editing select a component to edit from the list You can also open the Components dialog box in edit mode by double clicking
133. Load TotalChrom replaces the existing components in the component list with the components from the file Merge TotalChrom intersperses by retention time the existing components in the component list with the components from the file To use the Text File commands you must first generate an ASCII text file Each line of the text file represents a component that you want added to the list and each line must have the following format lt name gt time abs lt rel gt Two examples are Aldrin 8 6 5 0 1 Dieldrin 13 15 6 0 1 where lt name gt is the component name and time is the expected time for the component You must specify both of these values and you must enclose the name in quotes The remaining two values representing the size for the absolute search window and the size for the relative search window are optional You must separate all values on a line by commas The information in the component default file supplies all other values including the search window values if they are not defined in the text file gt To load components from a text result or method file 1 Do one of the following e Choose Load Text File or Load Result File from the Components menu to open the file selection dialog box for the specified type of file Skip to Step 5 e Choose Load Method File from the Components menu to open the Load From Method File dialog box Continue with Step 2 2 Leave C
134. OK Cancel Reset Display the conditions template for the selected instrument type 2 Do one of the following Enter the header text that you want to appear in the printed reports for this method To start a new line press Enter To erase the contents of the text box choose Reset Select a template for the instrument from the Template list 3 If you are working with a template edit the information as necessary 4 Choose OK to save your changes Creating Instrument Notes gt To change the template 1 Choose Instrument Notes from the Instrument menu The Instrument Notes dialog box appears and shows any current header information in the text box 2 Select the new template type from the Template list A confirmation box appears and asks if you want to erase the current header information 3 Choose OK 4 Edit the information or create new header text and choose OK Developing Instrument Parameters in the Method 6 5 Setting Data Channels Setting Data Channels 6 6 The Data Channels command in the Instrument menu controls how TotalChrom 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 The options available on the Data Channels tab depend on the type of instrument that you are using gt To set channel options for a LINK controlled instrument 1 Choose Data Channels from the Instrument menu to open
135. Offset text box enter the offset value that you want to appear at the bottom of the plot window The plot always appears above the actual bottom of the window to allow enough room for component names In the Full Scale text box enter a value to specify the height of the plot window The millivolt value assigned to the top of the plot window is equal to the full scale value plus the offset value A data point that has a voltage value equal to the sum of the offset and full scale is plotted at the top of the window A data point with a value equal to the offset voltage is plotted at the bottom of the window Choose OK to redraw the plot using the new values gt To redraw the plot at the default scaling Choose Entire Chromatogram from the Display menu TotalChrom redisplays the plot in its entirety showing the full time span and recalculating the full scale and offset values based on the maximum and minimum data values in the file Expanding Chromatograms By default TotalChrom displays the chromatogram and shows the complete run with the largest peak set to full scale You can quickly expand and reduce the plot display by using the mouse to rescale the plot manually You can also redefine scaling parameters in the Rescale Plot dialog box as shown in Changing the Plot Scale Editing Methods and Results Graphically 10 17 Changing Display Options To retain the plot scale that you defined for more than one file using eit
136. Only the index file represents a true picture of what occurred during a sequence run The Modify Active Sequence command is not available if the setup sequence includes bracketed calibrations To ensure that you obtain valid results you need to run a sequence of this type in its entirety without modifications gt To modify the active sequence 1 If the instrument is not bound choose Bind from the Instrument menu then select the instrument that you want to bind 2 Select the instrument in the Instrument panel then click the Modify button in the Navigator and choose Active Sequence Modify OR Choose Modify Active Sequence from the Instrument menu then select the instrument 13 16 Modifying a Sequence During a Run The Sequence Editor window opens The sequence file name appears in the title bar and the instrument name appears in the status bar S Sequence Editor D XPenExeXT cCSXVerb 1 0XE xamplesNgasmultmethods seq File Edi Change Build Format View Window Help uj amp ele ss tjv al E Sequence Information Channel A _ m xd 2600 Data Bw Type Sudyname Name Note Number Vel Ista So ESESE 3 sh cmm XR SA rr mM Ready Single lodified Rows 6 AD D PenExe TcCS Wer6 1 0 Examples 7 Although you can switch to other applications when you are modifying a sequence you cannot re access the Navigator until you close the Sequence Editor window 3 Edit the sequence as necessar
137. P is the second plot data value M is the multiplier applied to the second plot O is the offset applied to the second plot B is the baseline adjustment applied to the calculated plot 14 29 Calculating a New Chromatogram 14 30 10 11 The Normalization option you select determines how the values for M and O are calculated These options are None The operation is performed with no normalization applied to the second plot the raw data values are used from both plots for example M and O are equal to and 0 respectively From Data The offset and multiplier are derived from the minimum and maximum values in the two raw data files Changes in the actual display have no effect on the calculation max min max min O min M x min From Display The offset and multiplier are calculated in the same way as From Data except that the maximum and minimum values used are those from the displayed data range only they are the maximum and minimum values that occur in the raw data files between the Start Time and End Time set in the dialog box From Scaling The multiplier and offset values are calculated from the screen display as follows M Scale Scale O Offset M x Offset Manual Lets you set the values for the multiplier and offset If you select Manual as the Normalization option enter the values that you want to use for the Multiplier and Offset Offset This contro
138. P LaserJet 5 Print Range CAI Selector C page ETT To Print Quality 600 dpi Due E Iv Print file summary S ematogram 3 Select Print overlay in the Print dialog box and choose OK Only the contents of this overlay window will be printed Using Images in Other Applications The Copy To Clipboard command on the File menu allows you to copy a chromatogram and its scaling information for use in any Windows application that accepts black and white or color bitmapped files gt To copy a chromatogram to the clipboard 1 Select the chromatogram that you want to copy 2 Choose either Copy To Clipboard B W or Copy To Clipboard Color from the File menu You can then paste the image into any Windows application that accepts black and white or color bitmapped files The Save As MetaFile command in the File menu lets you copy an image of the screen to a Windows metafile gt To save the current chromatogram as a Windows metafile e Choose Save As MetaFile from the File menu then name the file The image in the file will be a color image 14 6 Controlling the Appearance of Chromatogram Windows Controlling the Appearance of Chromatogram Windows Because you can have multiple chromatograms open at the same time you might want to change the way in which they appear in the Chromatograms window Stacking Cascading and Tiling Chromatograms You use the following commands on the Window menu to control how chro
139. Parameters eeseseeeeseeeeeeeeene eene eene nre 11 26 Editing the Sequence Spreadsheet eese eene 11 27 Editing Basics C 11 27 Formatting Spreadsheet Views sessi enne nete nennen 11 28 Changing the Appearance of a Spreadsheet sse 11 30 Editing Individual Cells net br Ete ette teen delete etatis 11 32 Changing the Values in Multiple Cells seen 11 34 Editing ROWS 2 eet ete at tei e eee ca Dir rece E 11 35 Pasting Data from an External Spreadsheet Application esee 11 37 Editing Colum Y ales deeem e teer 11 38 Changing P ths 4i eei itia oq ep rd eal ied 11 44 Creating Notes About Your Samples esee eere 11 45 Including a User Program in a Sequence sees 11 46 Including a Serial Dilution Program in a Sequence serene 11 48 Appending New Cycles to a Sequence seen eene 11 48 Editing Global Parameters eo per e Het ca eee i fe eleme deste get 11 49 Changing Environments From Within the Sequence Editor esses 11 50 Switching tO Setup neo ee oe e rea e te erts 11 50 Switching to Batch Reprocessing esses nre nennen 11 50 Editing Method Files for the Current Sequence sese 11 50 Building a Sequence from a Text File esses nennen enne 11 52 Text File Form
140. Post Sequence Options tab will be available e Selecting Set Up With Specified Parameters will enable other options in the Post Sequence Options tab For additional information refer to Setting Post Sequence Options in Chapter 12 3 8 Configuring Instruments Configuring a 600 Series LINK Interface and Attached Instruments The 600 Series LINK interface lets you control instruments as well as acquire data A LINK interface can support one LC or up to a maximum of three GCs LINK Interfaces have no analog to digital conversion function Note the following exceptions e You cannot configure an AutoSystem with Headspace and a different type of GC on the same LINK e AnLC pump module must connect to Port A and the data source either a detector with digital output or a 900 Series interface must connect to Port B If used an ISS 200 or Series 200 autosampler must connect to Port C e A Model 7673 autosampler connected to an HP5890 Series II GC must appear on the port immediately following the HP5890 The following procedures explain how to configure LINK controlled GC and LC instruments These procedures assume that the instrument has not previously been configured Configuring a LINK controlled Instrument There are four steps to configuring a LINK controlled instrument for the first time e Choose a data acquisition port e Set LINK configuration options e Set GC or LC configuration options e Save the configuration Each step i
141. RIFY LOG The information in this file is also displayed in the Setup Problems window so you can quickly see the reason the setup failed You will be unable to complete the setup until you have corrected the problems described in the Setup Problems window Using the Instrument Errors Pop Up Menu You can access a pop up menu in the Instrument Errors window by clicking the right mouse button The menu includes commands to keep a separate log file print errors delete past errors and to toggle the display of new errors as they occur If you do not view new errors as they occur a message in the status bar indicates the number of new errors Acquiring and Viewing Data 12 25 Viewing Real Time Plots Viewing Real Time Plots The Real Time Plot button and its associated command in the View menu lets you view a real time plot of the data as it is acquired by an interface for each instrument that is performing a run Each real time plot appears in its own window in the Real Time Plot application As with other features clicking on the Real Time Plot button displays the plot for the instrument currently selected in the Navigator Choosing the command from the drop down menu opens the Real Time Plot window in which you select the instrument from a list of those available This does not change the instrument that is selected in the Navigator gt To open the Real Time Plot window e In the Navigator select the instrument for which you
142. Run Menu Lets you perform some of the same functions as the Run menu in the Navigator In addition the Start Monitor command lets you view the detector signal without starting a true run The Stop Monitor command stops the monitoring process Details Command Opens the Details window which shows instrument conditions during the run Acquiring and Viewing Data 12 27 Viewing Real Time Plots Viewing Multiple Real Time Plots You can open a window to display the real time plot for any instrument on your system that is currently set up Each plot appears in its own window The commands in the Options Run and Window menus as well as the Details command affect only the active plot Clicking in a plot window or choosing one of the instruments from the Window menu makes that the active plot it does not change which instrument is selected in the Navigator gt To view multiple real time plots 1 Choose an instrument name from the Instrument menu to view the real time plot for that instrument A new window opens in the Real Time Plot window 2 Continue choosing instrument names from the Instrument menu until all the real time plots you want to view are open gt To close a real time plot window e Close the window of the plot you want to close by clicking the close box in the upper right corner of the window Do not choose Exit from the Instrument menu or double click the Control menu box in the Real Time Plot window This will
143. Selecta path and choose Select TotalChrom will add the path as a quick path and list it in the Quick Paths dialog gt To remove all paths from the Quick Paths list 1 In the Configuration Editor choose Quick Paths from the User menu 2 Inthe Quick Paths dialog choose Clear 3 TotalChrom will remove all paths from the Quick Paths list If you change your mind choose Reset to replace the original paths Reporting This command opens a dialog box for you to select either TotalChrom Review and Approve or TcPublisher as the reporting program to review your data gt To select a Reporting Option 1 In the Configuration Editor choose Reporting from the User menu The Reporting Options dialog box opens Reporting Options x Which Reporting program would you prefer to review your data Changes will be seen the next time you start TC Navigator TotalChrom Review amp Approve C TePublisher Cancel 2 Select the Reporting program and choose OK The change will be seen the next time you start TC Navigator Project Directory Configuration This command opens a dialog box for you to type in or select via a Path Select dialog a Project Directory setting The Project Directory path the default is blank is used by all applications in place of all default path settings for all file types This includes all editors and Setup The specified project directory is saved with other user settings and will continue to
144. Setting Instrument Timed Events on page 6 36 For a complete definition of each LC parameter refer to the manual that came with the specific instrument module Setting Control Options Setting LC Autosampler Parameters gt To set autosampler parameters for liquid chromatographs 1 Select the Autosampler tab of the Instrument Control dialog box Instrument Control x Autosampler Pump Config Pump Program Detectors Instrument Timed Events Injection Source p Derivatization Dilution C Manual Off C Deiv C Dilution Program Sample Injection Flushes Injection volume pL oo Flush volume pL po Loop size pL p Flush speed Medium Fixed mode for Flush cycles D Excess volume uL fo Pre injection cycles E Air cushion pL B Post injection cycles 5 2x Sample syringe size uL 5 E Post method cycles Sample speed Medium Needle level 773 r Peltier Tray Control Ibiect debe inl NN Temperature C 4 10 v The autosampler will be used 2 If you are using manual injection select Manual If you are using an autosampler continue with Steps 3 through 19 3 In the Injection Volume text box enter the amount of sample that you want to inject Ensure that this value is less than 50 of the Loop Size that you specify in the next step 4 From the Loop Size list select the size of the injection loop fitted to your autosampler To e
145. Summary as 16 25 user programs 5 5 7 3 User Programs command 7 16 user values setting 8 38 user definable component values 8 19 xvii V V See valley to valley baselines timed event validation performance parameters C 2 procedures C 6 reports example C 15 specifications C 17 tests running C 14 valley height ratio 18 30 valley to peak ratio 18 14 valley to valley baselines timed event 18 33 valves adjusting for GC after setup 13 5 initial values for 6 18 vertical scaling 7 14 vial list building 12 17 overview 12 16 Vial List window 12 17 vial numbers incrementing 11 40 views of sequence 11 28 11 29 void time definition B 13 voltage range shifting 14 4 scaling 14 26 voltages changing in chromatograms 14 13 volume units parameter definition 8 4 W wavelength calibration for 785 detector 13 19 weighting factor definition 8 17 in calculation 18 64 selecting 17 9 width ratio definition 18 14 window See search window Wrapped error message 12 24 X X See exponential skim timed event xviii Z zone parameters setting 6 14 setpoints 6 13 zoom box 54 Zoom In A B command 12 30 Zoom Out A B command 12 30
146. This provides a type of chronological versioning capability If the method you use in Graphic Method Editor has auditing enabled then auditing is also enabled for result files created from it the Audit Trail dialog box will be displayed when you save the result file 10 10 Using Reprocess Results Using Reprocess Results To reprocess the data from a single run to improve the results of a single analysis use the Reprocess Results application The majority of the commands are the same as those in the Graphic Method Editor and you can see the effect of changing the parameters that were used to process the data immediately You can save the results in the existing result file or save them as a new file When you save the results you do not change parameters in the method gt To open the Reprocess Results window 1 Inthe Navigator click on the Results button or choose Results from the Reprocess menu ETTWNWNNS Results The Reprocess Results window opens The TotalChrom File Open dialog box appears in the foreground prompting you to choose a result file 2 Locate and select the result file you want to edit and choose Open TotalChrom opens the raw data file associated with the selected result file and processes it using the copy of the method embedded in the result file Therefore the results displayed are identical to the information in the selected result file Instead of opening result files by selecting them one
147. TotalChrom Workstation User s Guide Volume I Release History Part Number Publication Date N515 6003 B December 2004 User Assistance PerkinElmer 710 Bridgeport Avenue Shelton CT 06484 4794 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 O 2004 PerkinElmer Inc Tidestone Formula One Copyright 1993 2000 Tidestone Technologies Inc All Rights Reserved Portions copyright O 1999 Blaise Software Services Inc All Rights Reserved Portions copyright 1996 Microsoft Corporation All Rights Reserved Produced in the U S A Trademarks Registered names trademarks etc used in this document even when not specifically marked as such are prote
148. Undo command becomes disabled gt Toreturn multiple chromatograms to their previous level of expansion 1 Hx per NS Select Expand All Plots on the Options menu Click the right mouse button in any open chromatogram Choose Undo on the Chromatogram pop up menu Right click and choose Undo as many times as needed to further reduce the expansion When you can no longer reduce the expansion the Undo command becomes disabled If you have previously expanded any chromatograms with Expand All Plots deselected some plots will reach their original level of expansion before others Displaying Information in Chromatograms Rescaling Chromatogram Values The Rescale command on the Options menu lets you change the starting and ending times and the offset and full scale values by a specific amount for all open chromatograms except those displayed in overlay view gt To rescale the values for multiple chromatograms 1 Displaying Chromatograms Choose Rescale on the Options menu TotalChrom opens the Rescale dialog box which contains the file name starting and ending times and the offset and full scale values for all open files except overlays File Name Halo002 raw 35 275 803 508 4 9856587 37 959 4 857192 5 35 275 803 509 AutoScale Defaults ILL Cancel Enter new values in minutes in the Start Time and or End Time columns to define the X axis scale of the chromatogram These values determ
149. When you want to see a hidden label you can move it to the top of a stack of labels with the Move To Top command on the Labels pop up menu gt To move a label to the top of a stack 1 2 Click the right mouse button in the label that you want to move to the top of a stack of labels Choose Move To Top from the Labels pop up menu Linking and Unlinking Labels to Data When you choose the Link Position To Data option a label will keep the same position in terms of the time and intensity axes when you scale the chromatogram When you deselect this option the label maintains its same absolute position in the window When you create a label it is linked to data by default gt Displaying Chromatograms To link and unlink the position of a label to data 1 2 Click the right mouse button in the label that you want to link or unlink Choose Link Position To Data from the Labels pop up menu to toggle between linking and unlinking the position of the label to data appearing in the chromatogram A check mark will appear next to this command when you select it 14 19 Aligning Peaks in Two Chromatograms Aligning Peaks in Two Chromatograms 14 20 Use the commands on the Chromatogram pop up menu to shift or resize one chromatogram to align selected peaks baselines or other points with those on another chromatogram You can then compare chromatographic data in the two plots The procedures in this section expla
150. Window text boxes The total search window is the sum of the absolute and relative windows which TotalChrom applies to either side of the current retention time of the component The relative window is a percentage of the expected retention time of the component Changes are in increments of tenths of a second for the absolute window and tenths of a percent for the relative window The search window marker for the selected peak changes dynamically as you alter these values The example below shows the original search window on the left and a reduced absolute window on the right To identify the largest peak eluting within the search window as the component select Find Largest Peak In Window This option selects the largest peak as the designated component If you deselect this option TotalChrom identifies the peak closest to the expected retention time in the window as the component If you do not want to recalibrate the component skip to Step 13 To calibrate the component continue with Step 9 Select Update Calibration The Level and Amount text boxes and the Calibration Type settings become enabled This option only updates the calibration for the component you are currently working with To update all components use the Calibrate command in the Calibration menu In the Level field do one of the following e To select from existing calibration levels enter the name of the level or select it from the list e Tocrea
151. a component name in the Component List window This both opens the window and preselects the component that you want to edit For detailed information on the specific parameters contained in the Components dialog box refer to Understanding Component Parameters on page 8 9 Adding and Editing Components The following is the general procedure for adding and editing component information gt To add or edit component information 1 Choose New Component or Edit Component from the Components menu to open the Components dialog box Identification Calibration User Values LIMS Component Type Peak Named group Timed group Name Retention time 0 001 min Absolute window o oo s Relative window f 00 EX Find largest peak in window I This component is a retention reference Reference X This component is an intemal standard Internal Standard X Use this component as the RRT reference Next Brevious New Component DERECE New Component cot am The name by which the component is to be identified and labeled There are three tabs in the Components dialog box Identification Select this tab to set parameters for component identification The options on this tab change depending on the peak type you select Calibration Select this tab to set the calibration parameters you want to use User Values LIMS Select this tab to specify constants to
152. a LINK controlled GC 1 Select the Detectors tab of the Instrument Control dialog box Instrument Control x Autosampler Oven Inlets Carrier Detectors Instrument Timed Events m Detector A ECD m Detector B FPD Temp C 150 Range 1 Temp C 250 Range 0 E Time constant 200 7 Adjust m Time constant 200 x PMT oo Autozero Iv On Value fi Autozero Iv On Value fi Polarity Positive Negative Polarity Positive Negative Filament G Gh GF Shutdown Filament G Gh C Gi Shutdown m Gases m Gases None 0 0 iia H2 so Tuy inte Make up 30 0 min Air n mimi None Joss TUER None in Tol Zr REC REC Attenuation z Attenuation rz Offset po xs Offset p xs Lee ew Temperature of detector A 0 or 100 to 450 2 Inthe Temp text box enter a temperature value for the detector 3 Select a sensitivity setting for the detector in the Range 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 an AutoSystem 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 4 Select a value in the Time Constant list Developing Instrument Parameters in the Method 6 19 Setting Control Options 6 20 10 11 This value sets the detector f
153. a report format gt To create a report title 1 Choose Title from the User Notes menu to open the Report Format Title dialog box Title to appear at the top of the report 2 Enterthe title you want to use for this report and choose OK When you choose OK the dialog box closes and the title for this report format file appears at the top of the report After you have created a report title you can click the title area to reopen the Title dialog box The steps to create header and footer text are nearly identical and they have been combined into a single procedure gt To create header or footer text 1 Choose Header from the User Notes menu to open the Header dialog box OR Choose Footer from the User Notes menu to open the Footer dialog box The following shows the Header dialog box However except for the title the two dialog boxes look and function the same way Cancel Delete Enter text Use Ctrl M to start a new line Building a Report Format 9 5 Editing Report Columns 2 Enterthe text you want to appear as the report header or footer in the text area of the dialog box and choose OK When you come to the end of a line press Ctrl M to start a new line You can enter up to 512 characters To delete all existing text choose Delete When you choose OK the report header or footer appears in the report window After you have created a report header or footer you do not need to choose the
154. ach injection 9 Select how many Pre Injection Sample Washes and Post Injection Solvent Washes that you want to have If you are using an HP5890A HP 5890 Series II or an HP 6890 you can specify two sets of Post Injection Washes with solvents A and B Setting GC Oven Inlets Parameters The Oven Inlets tab of the Instrument Control dialog box 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 column 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 column Gives the temperature to which the oven is being raised during the ramp The initial setting is the temperature of the oven at the start of the run or throughout the run for an isothermal analysis Hold column Represents the period for which the temperature is held before starting the next ramp 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 Temperature and Hold fields are disabled until you set the Rate You can also adjust the Temperature and Hol
155. alibration information used to quantify the samples A single sequence can contain several brackets sets of calibration standards with intervening samples Cal Grand Avg Averages all occurrences of each calibration level in the sequence and uses that average to process and report all samples In the Injections Per Calibration text box enter the number of injections that you want to include for each calibration in the sequence If you want TotalChrom to enter sample numbers for calibration rows select Assign Sample Numbers To Calibrations If you selected Replace or Average as the First Injection type and are making more than one injection per calibration select from these same options for Replicate Injections This defines how TotalChrom will handle the replicate injections for each standard level within each set of calibration standards Enter a number in the Samples Between Calibrations text box to define where the calibration standards appear in the sequence When calibration cycles are to be inserted TotalChrom enters a row for each calibration level defined in the method Under Samples enter a Sample Number Pattern The sample number pattern is an alphanumeric entry that defines the basic form of the sample number Use characters to indicate the position and length of a numeric string within the sample number Numeric digits can be located anywhere in the sample number The following are valid patterns ABC
156. all unidentified peaks LIMS Results If you have Connect use this tab to specify which results to send to SQL LIMS 2 Inthe Volume Units text box enter the units you want to use for sample volume 3 Inthe Quantitation Units text box enter the units you want to use for amounts or concentrations 4 Inthe Sample Volume text box enter the value that represents the normal sample volume for the calibration standards you are using You only need to alter the default value if you plan to use different volumes for different samples 5 Inthe Void Time text box enter a time value that represents the elution time of an unretained peak Developing Calibration Parameters in the Method 8 7 Editing Global Calibration Information 8 8 10 11 12 13 Under Calibration select External or Internal Standard as the calibration type To exclude replicates that are outside a chosen limit select Reject Outliers During Calibration and enter the Allowed Deviation percentage you want to use To proportionally correct all calibration levels select Correct Amounts For Calibration Standards TotalChrom uses the amount you specify in the sequence file to adjust the calibration level Select Convert Unknown Samples To Concentration Units if you want TotalChrom to perform that function TotalChrom uses the amount you specify in the sequence file as a divisor for sample cycle types Under Unidentified Peak Quantitation en
157. alue will overwrite the sequence file value When you merge a text file with a sequence any parameters in a given cycle of the text file will overwrite those of the same type in the corresponding cycle of the sequence For example if a cycle in the sequence specifies DEFAULT as the method file and the corresponding cycle in the text file specifies SOLVENT as the method file SOLVENT will overwrite DEFAULT If the text file contains a blank parameter with commas to mark its place a blank value or 0 will overwrite the corresponding value in the sequence Certain numeric sequence parameters amount ISTD amount multiplier divisor and dilution factor are not allowed to be 0 so you must edit the sequence to correct these invalid entries gt To merge information from a text file 1 Open the sequence file that you want to change 2 Choose Merge Text File on the Build menu 3 Enter or select a text file name and choose Open This merges sequence information from the selected text file with the current sequence file Using a Text File from the Command Line You can run the Sequence Editor and specify a fully qualified text file name on the command line When you build a new sequence from the command line the text file name is used to name the sequence When you merge or append a text file the text file name must match the fully qualified name of an existing sequence CAM locks are asserted on existing sequence files the same way th
158. ameters are not available e For named group components select the component that you want to designate as the default internal standard for the open method e For timed groups select the default retention reference and or the default internal standard for the open method Setting the Calibration Defaults Calibration values affect how the software calculates component amounts You can choose among the following types of calibration for components e Using a constant calibration factor e Calculating an average calibration factor e Using the calibration curve of another component calibration reference e Solving the component s calibration curve The procedures for setting up each calibration type follow This section also provides instructions for working with calibration levels gt To calibrate using a constant calibration factor 1 Select the Calibration tab of the Component Defaults dialog box 2 Select Use Calibration Factor as the Calibration Type F Calibration Type C Calibrate by reference C Use curve 3 Enter a calibration factor value in the Cal Factor text box 4 Under Response select whether to use Area or Height Developing Calibration Parameters in the Method 8 23 Setting Component Defaults 8 24 gt To calibrate using an average calibration factor 1 2 Select the Calibration tab of the Component Defaults dialog box Select Avg Calibration Factor as the Calibration Type r
159. ample washes Post injection solvent washes 4 ENN gii Post injection solvent washes B Cancel aly The autosampler will be used 2 Ifyou are using Manual injection select Manual or a TurboMatrix select TurboMatrix When you select Manual or TurboMatrix all other controls are disabled If you select Autosampler the other controls are enabled or disabled according to the instrument type for example Clarus AutoSystem HP 6890 etc If you are using an Autosampler continue with Steps 3 through 9 3 Select the Syringe Capacity for the syringe in the autosampler 4 Selectan Injection Volume and an Injection Speed The actual injection volume is set here The sample volume that you enter in the sequence file is an optional mathematical correction used in quantitation 5 Select the number of Sample Pumps that you want to use 6 12 Setting Control Options This value specifies the number of times the syringe is filled and emptied before the final load 6 If you are injecting a viscous sample set the Viscosity Delay 7 If you are using an AutoSystem GC select the Wash Waste Vial Set that you want to use Wash Waste Vial Set 1 uses vials 1 and 2 Wash Waste Vial Set 2 uses Wash Waste vials 3 and 4 8 If you are using an AutoSystem 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 e
160. an be used as a correction for calibration standards and or to convert unknown samples to concentration units Int Std Amt Internal Standard Amount The total amount of internal standard component s in the sample Sample Vol Sample Volume The actual volume injected Dil Factor Dilution Factor The value that accounts for the diluents or aliquots used in preparing the sample Multiplier The value by which TotalChrom multiplies raw component amounts to get the adjusted amount 11 7 Using the Sequence Editor 11 8 Divisor The value by which TotalChrom divides raw component amounts to get the adjusted amount Addend The value TotalChrom adds to raw component amounts to get the adjusted amount A negative value is valid Norm Factor Normalization Factor The normalization factor used in reporting normalized amounts and normalized areas Baseline Baseline File The data file usually derived from a blank sample run that is subtracted from the raw data file to generate the modified file Modified Modified File The file containing the modified raw data Printer The printer to be used for printing reports See your application manager for information about default and other printers Plotter The plotter to be used for printing replots if specified in the method See your application manager for information about default and other printers Sample ID LIMS A read only col
161. an to put in the file Following is an example of the second line in a text file STUDY A SAMPLE A NUMBER A INST RAW A RESULT A PROC A SAMP A If you omit identifiers and the text file is intended to create a whole sequence or append cycles the Sequence Editor will enter default values for parameters corresponding to the missing identifiers Third and all subsequent lines Each of these lines represents a different cycle They contain parameters corresponding to the identifiers listed on line 2 No other parameters are allowed Here is an example of line 2 followed by a row of parameters to illustrate how the parameters must correspond to the identifiers TYPE A SAMPLE A AMOUNT A INST RAW A RESULT A PROC A SAMP A Sample HERBICIDE 2 PEST HERBOO1 HERBOO1 PEST PEST Building a Sequence from a Text File A file must contain at least as many cycles as specified in line 1 If there are more they will be ignored The following table lists the identifiers that you use when you import a text file into a sequence their corresponding parameters and whether each identifier must appear as a number or text You must enter the identifiers exactly as shown in the table including capitalization Otherwise TotalChrom will not be able to import the file For single channel runs using Channel B you must use the A identifiers for sample information If you use the B identifiers the sequence will not be built
162. and Printing a Report or Replot on pages 10 49 51 Saving Files in Reprocess Results When you work in Reprocess Results you can save modified result data with three commands on the File menu e To overwrite the original result file with the modified results choose Save e To save the modified results in a new file with the original name with a time stamp added choose Save With Time Stamp This provides a type of chronological versioning capability e To rename the modified result file choose Save As If a method that is referenced in a result file has auditing enabled then auditing is also enabled for result file that was created from it the Audit Trail dialog box will be displayed when you save the result file Editing Methods and Results Graphically 10 15 Changing Display Options Changing Display Options Display menu commands let you change how chromatographic data appears as well as other attributes of the Graphic Method Editor and Reprocess Results windows You can e Display report information above the chromatogram to review the peak report or report header select another report format file or print a report e Use raw data points or bunched points to display the chromatogram e Show or hide the reference chromatogram e Display the entire chromatogram if you have expanded it e Redefine the plot scale by entering specific values e Expand both chromatograms together by expanding the reference chromatogram Th
163. and Reprocess Results windows The dialog box allows you to scale the chromatogram manually by entering minimum and maximum values for each axis Select Header On All Replot Pages to print the header on all pages or leave it unselected to print the header on the first page only The header appears at the top of the printed plot This applies to replots generated automatically at the end of a run Configuring User Options 4 Leave Show Reference Chromatogram selected if you want to display both the reference and working chromatograms in the Graphic Method Editor and Reprocess Results windows The Reference Chromatogram Size text box becomes active 5 Use the scroll arrows to change the reference chromatogram size The percentage of the screen the reference chromatogram occupies can be between 596 and 5096 6 Under Plotting Style select whether you want the chromatogram to appear by default as Line Segments Data Points or Bunched Points in the Graphic Method Editor and Reprocess Results windows You can also change the plotting style from within these windows Note that these are display modes only and have no effect on data analysis or printed chromatograms Line Segments Displays chromatograms as a series of line segments connecting each raw data point Data Points Displays chromatograms as a series of unconnected raw data points Bunched Points Displays chromatograms as a series of raw data points and includes
164. and how many report formats are used Data Processing and Reporting Replot Pages 1 Scale Factor 1 000000 Offset Scale 0 000 V 1000 000 V B NT AT Timed Events 0 24 2 uy User Programs 0 Report Files 100 00 uv Component List and Calibration Shows the number of components that are identified in a sample using this method the number of named and timed groups the type of calibration you are using and global calibration parameters Component List and Calibration Components 213 Named Groups 0 Timed Groups 0 Calibration EXTD Volume Unis UL Unidentified Peaks Sample Volume 1 000 Quant Units ng Reject Outliers Void Time 0 000 min Outlier Tolerance Use Nearest Component Global Calibration Factor 1 000000e 06 3 00 Component List Window There are three panes in the Component List window The left pane shows the component list for the method the middle pane shows the calibration parameters for the selected component and the right pane shows the calibration curve for the selected component You can change the relative size of the panes by dragging the dividers Component List 3 300 17 400 31 700 41 300 47 200 58 400 66 400 70 000 73 500 80 000 85 000 31 500 38 500 107 211 116 951 ETHANE PROPANE BUTANE levell 1 0000 METHANE Single Peak Component 6 330min 0 00s 5 00 PENTANE PENTANE Pea
165. application You can also use the Rescale command on the Options menu to change the scaling factor and plot offset Refer to Rescaling Chromatogram Values on page 14 13 Displaying Chromatograms 14 11 Displaying Information in Chromatograms 14 12 gt To expand an individual chromatogram 1 3 If more than one chromatogram is open in the Chromatograms window deselect Expand All Plots on the Options menu Highlight the part of the chromatogram that you want to expand TotalChrom redraws the chromatogram at the expanded scale If you want to further expand the chromatogram repeat step 2 gt To expand all open chromatograms 1 3 Select Expand All Plots on the Options menu This command functions as a toggle it is selected by default and has a check mark next to it Select an area to expand in one of the chromatograms When you release the mouse button TotalChrom expands all open chromatograms Repeat step 2 to further expand all chromatograms gt To return a chromatogram to its previous level of expansion 1 To reduce only one chromatogram deselect Expand All Plots on the Options menu Click the right mouse button anywhere in the chromatogram that you want to return to a previous level of expansion Choose Undo on the Chromatogram pop up menu Right click and then choose Undo as many times as needed to further reduce the expansion When you can no longer reduce the expansion the
166. apter 7 Modify these values with caution If you change these parameters without fully understanding the potential consequences you might obtain invalid results 10 30 Setting Processing Parameters gt To change the peak separation and exponential skim criteria for a peak 1 Choose Peak Separation Expo Skim from the Process menu to open the Peak Separation Expo Skim dialog box Peak Separation E xpo Skim x p Peak Separation Criteria Width ratio 0 200 Valley to peak ratio fo 010 r Exponential Skim Criteria Peak height ratio 5 000 Adjusted height ratio 4 000 Valley height ratio s 000 E anc Peaks overlapped if ratio below this value 0 000 to 5 000 2 Make any changes to the values for the Peak Separation Criteria A peak must meet both of the following criteria to be considered separated Width Ratio The ratio of the distance between two peaks to the width of the base of the second peak If the actual value of this ratio for two peaks is greater than the value set here TotalChrom considers the peaks separated Otherwise TotalChrom marks them as overlapped Valley To Peak Ratio The ratio of the height of the valley between the peaks to the height of the smaller peak If the actual value of this ratio for two peaks is less than or equal to the value set here TotalChrom considers the peaks to be separated Otherwise TotalChrom marks them as overlapped
167. arameters for a range of components 1 Choose Change Calibration Info from the Components menu to open the Change Calibration Information dialog box Change Calibration Information x Iv 3 C Use calibration factor 1 000000 C Average calibration factor C Calibrate by reference Use curve Change response Change scaling None E Change weighting None Change curve Eirst component Last component Select to change the calibration type To change the calibration type select Change Calibration Type and select an option For detailed information on each of the options refer to Setting Calibration Parameters on page 8 33 To change the peak response you want to use for calibration select Change Response and select Area or Height To change the origin option select Change Origin and select Include Origin Force Origin or neither to reset a previous origin option Changing Parameters for Multiple Components Simultaneously 5 Tochange the plot scaling select Change Scaling and select an option from the list 6 Tochange the regression weighting select Change Weighting and select an option from the list 7 To change the curve fit type select Change Curve and select an option from the list 8 In the First Component text box enter the first index number in the range of components that you want to change 9 Inthe Last Component text box enter the last index number in the
168. at you select affects which options are available through the other commands in the Instrument menu gt Toselect an instrument 1 Choose Name from the Instrument menu to open the Instrument Selection dialog box 2 From the list of configured instruments select the instrument that you want to use with this method and choose OK AutoSystem XL GC The Method Summary window changes to reflect the parameters associated with this instrument Developing Instrument Parameters in the Method 6 3 Creating Instrument Notes Creating Instrument Notes 6 4 The Notes command in the Instrument menu lets you create original text or use a preset template to record information for the instrument section of the method The information you enter has no effect on data analysis The maximum number of characters allowed in the Instrument Notes field is 1641 To print these notes as part of the header in the analysis report select the Instrument Control Parameters option in the Report Format Options dialog box You access this dialog box in the Report Format Editor gt To create or edit header information 1 Choose Notes from the Instrument menu to open the Instrument Notes dialog box Header text Liquid Chromatography Instrument Column C18 Column Length 3x3 Particle Size 3u Column Diameter 46 cm Mobile Phase Flow Rate Back Pressure Temperature Detector 1 Detector 2 Notes off Template a
169. ation Editor menus 3 3 opening 3 2 configuration file A 4 configuration information printing 3 25 configuration parameters 11 12 configuration saving 3 14 Configure command 3 4 3 10 constant calibration factors 8 23 8 34 18 75 Control Options command 6 2 6 11 control options parameters setting 6 11 conventions used in manual 1 11 Convert application overview 19 1 coordinates showing and hiding 14 14 Copy command 17 14 Copy To Clipboard command in Chromatograms 14 6 in Fit Analysis 17 17 in Graphic Method Editor Reprocess Results 10 55 Create ASCII File command 19 2 CSV file extension 16 24 curve fit types 17 9 Curve Info command 17 11 curves calibration 18 70 custom expressions definition 9 10 16 19 multiple 9 12 16 22 customized component defaults 8 20 cycles appending 11 48 definition 11 2 D data acquisition controlling overview 12 19 effect of breaking communication 12 24 pausing and resuming 12 22 port choosing 3 9 setting up overview 12 2 starting 12 20 12 21 stopping 12 21 viewing run information for 12 32 with 785 Detector 13 19 with Method 12 3 12 6 with Quick Start 12 2 12 4 with Sequence 12 3 12 8 analysis definition 18 2 icons 18 3 overview 18 3 18 4 parameters 18 2 collection Index by interfaces A 2 determining length of A 8 setting channel s for 6 6 compression A 10 expected retention time updating 18 55 points calculating collected 6 7 recalibrating 15 4 repro
170. aults for peak components If you are setting up default internal standards or reference peaks the components you want to designate must appear in the component list for the open method For example if you want to set Methane as an internal standard for new peak components you must first add it to the method and then specify that it is an internal standard in the Components dialog box gt Toseta single peak component as the default type 1 2 3i Select the Identification tab of the Component Defaults dialog box Select Peak under Component Type In the Absolute Window text box enter the time you want to use for the default absolute search window In the Relative Window text box enter the percentage you want to use for the default relative search window Select Find Largest Peak In Window if you want the default to be to identify peaks by size based on height not area When you deselect this option TotalChrom identifies the peak closest to the expected time as the component To designate a component as the default reference peak select it from the Reference list To designate a component as the default internal standard select it from the Internal Standard list Setting Component Defaults gt To set defaults for new named and timed group components e The procedures for setting identification defaults for named group and timed group components are very similar to that for peak components except that many par
171. bdirectories for raw files This user is required to use the default path or subdirectories for result files m Other paths Method path CAPenExe TCWSWerb 3 0 Examples Sequence path CAPenEwe ToWSWerb 3 0 Ewamples Report format path CAPenEwe TCWSWerb 3 0 Examples Program path R r Default base names OK Raw data file kInst_ lt Usen_ E Cancel Result data file kinst User sit el Modified data file sinst _ lt DOM gt _ lt Mon gt _ lt Yean_ itt The user cannot edit these base names Browse to define the default modified data file tokens For this user TotalChrom Basics 2 7 Entering Descriptive Information About a File Entering Descriptive Information About a File 2 8 You may enter descriptive information about a file on the Description tab in the Documentation dialog box and in the Audit Trail dialog box 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 box always 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 Your application manager may set up the Description tab to appear every time you save a non audited file e fauditing has been started for a file the Audit Trail dialog box appears every time you sa
172. be used for all TotalChrom sessions of that user until a further change is made 3 23 Configuring User Options gt To seta Project Directory 1 2 3 3 24 In the Configuration Editor choose Project Directory from the User menu The Project Directory Setup dialog box opens Project Directory Setup In the Project Directory Setup dialog click on the file folder The TotalChrom Path Select dialog box appears TotalChrom Path Select Tools_95 TotalChrom Project Files EC Webshare H Windows Windows Update Setup Files emovable Disk D 010102 1630 E Users on Usnomw3 L E Users on Usnomw3 M H Data on Usnomw3 P E Data on Usnorlug U Select a path and choose OK The Project Directory path displays Printing Configuration Information Project Directory Setup x The project directory specified below will be used by all applications in place of all default path settings for all file types Default project directory er otalChrom Project Files teen Browse for your own personal project directory 4 Choose OK Printing Configuration Information The Print command in the File menu lets you print a copy of the configuration information for each interface and instrument Configuration information includes plot compare curve and edit colors font choices options quick paths and instrument and interface data Configuration 3 25 Printing
173. box Choose OK to close the dialog box and move the column to the new location 9 9 Creating a Custom Expression Creating a Custom Expression 9 10 Custom Expressions let you include information that is the result of a calculation that is performed when the report is generated For example you must use custom expressions to calculate scaled percentage values To obtain scaled values the largest peak is assigned a value of 100 or some other percentage and percentage values for other peaks are scaled proportionately You can use the following expressions Scaled area PA MA 100 Scaled height PH MH 100 Scaled amount AA MC 100 In these expressions PA PH and AA represent peak area peak height and adjusted amount respectively MA MH and MC represent the maximum peak area maximum peak height and maximum adjusted amount respectively Creating a custom expression is much like building a mathematical expression except that you use the data values and operators provided in the Custom Expression Editor e Data values can be numbers or predefined values such as Area Percent and Sample Volume e Operators can be arithmetic exponential or logarithmic e Calculations can be binary performed with two values or multi level Use US conventions for all number formats in the Custom Expression Editor For example although a Windows system may be set up to use German number formats such as using a comma to
174. bration Parameters in the Method 8 37 Adding and Editing Components 8 38 4 Enter a value in the first empty cell in the Amt column TotalChrom adds a new row to the table after you complete the columns for the current level The value displayed in the Area Height column is grayed out because it is not relevant for default components 5 Repeat Steps 2 to 4 to add additional levels gt To change an existing calibration level 1 Inthe table showing the levels select the cell that contains the parameter you want to change 2 Edit the parameters as necessary If you change level entries that contain any replicates TotalChrom will delete the replicates gt To delete a calibration level 1 Click inside the row you want to delete 2 Press the Delete key Setting User Values and LIMS Options You can use the User Values LIMS tab to e Specify a number of constants associated with the component e Setup SQL LIMS reporting for the component if you have Connect You can specify constants and then use these values in custom expressions which you create in the Report Format Editor For example you can multiply the peak area or the peak concentration or other value by a constant factor for each individual component If you are using Connect you can also use this tab to specify whether to send the results for the component to LIMS gt To set user values for the component 1 Select the User Values LIMS tab in the
175. bunched points Bunched points are calculated points representing the average of every n raw data point where n is the bunching factor Displaying bunched points allows you to see the actual data values TotalChrom used when detecting peaks in the chromatogram 7 Choose OK to close the Plot dialog box Quick Paths You can configure TotalChrom so that file open file selection and file save dialog boxes display a preset list of up to 20 commonly used paths This feature lets you quickly choose a path instead of scrolling and clicking through a complicated file hierarchy with the default Windows file selection method gt To add a path to the Quick Paths list 1 In the Configuration Editor choose Quick Paths from the User menu Configuration 3 21 Configuring User Options 3 22 3 The Quick Paths dialog box opens and displays the current quick paths Quick Paths Choose Add The TotalChrom Path Select dialog box opens TotalChrom Path Select C SPenE xeXT cw SNVerb 2 NE amples Select a path and choose OK TotalChrom will add the path as a quick path and list it in the Quick Paths dialog gt To insert a path in the Quick Paths list 1 2 In the Configuration Editor choose Quick Paths from the User menu In the Quick Paths dialog highlight the path above which you want to insert a new quick path Choose Insert Configuring User Options The TotalChrom Path Select dialog box appears 4
176. can load append or merge the information from an ASCII text file to build a sequence e Loading a text file lets you use it as the source for an entire sequence e Appending a text file lets you append sequence information from a text file to the end of a sequence file e Merging information from an ASCII text file lets you merge it into the cycles of a sequence In this case the text file provides missing parameters in the sequence and overwrites existing parameters You can create an ASCII text file with sequence parameters by using any text editor or word processor that can convert its files to ASCII text You can also create a text file automatically by using certain laboratory information management system such as SQL LIMS Text File Format You can import a text file into a sequence but it must be formatted in a precise file format in order for TotalChrom to recognize it The file format is as follows First Line The first line of the text file must contain only the number of cycles defined in the text file and nothing else Second Line The second line of the text file contains a series of identifiers separated by commas that specify which parameters are included in the text file and the order in which they will appear The identifiers are listed in the table that follows this discussion You can list some or all of the identifiers on the second line Enter only the identifiers that represent the parameters you pl
177. cation for the instrument Configuration Editor 9 Check communication for Instrument LINK at Port lortonlj1 GpibO 1 LINK Port A Note it must be connected to the LINK box and turned on If the named instrument is connected and turned on choose Yes TotalChrom will attempt to check the physical connection with the instrument by taking and then releasing control of the instrument The Confirm Configuration message box appears with AutoSystem and HP 6890 devices Choose Yes to compare the configuration options you selected with those that are being reported by the instrument If the two do not match a message box appears Choose Yes to modify the configuration settings in TotalChrom so that they match those of the instrument When TotalChrom is finished the Configuration Editor appears YES appears in the Configured column if an instrument is adequately configured If NO appears you need to complete the configuration options for the instrument before you can acquire data 3 14 Configuring Instruments Resetting a LINK Configuration A severe incompatibility between a LINK s physical configuration and the logical configuration as defined by the Configuration program may result from moving the LINK or other reasons The Reset LINK command from the Interface menu lets you clear the LINK of all IPM and instrument and port configuration data gt To clear a LINK of all configuration data 1 Select the LINK inter
178. ce or index file is reprocessed Programs used to process data should be identified as Process programs while programs that interact with an instrument for example to switch sample streams or columns should be specified as Real Time programs When you reprocess only the Process Time programs are run Building a Sequence Editing the Sequence Spreadsheet gt To include a user program in a sequence 1 In the Type cell of the row for which you want to include a user program select Program from the list The Program Information dialog box opens and TotalChrom disables all columns for the Program row except Type Name and Note Program Information Eg Program name T cmmrana life kad Carcel Dee The full path and file name of the program to be run Select the program name If you have unlimited access to programs you may type in a program name You must include the complete path so that TotalChrom can find the program You can enter a program name that does not yet exist as long as you create it before you run the sequence In the Command Line text box enter any text that you want to pass to the user program A command can contain no more than 256 characters Make sure that the sum of the path program name and command line arguments including expanded tokens are within this limit When TotalChrom runs a user program it adds the command line by taking the specified information and by providing
179. ce you create a replicate you can either exclude it from the current calibration or delete it altogether gt To work with the replicate list 1 Choose Edit Component from the Components menu or double click the component name in the Component List to open Components dialog box 2 Select the Calibration tab to view the level settings for the selected component Developing Calibration Parameters in the Method 8 47 Performing a Manual Calibration 8 48 Open the Replicates dialog box by double clicking any level that is marked with an asterisk or by clicking the Replicates button Replicates x File 1 Mmarheiusersymikeldatoi d2 idat 04 28 98 07 14 12 AM davisma 10 00 8475235 2 _ martha users mike data 0428 dat 04 28 98 07 14 30 AM davisma 10 00 35578 07 eet Delete Cancel Select the replicate you want to act on by clicking its row number Use Ctrl Click and Shift Click to select multiple replicates To exclude a replicate from the list choose Exclude Replicates that you exclude are shown in red on this list The points that represent replicates will appear in a different color on the calibration curve for that component TotalChrom excludes these replicates from the analysis and the plot but the replicates still exist in the result file You cannot exclude all replicates or delete the last replicate if all other replicates are excluded To remove all calibration data from a lev
180. cessing 10 25 15 4 15 8 storage 6 7 12 31 validation C 2 Data Channels command 6 2 6 6 6 8 Data File command 15 10 data files renaming 11 41 renumbering 11 42 Data List command 17 12 Data List spreadsheet overview 17 12 default component information setting 8 20 Defaults command 8 20 8 21 delayed time data collection programming 6 7 Delete All Components command 8 42 Delete Column 9 8 Delete Column command 16 18 Delete command 14 17 Delete Component command 8 42 Delete Events command 10 23 10 24 10 34 Delete View command 11 30 delta modulation A 10 derivatization programs 6 38 descriptive file information 2 8 Detach command 12 24 Details command 12 27 12 28 Details window 12 32 detector signals viewing 12 30 detector GC adjusting after setup 13 5 setting parameters 6 19 detector LC adjusting after setup 13 10 setting parameters 6 30 Dilution command 6 42 dilution programs 6 38 6 40 Disconnect command 3 15 downloaded method modifying 13 13 downloading parameters overview A 6 dropline integration 18 27 dual injection versus dual channel 11 18 dual channel instrument processing parameters 7 2 dual injection sequence sample identification 11 20 E E See end peak timed event Edit Calculation Plot command 14 31 Edit Component command 8 28 Edit Component List command 16 10 Edit Components command 10 37 10 38 10 39 10 41 10 43 10 44 Edit File List command 16 4 16 8 Edit Format command 16 3 Edit List
181. ch data is included in Small Medium and Large report headers im oron Wedium taro 9 13 Editing Report Format Options em Sm Wedium ions wmm o ec Bere f o wem x metes 5 5 wwe x wem S o mam Tel wwe samp vous x wma L5 nnn stone Processie menase umwemsewne meram ee aree Pied ara tend OO niente ome nenca Menos possen usse memmeerpanzee 9 14 Building a Report Format Editing Report Format Options A process number is included in every standard report header generated i e produced from an RPT file when a raw file is processed starting with peak detection A process number is a unique number specific to the analysis server and execution of Client Server Analyze that created the report If a method specifies a number of different reports then when a file is analyzed with that method the set of resulting reports all contain the same number but that number is different each time the method is used to process data Since the process number only appears when processing starts with peak detection it will be printed on a line by itself just below Software Version with the caption Process Number The first time a report is generated the Analyze software sets the proc
182. ch of the tabs in the Process dialog box Developing Processing Parameters in the Method 7 3 Entering Peak Detection and Integration Parameters Entering Peak Detection and Integration Parameters 7 4 The Integration command in the Process menu lets you enter the parameters that affect peak detection and integration Peak detection The process by which TotalChrom examines raw data points to determine where peaks exist Your entries for basic integration parameters are used in this process Peak integration The process of determining peak area Your entries for advanced integration parameters are used in this process For technical information about peak detection and peak integration and how baseline timed events affect them refer to Chapter 18 Discussion of Data Analysis You seldom need to modify the advanced parameters because their values have been optimized for normal chromatographic situations Modify these values with caution If you change these parameters without fully understanding the potential consequences you might obtain invalid results gt To edit peak detection and integration parameters 1 Choose Integration from the Process menu to open the Process dialog box with the Integration tab selected Integration Baseline Timed Events ptional Reports Replot User Programs m Basic Parameters Bunching factor pts jz Noise threshold iV fi 2 Area threshold uy fi 2 00 m
183. ch will in turn send a message to TotalChrom via the LINK that the run has started LINK Controlled GCs Without Autosamplers The Start Run command will begin the GC s program run starting with the equilibration step Alternatively if you make an injection at the GC and then press its run button TotalChrom will receive a message via the LINK that the run has started gt To start data acquisition for the selected instrument e After you have completed the Setup procedure click the Run button in the Navigator and choose Start Run The immediate effect of choosing Start Run will depend on your instrument configuration as described above At this point you may want to view instrument information in the Details window or open the Real Time Plot window to wait for the run to start if it has not already and watch TotalChrom plot the data Refer to Viewing Real Time Plots on page 12 26 and Viewing Data Acquisition Information on page 12 33 You may also send the Start Run command to a LINK controlled instrument when it is not ready It will start as soon as it is ready Stopping a Run You can stop data acquisition by choosing the Stop Run command This command is only available when a run is in progress When you stop a run TotalChrom retains the data that has been collected up to that point analyzes it and prints a report and plot based on the data collected unless you suppressed processing or the printing of a report and p
184. ciated with the tab Columns in the Spreadsheet A sequence spreadsheet consists of the columns listed in this section Columns that must have the same value for both channels appear with a yellow background Columns that can have different values for each channel have a blue background For a dual injection sequence the instrument method column is the only yellow column If the TotalChrom applications manager has designated columns as read only they will appear with a gray background indicating that they are unavailable for editing Type Defines the nature of a row which can be an analysis a calibration an external program or a cleanup A description of each type follows this list Study Name The name of the analytical study Name The name of the sample Note Displays an X when text program or serial dilution information has been entered for a row Number Sample Number The identification number of the sample Site Injection Site Whether the autosampler will inject into the front or back injector for LINK controlled GCs only Rack The rack number of the vial used for the injection when Varian or Micromeritics autosamplers are used Vial The vial number for the sample Building a Sequence Using the Sequence Editor Method If you select One Per Row in the Global Parameters dialog box TotalChrom will use the same method for the instrument processing and calibration paramet
185. ck bits 0 to 5 Autosampler code ND0044 Reset Finish Cancel Autosampler uses low logic level to output rack vial number Selecting the autosampler name changes the information in the Rack Vial Mask Info area of the dialog box These values are preset and cannot be changed The Autosampler Code shows which device is selected 2 If your autosampler was listed skip steps 3 through 6 and go to the following To save the configuration procedure OR If the autosampler was not listed choose Other Type from the top of the Autosamplers list 3 6 Configuring Instruments All of the options in the A D Configuration dialog box become available You may need to refer to the manual that came with your autosampler to complete this information 3 Select Positive or Negative as the appropriate Logic Sign 4 Select Binary or BCD binary coded decimal as the Logic Type 5 Specify the Number Of Vial Bits by entering the number or clicking on the up or down arrows This is the number of binary digits or signal lines that are sent to represent a vial number The options are 1 through 8 indicating how many of pins 1 through 8 on the 900 Series Interface will receive vial information 6 Specify the Number Of Rack Bits This is the number of binary digits or signal lines that are sent to represent a rack number The options are 0 through 6 indicating how many of pins 9 through 14 on the 900 Serie
186. column Building a Report Format Choose Report to display the available column types Normalized Area Percent Component Name ISTD Response Ratio Reference Component ISTD Amount Ratio Betention Time ISTD Component Delta Retention Time Adjusted Amount k Prime Raw Amount Relative RT Percent Amount Peak Area Normalized Amount Peak Height Area Amount Ratio Baseline Type Calibration Range Area Percent Voltage Range Area Height Ratio eee Custom Expression Peak Purity Index Pl Blank Column Absorbance Ratio Spectral Standard Confirmation Spectral Library Confirmation Peak Library Search Mobility Choose one of the column types listed in the menu except Custom Expression The Column Information dialog box appears The word lt none gt appears next to Current Column until you add this column to the report Once the column is added you can click on the column name to open this dialog box rather than choose the name from the Report menu Percent Amount x Current column lt none gt Insert Add E I Column number Column width b Digits R Hove Column label pmut ooo Deae Second label oOo i Cancel v Calculate total for this column Location of this column across the page 1 to 9 Enter a column number in the Column Number text box This establishes the location of this column relat
187. command to edit the header or footer just click anywhere in the header or footer text in the Report Format Editor window to open the corresponding dialog box Editing Report Columns 9 6 The Report menu in the Report Format Editor displays a list of the types of columns you can include in a report For an explanation of each type of column refer to the Glossary The Report menu also includes the Custom Expression command Custom Expression is a special type of data column that allows you to include mathematical operations within a column Refer to Creating a Custom Expression on page 9 10 Choosing any of the column types from the Report menu or clicking the column name in the report itself opens the Column Information dialog box which is described in the procedures that follow You can edit the column information including the name and place the columns wherever you want them to appear in the report You can also create blank columns in a report by choosing this command in the Report menu The Blank Column dialog box is the same as the Column Information dialog box except that it inserts a blank space between columns or it adds space in the margin if you make it the first or last column on the page Adding and Deleting Columns The default report format file shipped with TotalChrom includes the following columns You can add new columns or delete report columns as desired Editing Report Columns gt To adda report
188. ct the Absolute Window option and enter a new value in seconds in the text box 3 To redefine the relative window size as a percentage of the expected retention time select the Relative Window option and enter a new value in the text box 4 To change the peak identification select the Peak Identification option Select Find Largest Peak if you do want to identify the largest peak based on height not area in the search window as the component 5 To change the reference component select the Reference Component option and then choose a name from the list Choose no reference to remove an existing reference component Developing Calibration Parameters in the Method 8 43 Changing Parameters for Multiple Components Simultaneously 8 44 6 To change the internal standard component select the ISTD Component option and then choose a component name from the list In the First Component text box enter the index number of the first component in the range that you want to change In the Last Component text box enter the index number of the last component in the range that you want to change Choose OK TotalChrom updates the component list to reflect the changes you specified The Change Calibration Info command in the Components menu allows you to change the calibration data for more than one component For example you can change all components to use peak height instead of peak area gt To change calibration p
189. ctangle in the reference chromatogram The mouse cursor changes to a double headed arrow 2 Drag the selected edge until the rectangle is the size you want 3 Release the mouse button Hiding or Showing the Reference Chromatogram By default TotalChrom displays the reference chromatogram above the working chromatogram in the Graphic Method Editor or Reprocess Results window You use the Reference Chromatogram command as a toggle to hide or show the reference chromatogram gt To hide or show the reference chromatogram 1 Choose Reference Chromatogram from the Display menu to deselect the command TotalChrom redraws the working chromatogram to fill the entire window 2 Choose Reference Chromatogram again to show the reference chromatogram Editing Methods and Results Graphically 10 21 Setting Processing Parameters To hide the reference chromatogram as the default or to change how much space it occupies as a percentage of the total window area deselect Show Reference Chromatogram or change its size in the Plot Options dialog box in the Configuration Editor The change takes effect the next time you open the Graphic Method Editor or Reprocess Results For more information refer to Chapter 3 Setting Processing Parameters 10 22 Most of the commands in the Process menu affect peak detection and integration For detailed information on the basic concepts terminology and effects of setting these parameters refer to
190. cted by law PerkinElmer is a registered trademark of PerkinElmer Inc TotalChrom and 900 Series Interface are trademarks of PerkinElmer Inc Turbochrom is a trademark of Applera Corporation Microsoft MS and Microsoft Visual Basic are registered trademarks and Windows is a trademark of Microsoft Corporation HP LaserJet is a trademark of Hewlett Packard Corporation Tidestone is a trademark and Formula One is a registered trademark of Tidestone Technologies Inc Table of Contents Volume Chapter 1 Introduction and Overview Tot lChrom Eunctons 5 a ob tn pt E e t e ette o ebat o etse 1 3 Acquitang Data srren ies te E EUR e EUR U HEN N Histo et ads 1 3 Analyzing Dat tee Ret ERR ED ERR et ED Ee e de ette teet itee 1 3 Creating Data Acquisition Methods essseeseeeeeeeeeeen eene ener ene 1 4 Setting p Sequence esto eed ren e e ect ee Ee erede eres 1 4 Reprocessing Data e Up aee eg ee eR 1 5 Viewing Chromatographic Data eee eene enne eene nee 1 5 Generating Summary Reports x sessionerna eneee rane eene nennen trente nein 1 6 Review and AppIOVE ze piri rapa inion lap aree eg 1 6 Using this Guide chiens ene eae e eU ea Guetta 1 8 Chapter Topics nee pt egest RN ea te E a RENI 1 8 Conventions Used in This User s Guide esee eee 1 11 They Help Systems 2 etre ere prO tees equ pb P REO e pro Ere 1 12 Chapter 2 TotalChrom Basics Using Common Dialog Boxes
191. cur before this time 5 From the Reference list select the component you want to use as a reference component If you specify a reference component TotalChrom adjusts the actual start and end times used to define the group based on the actual retention time of the reference peak in each run 6 If necessary select the name of a component you want to use as an internal standard from the Internal Standard list Setting Calibration Parameters Calibration values affect how TotalChrom calculates component amounts You can choose among the following types of calibration for components e Using a constant calibration factor e Calculating an average calibration factor e Using the calibration curve of another component calibration reference e Solving the component s calibration curve The procedures for setting up each calibration type follow This section also provides instructions for working with calibration levels If you select Use Calibration Factor TotalChrom divides the component s response by the calibration factor to obtain an amount Developing Calibration Parameters in the Method 8 33 Adding and Editing Components gt To calibrate using a constant calibration factor 1 Select the Calibration tab of the Components dialog box 2 Select Use Calibration Factor as the Calibration Type Identification Calibration User Values LIMS Calibration Type 3 C Calibrate by reference C
192. d its related information is deleted and the Component List window changes to show information on the next component gt To delete all components levels and replicates e Choose Delete All Components from the Components menu After asking you to confirm the command TotalChrom deletes all components from the component list for this method file 8 42 Changing Parameters for Multiple Components Simultaneously Changing Parameters for Multiple Components Simultaneously The following commands in the Components menu allow you to make changes simultaneously to multiple components Change Component Info Changes the search window and reference peak information for a range of components Change Calibration Info Changes parameters for a range of components The changes apply to the range of components and parameters that you specify in each dialog box You specify the component range by using the index numbers for each component which appear next to the entry in the component list gt To change component information for a range of components 1 Choose Change Component Info from the Components menu to open the Change Component Information dialog box Relative window E 00 Peak identification Find largest peak Reference component z GTO component z First component 1 Last component 16 Cancel Select to change the absolute retention window 2 To redefine the search window size sele
193. d values by dragging the corresponding points on the curve to the desired position Developing Instrument Parameters in the Method 6 13 Setting Control Options gt To set oven temperature and zone parameters 1 Select the Oven Inlets tab of the Instrument Control dialog box Instrument Control x Autosampler ven Inlets Carrier Detectors Instrument Timed Events gt Program time min Oven 20 00 440 Sn In PS TOUT 220 Inj B PSSI 20 00 110 Dataendtime 2000 Cryo Oven Ramp Rate Temp Hold for gt Initial 50 20 00 eee 1 0 0 0 6 00 Cuintemp c oo 2 0 0 g 0 00 3 0 0 n 0 00 Timeout min 999 41h OvenRamp AinjBRamp fo Heated zone setpoints C m Oven Injector amp On Jxuillam Joo Max temp C a50 Injector B On Equil time min 2 0 Cancel Bus Rate at which to increase Temperature for this program step 0 0 0 0 deg min 2 From the available program tabs under the table choose 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 3 In the Initial Temp field of the table set the temperature for the start of the run 4 Inthe Initial Hold field enter the amount of time that you want to hold the initial temperature To hold the temperature indefinitely for most instruments enter 999 5 Setthe Ra
194. data Press the Control M key combination to start a new line Gen Enter text press Critrl M to start a new line 2 Enter a text note pressing Ctrl M to start a new line 3 Choose OK An X appears in the Note column to indicate that a note exists Including a User Program in a Sequence To include a user program in a sequence you select Program as the cycle type and then complete the Program Information dialog box For specific information about running System Suitability Fit Analysis or Summary as a user program see the corresponding chapter in this manual Contact your application manager for information about your access to programs When you designate a program in one channel for a single injection sequence TotalChrom adds the same program to the second channel You can specify different programs for each channel only in dual injection sequences Real Time programs will be run by Acquire when that cycle is reached during sequence execution These programs are run in a manner that is synchronized with Analyze That is the program will not run until the previous row has been completed and processed if processing is taking place A Real Time program does not run when a sequence or an index file is reprocessed Process Time programs are also run in a manner synchronized with Analyze The difference between a Process Time program and a Real Time program is that the Process Time program is also run when a sequen
195. data in an external spreadsheet application then paste that data into a sequence You can paste in every column in a row or only certain columns You can reverse the process and copy visible contiguous sequence spreadsheet data for pasting into an external spreadsheet application 11 37 Editing the Sequence Spreadsheet gt To paste data from an external spreadsheet application 1 In the external application create the data then copy them to the Windows clipboard In the sequence display the columns that correspond to the data to be pasted If the columns do not match the incoming data validation is likely to fail Identify the paste location by selecting the cell that is the upper leftmost in the block Choose Paste Each cell in a pasted block must pass a validation check for format such as length or numeric range If any single cell fails validation the entire paste operation is canceled and all cells remain unchanged The basic rules of validation for pasting are e Alphanumeric cells such as Sample Name can accept from any cell within length constraints e Numeric cells such as ISTD Amount can only accept numbers within the allowed range e Cells with enumerated lists such as Type can only accept strings that match one of the allowed entries exactly except for case e Method cells which require a path will accept a string If the string does not include a valid path the default path will be added E
196. designate a decimal point the Custom Expression Editor only accepts a period as a decimal point When a calculation is invalid for example division by zero a dashed line appears in the report instead of a numeric value After you build the calculation for an expression you specify column parameters in the Custom Expression column information dialog box This dialog box is identical to the column information dialog box that is used for all other report columns Once you create a custom expression it can be edited moved or deleted just like any other report column Predefined Custom Expression Data Values When you develop a custom expression you select from a list of predefined data values Most of the items refer to individual peak values such as PA for Peak Area others refer to the entire run such as TA for Total Area Creating a Custom Expression Predefined values for the items with the phrase from Suit are available only if Suitability has been run on the data before this report is generated Values for SA Lambda Max SP Peak Purity Index SR Absorbance Ratio are available only if they are present in the result file Additionally for SP the LC235 must have been set to AUTO mode for spectra gt To create a custom expression 1 Choose Custom Expression from the Report menu to open the Custom Expression Editor dialog box Custom Expression E ditor x Available column values Available operations HAA Adj
197. dialog box appears 3 Make any changes to the options and choose OK 10 54 Using Images in Other Applications Using Images in Other Applications The Copy to Clipboard command in the File menu lets you use a copy of the chromatogram image in another Windows application gt To copy the current chromatogram to the Clipboard e Choose either Copy To Clipboard Color or Copy To Clipboard B W from the File menu TotalChrom captures the screen image of the working chromatogram and copies it to the Windows Clipboard The image is either a color or monochrome bitmap You can now copy the screen image from the Clipboard into another program or a file A color bitmap requires many times more memory than a monochrome bitmap The Save As MetaFile command in the File menu lets you copy an image of the screen to a Windows metafile gt To save the current chromatogram as a Windows metafile e Choose Save As MetaFile from the File menu then name the file The image in the file will be a color image Editing Methods and Results Graphically 10 55 10 56 Chapter 11 Building a Sequence This chapter explains the function of a sequence and describes how to use the Sequence Editor to build and edit sequence files To learn about Go to page How a Sequence Works Using the Sequence Editor Defining Global Parameters Building a Sequence by Template Building a Sequence Vial by Vial Editing the Sequence Spreadsheet Changing Env
198. diting Column Values You use the Fill Renumber Files and Path commands from the Change menu or the shortcut menu to edit column values Smart Fill Increments the sample and vial values and data file names in a single column Renumber Files Renumbers the base data file name selectively in multiple columns Fill Down Duplicates the value in a selected cell to all cells in the rows below it Sample Fill In Ensures that sample information for replicate injections is the same Path Changes the path that is associated with method and or data files Using Smart Fill to Increment Sample Numbers Many editing operations apply only to the cell you have selected After you insert copy move or delete rows in a spreadsheet it is a good practice to check the 11 38 Building a Sequence Editing the Sequence Spreadsheet accuracy of values in other rows For example if you change a sample number the values in the remaining Number cells retain their original values You use the Smart Fill command to increment sample numbers in the same column gt To increment sample numbers 1 If this is a dual injection sequence select all or part of the Number column in the channel for which you want to make changes For a single injection sequence changes will apply to both channels Select the Smart Fill command from the Change menu or the shortcut menu Smart Fill x Starting row f Ending row 2 Sample n
199. e Tv Store data ImgoByE Batts GT sul ES itp atis BHSETIETTIGIIE Li aroaren Isaiam lire Any path typed into the constrained field s must be on the default path tree Entering an invalid path produces an error message when you leave the field or click on a button If you click the file folder button associated with a constrained field then the displayed dialog box only allows selection of directories in your default path tree Acquiring and Viewing Data 12 11 Setting Up Data Acquisition 12 12 10 In the Starting Row text box you may change the row number with which you want to begin the sequence operation This may be an analysis cycle or a user program to be run In the Ending Row text box you may change the sequence row number with which you want to end the sequence operation This specifies the last row of the sequence that will be run If you are using a LINK controlled autosampler TotalChrom will stop acquiring data at this point If you are using a LINK without a controlled autosampler or a 900 Series Interface you may continue to collect data from runs by using manual injections However the sample information for all subsequent injections will come from this last row and TotalChrom will build all file names for the data from the last row s file name Select Start Run When Ready to start the run as soon as the instrument is ready You use this option when you want a L
200. e Adds a new replicate to the existing replicate list at the specified level for each component in the current method file Replace Deletes all replicates in the current method file at the specified level and replaces them with one replicate for the current data file Using the Components Commands in Reprocess Results The only component operations you can perform in Reprocess Results are identifying peaks manually and displaying search windows Identifying Peaks Manually 10 48 Working with Components The Manual Identification command in the Reprocess Results window lets you override normal component identification and directly assign component names to peaks in the result file gt To identify a peak manually 1 Choose Manual Identification from the Components menu The window changes to display the Manual Identification list and the Reassign button above the working chromatogram ata Reprocess Results C PenExe TcCS Ver6 1 0 Examples Solv001 rst Return Help b a 1 MIBK ISOBUT AD TOLUEN EPenExeXT CCS NVerB 1 ONE xamples NS OLVOOT rav 1 375 min For Help press F EMEN 2 Click the peak that you want to rename If this peak has already been identified as a component the name appears in the text box Select a component name from the list 4 Choose Reassign to give the selected peak a new name The new component name appears beneath the sel
201. e In this situation breaking communication between TotalChrom and the interface will eventually cause an Overflow or Wrapped error state when the interface memory fills up Controlling Data Acquisition gt To break communication between TotalChrom and an instrument e Click the Run button and choose Detach from the pop up menu TotalChrom will no longer be able to receive information from or give information to the selected instrument Instrument Errors Failures of communication between TotalChrom and an instrument could possibly occur at any time The two most likely situations when a problem will be detected are when you open the Navigator window or when you set up an instrument A list of the errors that have occurred since the Navigator was started is shown in the Instrument Errors window By default this window is displayed whenever a new error occurs you can change this default from the Instrument Errors pop up menu You can open the window at any time by choosing Error Messages from the View menu A list of all errors that have occurred since the last time the list was cleared is maintained in INSTRUMENT ERRORS LOG in the user s directory Config Users lt username gt in the TotalChrom path When you set up a sequence each method specified in the sequence must be checked to see if it is valid for the selected instrument Errors detected during this process are saved in a file in the user s directory under the name VE
202. e Series 200 Autosampler This application lets you create a Serial Dilution method which can be used to perform multiple vial to vial transfer and mixing operations Introduction and Overview 1 10 Using this Guide Conventions Used in This User s Guide NOTE TotalChrom is the updated version of the software previously marketed as Turbochrom This guide designed for Windows users assumes that you will be using a mouse or similar device to perform your TotalChrom operations Many shortcut keys are listed on the TotalChrom 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 Capitalization All menus commands and dialog box 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 Terminology Throughout the TotalChrom documentation the following terms are used to refer to program elements and the actions that you perform to carry out tasks Chromatogram Plot and Replot A chromatogram plot or replot is the graphical representation of chromatographic data in TotalChrom The terms chromatogram plot and replot are used interchangeably in th
203. e GC The GC Hands On dialog box appears showing the current zone setpoints and valve settings GC Hands On mini ITA TTT laici mrs Det tiov ene ene solui saline 2 Inthe Zones Setpoints text boxes enter the temperature and flow setpoints for this GC and choose Set Zones to implement the settings 3 Choose Autozero if desired 4 In the Valves area of the dialog box select the valves you want to switch by clicking the ON or OFF button as appropriate and choose Set Valves to implement the settings Working with Instruments Interactively 13 5 Setting Zone Setpoints and Valves for a GC 5 Choose Close You must choose Set Zones Set Valves or Autozero before choosing Close in order to change settings 13 6 Setting LC Parameters Setting LC Parameters If you are using a LINK controlled LC system the Hands On command enables you to change a variety of instrument parameters for the different modules Most of these settings are only available when a run is not in progress LC Hands On is available after the LC instrument is set up and the hardware e g pump autosampler and detector is ready for pre run startup For example purging the pump autozero A Z the detector and flushing the autosampler LC Hands On is not available during the actual run analysis and it is disabled at the end of a running sequence gt To set parameters for an LC 1 Select the LC in the Inst
204. e Level text box either enter the name of the calibration level represented by the data file or select a level from the list In the Amount text box enter the sum of the standard amounts for each of the member components of the group Select Average or Replace under Calibration Type Average Adds an entry to the calibration replicate list for the component in the current method Replace Deletes all calibration replicates for the current component in the current method and replaces them with one replicate for the current data file For a new component Average and Replace act in the same way because there is no current calibration information Choose Next or Prev to implement the change and move to the next group When you are done creating named groups choose Return to close the Edit Components dialog box To edit a named group l Choose Edit Components from the Calibration menu The Edit Components dialog box appears and shows the options for single peak components Choose Named Group from the Type menu The name of the first group appears in the Name text box followed by a list of all components in the method with the group members selected in the list and on the plot In the Group Members list box click each component that you want to include in or delete from the group Choose Next or Prev to implement the change and move to the next group When you are done creating named groups choose Return to cl
205. e Name command 15 8 baseline See also baselines penetrations 18 24 18 26 resolution improving 18 23 subtraction 18 3 18 5 timed events adding 7 8 deleting 10 24 entering 7 6 overview 7 6 18 15 18 32 setting 10 22 Baseline Events 68 Baseline Events command 10 23 10 24 Baseline Timed Events command 7 6 7 8 baseline to point timed event 18 34 baselines See also baseline adjusting preliminary 18 24 hiding or showing 14 14 horizontal backward 18 38 horizontal forward 18 36 indicating for peaks 10 32 preliminary establishing 18 24 printing 7 14 redrawing manually 10 32 theoretical repositioning 18 35 valley to valley 18 33 Batch command 11 50 15 3 batch reprocessing overview 15 2 steps 15 3 versus single file reprocessing 15 4 BF See bunching factor timed event bipolar interfaces testing C 4 BL See baseline to point timed event blank column in reports 9 6 16 17 build parameters entering 11 11 bunching factor overview 18 6 setting 10 28 bunching factor timed event 18 15 C Calibrate command 8 46 10 48 calibrating by reference 8 35 calibrating components 8 9 8 35 calibration amounts correcting 8 6 11 24 automatic 18 55 by average calibration factors 18 59 commands overview 10 36 components controlling 10 36 curve labels changing 17 7 curves changing display of 17 6 changing fit parameters 17 8 computing overview 18 56 creating 8 16 defining 8 37 defining scaling limits for 17 6 displaying informa
206. e SSS Start time opo min End time so min T Include only unidentified peaks Reference fo Intemal Standard hd New Component Rreviaus Delete Bomponent Next New Component Cancel Apply The name by which the component is to be identified and labeled A variant of the timed group component type groups all unidentified peaks in a specified time zone of the run and quantitates them as a single component This is set up by selecting the check box labeled Include only unidentified peaks When this is checked any identified components that fall within the group time limits will be excluded from the group When this option is set for a timed group component that fact will be included in the method printout for that component Understanding Component Parameters Setting Up Search Windows When setting up peak components you need to define a search window to enable TotalChrom to match components with the correct peaks in a run A search window is a time tolerance before and after the expected retention time of the component This window allows TotalChrom to identify components despite small variations in retention time from run to run TotalChrom must find a peak within a component s search window to identify it as that component If the component s search window contains no peaks TotalChrom will not be able to find the component in the sample If more than one peak occurs within the search window yo
207. e a TT T a TNT a a O aA TTTT UT PEETI IEN 14 TY 05 10 15 20 25 3 0 35 4 0 45 For Help press F1 Start 0 000 End 2 998 Offset 37 036 Scale 915 552 7 2 Right click in the target chromatogram and choose Scale Voltage Displaying Chromatograms The target chromatogram is scaled such that the low and high voltage align with the reference chromatogram Chromatograms Solv_001 raw File Operation Options Window View Help alale Haj sajes m 2i s Mi Solv_002 raw M Solv_001 raw T E Trt tt hp S TET T T T A L et Tt 0 5 10 15 20 25 30 35 40 45 For Help press F1 Start 0 000 End 2 998 Uffset 37 036 Scale 915 552 7 14 27 Calculating a New Chromatogram Calculating a New Chromatogram 14 28 The New Calculation Plot command on the Operation menu enables you to create a new chromatogram by performing a mathematical operation on two chromatograms You can add subtract or divide the data from two raw data files to create a new data file After completing the calculation TotalChrom plots the results in a new window You can save the data resulting from the calculation in a new raw data file and use it like any other raw data file in TotalChrom This data file which is called the modified data file uses the method parameters associated with the first file This includes the sampling rate and voltage range gt To create a new chromatogram from two existing chromatograms l 2 Open th
208. e accuracy you can choose to inject more than one standard sample where each sample contains the same component but in different amounts These varying samples are called calibration levels The response produced by the component at each calibration level plotted against the level amount defines the points on which the component s calibration curve is based Some notes about calibration levels e You can add calibration levels only with the Avg Calibration Factor and Use Curve calibration types e A component can have up to 100 calibration levels but the level names for all components in a standard sample must be the same e Use unique level names for different levels e Ensure that two different levels have different amounts unless the component is an internal standard component You can also revise an existing calibration level or delete it from the list if it no longer applies to a specific method or component If you are using named or timed groups these actions apply to a group of components gt To add a calibration level 1 Choose Avg Calibration Factor or Use Curve as the Calibration Type r Calibration Type C Use calibration factor C Avg calibration factor Calibrate by reference 2 Under Response select Area or Height as the option you want to edit 3 Enter a level name or number in the first empty cell in the Level column The level name must be between 2 and 40 characters Developing Cali
209. e as follows e Point To Point 1 e Ist Order Polynomial 2 or 1 if you include the origin e 2nd Order Polynomial 3 or 2 if you include the origin e 3rd Order Polynomial 4 or 3 if you include the origin 5 Select the Scaling factor you want to use from the list For definitions of the options refer to Selecting Fit Parameters on page 8 16 6 Select the Weighting factor you want to use from the list For definitions of the options refer to Selecting Fit Parameters on page 8 16 7 Under Origin Treatment select Include or Force as the origin option if required Include origin adds point 0 0 to the calibration zero amount to zero response Force origin prevents any offset forcing the curve to go through the point of origin Leave both options deselected to omit the origin from the calibration 8 Editthe Level Amount and Area Height values as necessary For more information on how to create new calibration levels refer to Working with Calibration Levels on page 8 37 8 36 Adding and Editing Components Working with Calibration Levels If you did not build calibration levels in the Component Defaults dialog box or if you need additional levels you can add new levels in the Components dialog box To determine unknown component amounts TotalChrom compares the component s response peak area or height to the response of a known amount of the same component in a single standard sample To improve th
210. e coordinates title bars axis labels baselines component names and retention times Window Menu Allows you to automatically size displayed chromatograms overlay two or more chromatograms stack cascade and tile open windows and arrange icons View Menu Allows you to switch from window to window Status Bar At the bottom of the window the status bar displays the file name and path of the active chromatogram the starting and ending times of the run and the offset and scale You can substitute the X and Y coordinates of the mouse cursor for Start and End times if you choose Show Coordinates from the Options menu Displaying Chromatograms 14 3 Using the Chromatograms Application Using the Chromatogram Pop up Menu After you open one or more chromatogram files you can access additional commands by clicking the right mouse button in any chromatogram The Chromatogram pop up menu lets you add labels to chromatograms and perform other tasks Your access to pop up menu commands will vary depending on the type of file you have open and the way in which chromatograms appear command Amm O Add Label Adds labels to chromatograms Set Start Time Allows you to set markers for the starting time of peaks in chromatograms Set End Time Allows you to set markers for the ending time of peaks in chromatograms Set Low Voltage Allows you to set low voltage values in chromatograms Set High Voltage Allows you to set the high
211. e current data point is plotted at 5 above the X axis The height of the plot window remains unchanged Do not choose this command while a peak is eluting or the remainder of the peak will be clipped at the X axis gt To autozero the plot origin for a real time plot e Choose Autozero A from the Options menu The plot changes by adjusting the offset so that the current detection signal level is visible just above the X axis You can choose the command for Channel B if you are using a dual channel instrument Controlling a Run from the Real Time Plot Window The Run menu in the Real Time Plot window is similar to the one in the Navigator The differences are that this Run menu lets you control a run while viewing the data being plotted for one or more instruments you cannot take or release control of an instrument but you can use monitor mode to view the detector signal without starting a true run Refer to the next section Using Monitor Mode For specific information on how to use the commands in the Run menu except Start Monitor refer to Controlling Data Acquisition on page 12 19 Using Monitor Mode The Start Monitor command in the Run menu of the Real Time Plot window lets you view the detector signal coming from an instrument without actually engaging in a run All of the Options commands are available during monitor mode plotting 12 30 Viewing Real Time Plots gt To view the detector signal without starting a
212. e current tray number Flush The autosampler is performing a flush cycle No Vial There is no vial at the requested sampling position Not Ready The autosampler is not ready Off The autosampler is off Ready The autosampler is ready Sampling The autosampler is withdrawing a sample from a vial 12 43 12 44 Chapter 13 Working with Instruments Interactively This chapter explains how to use the Hands On and Modify functions in TotalChrom to work interactively with instruments before during or after a run To learn about Go to page Using Hands On Setting Relays for a 900 Series Interface Setting Zone Setpoints and Valves for a GC Setting LC Parameters Modifying a Downloaded Method Modifying a Sequence During a Run 785 Detector Wavelength Calibration 13 1 Using Hands On Using Hands On 13 2 The Hands On button and Hands On command in the Instrument menu let you control certain instrument settings after you have set up an instrument The actual parameters available depend on the type of instrument that is selected and whether or not a run is in progress The Hands On button and command are not available until you set up and bind an instrument As with most other functions in TotalChrom clicking the Hands On button in the Navigator opens the dialog box for the instrument that is currently selected in the instrument selection panel In contrast selecting the Hands On command from the
213. e enabled you must enter your TotalChrom password after you complete the Audit Trail dialog box in order to save the file gt To enter your electronic signature 1 In the Electronic Signature dialog box enter your TotalChrom password The entry in the User Name field is the name of the current user The password must correspond to this name 2 Choose OK Retaining the Requirement for Electronic Signature on a New File When you use Save As to create a new file from a file that has electronic signature enabled you have the option to retain the requirement for electronic signature for the new file gt To retain electronic signature e Inthe Audit Trail dialog box leave Retain Electronic Signature selected 2 14 Selecting an Instrument Selecting an Instrument Use the Instrument Selection panel in the Navigator to select an instrument The panel also appears in other applications whenever you have to select an instrument In the Method Editor access the panel by choosing Name from the Instrument menu In the Sequence Editor choose Global Parameters from the Change menu Then click the button to the right of the Instrument list The Instruments That You Can Select You have access to instruments for which you have rights as assigned by your application manager To change your access level to different instruments see your application manager Using the Instrument Selection Panel The Instrument Selection pa
214. e file contains only the base file name and the cycle number The actual file name may be more than a combination of these two parts however because if that name already exists at the time of the run a timestamp will be added to create a unique file name Because you can modify completed rows during data acquisition you cannot use the sequence file as documentation for a series of runs Only the index file represents a true picture of what occurred during a sequence run TotalChrom does not add file names to the index file until the run is complete so the index file that is generated from a sequence that has not run to completion will contain fewer rows than the sequence You can view index files in the Sequence Editor but you cannot edit them However you can save an index file as a new sequence file with the Save As command gt To view an index file 1 Choose Open from the File menu 2 Select IDX Files from the List Files Of Type list 3 In the File Name text box enter or select the name of the index file that you want to edit 4 Choose Open You can print the index file by choosing Print from the File menu Building a Sequence 11 59 Printing Sequence Information Printing Sequence Information 11 60 The Print command on the File menu allows you to select from a variety of printing options and print the information in a sequence Two print related dialog boxes will appear one for sequence options and one for s
215. e file name with a number since it will be treated like a cycle number If you must enter a number then follow it with a legal separator for example hyphen or underscore_ Do not use a period TotalChrom creates a result file RST for every raw data file RAW The base name you enter here is used to name these files along with a three digit cycle number starting at 001 that TotalChrom appends to them If you run a sequence more than once TotalChrom appends a timestamp to file names when necessary to keep them unique Your application manager may have set up your system to append a timestamp to all files 4 If this is a dual channel sequence repeat steps 2 and 3 for Channel B The method you enter for Channel A determines the instrument parameters that are used for both channels because these must be the same If you enter a different method for Channel B TotalChrom uses only the processing and calibration parameters from that method for Channel B 5 If you want to run calibration standards to calibrate the method select Include Calibration Standards under Calibration This option is only available if the method you specify includes calibration information If you select Include Calibration Standards the other options in the group box are available TotalChrom will create a row for each calibration level that is defined in the method and the first rows entered in the sequence will be calibration levels Additiona
216. e following sections explain how to perform each task For information on how to use the report commands see Displaying and Printing Information on page 10 49 Changing the Plot Display You can choose to display the chromatogram as raw data points raw and bunched data points or as line segments gt To change the display of the plot e Choose Raw Points Raw Points With Bunching or Lines from the Display menu Changing the Plot Scale The Rescale Plot command in the Display menu lets you change the parameters that affect which part of the run the chromatographic data you see in the main window These parameters include starting and ending times the offset and the full scale values gt To edit the scaling parameters 1 Choose Rescale Plot from the Display menu Start time min Jm o End time min ooo Offset mV pao Eull scale mV 770 156 Cancel Enter plot start time 0 000 to 10 000 10 16 6 Changing Display Options In the Start Time text box enter the time you want at the start of the plot window The start time must be the same as or greater than the delay time for the start of data acquisition This time must also be less than the total run time for the chromatogram In the End Time text box enter the time you want at the end of the plot window The end time must be later than the start time and be less than the total run time for the chromatogram In the
217. e requirements of FDA Final Rule in 21 CFR 11 Electronic signature works in conjunction with audit trail you can enable electronic signature only on files for which audit trail has been enabled Once electronic signature has been enabled for a file it cannot be turned off Electronic signature makes the following entries in the audit trail e When electronic signature is enabled for an file an entry is made in the audit trail to record the fact that signature requirement has been started e When a user enters the correct password for a file that has electronic signature enabled the audit trail entry for the transaction will show that the electronic signature was verified Starting Electronic Signature You start electronic signature on the Description tab in the Documentation dialog box You can do this either at the time you create a file or later Your application manager may have set up this option so that the Start Electronic Signature check box is always selected and unavailable gt To start electronic signature 1 On the Description tab in the Documentation dialog box enable Start Audit Trail if necessary 2 Select the Start Electronic Signature check box TotalChrom Basics 2 13 Using Electronic Signature Documentation x Description Description Logon Name manager Begin recording changes made to the file Entering Your Electronic Signature When you save a file that has electronic signatur
218. e run data buffering and the interface is detached or if the Navigator is closed during data collection TotalChrom will automatically stop the run when this occurs Ovrflw Wrp A combination of the two previous situations This can occur if the Navigator is closed while the interface is in the Wrapped state Pre Run A LINK controlled autosampler is preparing the next injection Post Run A LINK controlled autosampler is cleaning up after the previous injection Ready The interface is ready to collect data and is waiting for the run to start Released TotalChrom does not have control of the instrument Sampling A run is in progress and the interface is collecting data Ser Dil The instrument is performing a serial dilution 200 Series LC only Understanding Status Messages Started A Start Run command has been given but the run has not yet started This will occur if the Start Run command is given before a LINK controlled instrument is ready Wrapped The run has produced more data than the interface can store Some data have already been uploaded from the interface and TotalChrom is using that part of memory to store new data This can only occur when the interface has been set up in single run data buffering and the Navigator is open No data is lost in this situation and the run can continue Command Messages Line 4 None No command is currently being processed Attaching TotalChrom is attach
219. e the title bars to enlarge the chromatograms When you hide the title bars you can distinguish the active chromatogram by their color and by the file name that appears in the status bar gt To hide the title bars of all chromatograms e Choose Show Title Bars from the Options menu to deselect it TotalChrom removes the title bars from all open windows and redraws the chromatograms slightly larger than before To show the title bars choose the command again Showing and Hiding Axis Labels For some operations you must have the axis labels displayed in each chromatogram When you do not need this feature you can hide the axis labels gt To hide axis labels for all open chromatograms e Choose Show Axes from the Options menu to deselect it TotalChrom redraws the display without axis labels To redisplay axis labels choose Show Axes Showing and Hiding Baselines Component Names and Peak Retention Times If you display chromatograms based on result files rather than raw data files you have the option of displaying or hiding the baselines component names and peak retention times for each chromatogram The first time you run Chromatograms after installing TotalChrom it displays the baselines for result files To hide baselines deselect Show Baselines on the Options menu Displaying Information in Chromatograms To show component names or retention times however you must choose Show Components or Show Retention Times T
220. e to the next timed group The name for the timed group appears beneath the chromatogram at the midpoint of the timed group marker Working with Components You can select the timed group component by selecting anywhere on the timed group window marker 13 When you are done creating timed groups choose Return to close the dialog box Displaying Search Windows To identify a peak as the correct component in a run you define a search window which is a time tolerance before and after the expected retention time for the component This enables TotalChrom to identify components despite small variations in retention time from run to run The Show Windows command in the Calibration menu displays the search window for each single peak component that is defined in the method This allows you to check for any component identification problems caused by incorrect search windows The Show Windows command is a toggle so you choose the command again to hide the search windows 4 Graphic Method Editor C PenExe TcCS Ver6 1 0 Examples solvent mth G x File Process Calibration Display Other View Help sil eje sjej elua x uj epe si MEK ISOBUT ETHYLA CYCLO EAPenExeXT CS Werb 1 O Examples Solv001 rav 788177 mV 1200 pts For Help press F1 gt To hide all search windows for single peak components e Deselect the Show Windows command from the Calibration menu
221. e two files that you want to use to create a new chromatogram Choose New Calculation Plot from the Operation menu The Calculation Plot Properties dialog box appears Plot 1 Plot 2 Halo raw Minus e Halooo m Start time min nono Start time min non End time min so Endtime min 5 000 Scaling for Calculated Data Baseline Adjustment Normalization for Second Plot Automatically calculate None x Set uv SEE Uy fi 000 OK Multiplier aa First plot for generating calculation plot Select the name of the raw data file that you want to use in the calculation from the Plot 1 list If you have aligned this chromatogram with another one by using one of the commands on the Alignment menu the starting and ending times resulting from this alignment will appear in the Start Time and End Time text boxes Select the operation that you want to perform to create the modified data file Plus Adds the data in Plots 1 and 2 Minus Subtracts the data in Plot 2 from that in Plot 1 Divide Divides the data in Plot 1 by that in Plot 2 Displaying Chromatograms Calculating a New Chromatogram From the Plot 2 list select the name of the second file that you want to include in the calculation In the Start Time text boxes for each file enter the time at which you want the chromatogram to begin This defines the starting point for the new data If you enter a
222. ected by building a vial list through the Setup Instrument dialog box You can build a vial list for any instrument although it is only required if you are using a controlled autosampler The Vial List button opens a limited version of the Sequence Editor Use this editor to build a sequence when you use the Quick Start Setup type or to edit a sequence when you use the Sequence Setup type In addition to entering vial numbers for a LINK controlled autosampler you can also enter the sample name number rack number if applicable and injection site if you are using a LINK controlled GC The limited version of the sequence spreadsheet also has columns for Sample Amount ISTD Amount Sample Volume and Dilution Factor However these are Setting Up Data Acquisition not used in a normal Quick Start setup because the Quick Method only performs an area percent calculation If you are setting up a standard TotalChrom method these parameters will be used if the method includes calibration information If an instrument has no autosampler and the user does not create a vial list TotalChrom automatically creates a one row sequence when the user chooses OK in the Setup Instrument dialog box The files generated by a vial list include cycle numbers that are appended to the base file name These cycle numbers increase automatically by an increment of one such as TEST001 TEST002 TEST003 etc For a detailed explanation of Sequence Editor commands
223. ected peak TotalChrom also removes the new component name from any peak to which it was assigned previously 5 Repeat Steps 2 through 4 to identify another peak Editing Methods and Results Graphically 10 49 Working with Components 10 50 6 When you finish identifying peaks choose Return to restore the main Reprocess Results window Displaying Search Windows To identify a peak in a run as the correct component you define a search window which is a time tolerance before and after the expected retention time for the component This window allows TotalChrom to identify components despite small variations in retention time from run to run The Show Windows command in the Components menu displays the search window for each single peak component defined in the method You can use the display to check if incorrect search windows are causing any component identification problems The Show Windows command acts as a toggle so you choose it again to hide the search windows Timed groups do not use a search window but instead have their own time window defined Therefore the Shows Windows command does not display timed group windows gt To show the search windows 1 Choose Show Windows from the Components menu A check mark appears next to the command and TotalChrom adds search windows to the working chromatogram 2 Toremove the search windows choose the Show Windows command again For more information on how TotalChrom us
224. ecting a file name from the File Select Introduction and Overview I 11 The Help System dialog box After you display this dialog box you must locate and select the file name that you want to use by browsing for that file on your computer or network Illustrations 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 The Help System The TotalChrom help system is a collection of help files one for each TotalChrom application You access help in several ways Context sensitive help When you press F1 TotalChrom displays information related to the dialog box or window you are currently using Press Escape to close the help Help menu When you choose Help Topics from the Help menu TotalChrom displays the list of help topics for the current application From within help TotalChrom offers two additional sources of information e Other Help Displays a list of help files for other TotalChrom applications e Glossary Lets you access a list of terms and definitions Introduction and Overview 1 12 Chapter 2 TotalChrom Basics TotalChrom is a collection of applications such as the Sequence Editor and the Method Editor rather than a single program These applications have many elements in common how files and instruments are accessed dialog boxes and user interface feature
225. ed with the data file or selected using the New Report Format command epeek enes EE TCT eee een eo a 3 3227285 50 oe 1B 71 18 71 58 gu 4143312 50 716219 90 4169100 25 716670 75 1897635 19 306645 89 i 3 2 5 3 3234299 75 584924 88 5 4 5 5 6 The example above shows the default report format For information on report data and formats refer to Chapter 9 In the chromatogram click on the peak for which you want to review information TotalChrom highlights the line for that peak in the report To sort the display on something other than Peak click a different column header gt To change the report format file 1 Choose New Report Format from the Report menu to open the TotalChrom File Open dialog box Locate and select the report format file you want to use and choose Open The report information display changes according to the new format you select Displaying and Printing Information Printing a Report or Replot You can print a report or replot from either the main application window or from the report information display You can select to print the report and replot that would be printed at the end of a run or you can print the plot as currently displayed gt To print a copy of the current report or replot 1 Do one of the following e Inthe Graphic Method Editor or Reprocess Results window choose Print Report from the File menu e In the report information display choose
226. ed event 18 41 Start Run command 12 20 12 21 12 22 Startup dialog box 2 2 Static Overlay Plot 53 Static Stacked Plot 53 Status command 4 4 12 37 status messages acquisition 12 40 XV autosampler 12 43 displaying 12 37 12 38 global 12 39 instrument 12 42 interface 12 40 Status Tab 20 108 Stop Monitor command 12 31 Stop Pump command 12 23 Stop Run command 12 21 SUI See System Suitability files Suitability See System Suitability Suitability command B 8 summary reports including historical IVM data in C 17 Summary See also summary report format editor menus and commands 16 3 overview 16 2 report definition example 16 12 including in a sequence 16 25 printing 16 4 16 11 selecting components for 16 4 16 6 16 9 selecting format for 16 11 selecting result files for 16 4 16 6 16 8 window 16 3 Summary Properties 20 133 summary report format editor See also Summary menus and commands 16 13 overview 16 12 report format custom expressions in 16 19 designing columns 16 16 general procedure 16 13 headers and footers 16 16 printing content of file 16 24 printing options 16 23 selecting ASCII text file output 16 24 title 16 15 Synchronize Column Widths command 11 32 synchronized programs 7 16 System Suitability calculations B 22 commands and menus B 8 files B 11 method creating B 9 developing component lists for B 12 modifying B 11 using an existing B 11 opening B 8 options defining B 13 overview B 3 parameters used
227. ed with the CDF file extensions e Select Create SOL LIMS File to create a special data file that can be exported to SQL LIMS These files are saved with the PRC file extensions e Select Formfeed Between Reports to start any optional report specified in the method on a new page Otherwise the optional report will immediately follow the primary report on the same page If you selected Print Replot With Report to print a plot on the same page as the report enter a value in the Replot Size text box to indicate the height of the chromatogram replot on the page Other parameters needed for the replot such as the axis labels are supplied from the method used to process the run Choose OK Printing Report Format Files Printing Report Format Files The Print command in the File menu lets you print a copy of the current report format file optionally with its audit trail information This output lists the contents of the report format file it does not print an example of the report format like the one you see in the Report Format Editor window Building a Report Format 9 17 9 18 Chapter 10 Editing Methods and Results Graphically This chapter explains how to create an optimal data processing method for an analysis by manipulating a typical chromatogram in the Graphic Method Editor It also explains how to optimize the results for a single analysis by using the Reprocess Results function To learn about Go to page Opt
228. eeeeeeeeeenee eene nennen nennen nee 20 148 Set Up COndltiOlis s cett c ede ipt tet eee 20 148 How Review and Approve is used in this Example seen 20 148 System Configuratio 1a I eo PERENNE HUE e EH e ene eee 20 152 About External Programs eese nennen nen neen rene enne enne 20 155 Abbreviations and Acromy mss ipei teer rp prb DOO pr re dep berti 20 156 Appendix A How Interface Collect Data Using Interfaces to Collect Data eiie teintes repente deett ttc nene fen A 2 How the 900 Series Interface Converts Analog Signals to Digital Values A 2 How the 900 Series Interface Interacts with an Instrument eee A 3 Using a 600 Series LINK Interface sees A 4 How the LINK Communicates with an Instrument esee A 5 Downloading Parameters to the Interface eese enne A 6 Stoung Data n the Interface sS gb A eau nn RR ei t ER eiie td A 7 Memory Segmentation 52 esee arte at tete Db eee he A 7 Unsegmented Mernory notte erheben bester A 7 Backlog ged Data entes eerte Eee ite A 8 Data COIBpIeSSIOIN c r ee e oii Pet mite he ei Mek terns A 10 Appendix B System Suitability Testing What Is System Suitability Testing esesssessseseeeeseeeeeeenen enne enne enne nenne B 2 System Suitability Parameters esee nennen rennen enne ne ennenren nennen nennen B 2 Pro r in Operation
229. eference and working chromatograms 1 Click the right mouse button inside the working chromatogram TotalChrom restores both plots to the previous scaling If you click the right mouse button inside the reference chromatogram after you start to reduce the view in the working chromatogram an update message appears Choose Yes and click the right mouse again to continue reducing the view Changing Display Options Manipulating the Reference Chromatogram If you have not expanded the reference chromatogram TotalChrom displays visible portion of the working chromatogram as a selection rectangle in the reference chromatogram You can manipulate this selection rectangle to change which part of the plot appears in the working chromatogram window gt To display a different part of the chromatogram 1 Move the mouse cursor over the selection rectangle in the reference chromatogram The mouse cursor changes to a cross 2 Drag the outline of the selection rectangle to the part of the chromatogram you want to view 3 Release the mouse button TotalChrom displays the selected part of the reference chromatogram in the working chromatogram In addition to changing which part of the chromatogram appears in the working area you can also change the size and proportions of the selection rectangle in the reference chromatogram gt To change the size of the displayed region 1 Move the mouse cursor to an edge of the selection re
230. el you must delete all replicates or delete the level itself The next topic describes how this can be done for all components and all levels simultaneously using the c command line parameter 6 7 To include a replicate that you have excluded choose Include To delete a replicate from the list choose Delete Points associated with replicates will be removed from the calibration curve Choose OK to return to the Components dialog box Deleting All Calibration Replicates Deleting All Calibration Replicates You can delete all calibration replicates from a method in one operation by running the Method Editor from the command line typically by setting it up as a user program in the Sequence Editor You will need to use the following information to fill in the Program Information dialog box Program Name MethEdit exe Command Line filename mth c This will delete every replicate for every component in the method Refer to Chapter 11 for complete information and instructions on how to include a user program in a sequence Developing Calibration Parameters in the Method 8 49 8 50 Chapter 9 Building a Report Format This chapter explains how to use the Report Format Editor to build a report format file This file controls which parameters are included in the printed report that follows data analysis You can use TC Publisher to produce highly customized reports Refer to the TC Publisher Help file for instructi
231. ement whose color you want to change Color Selection a Component names Retention times Timed events xj The list of items in the Color Selection list box changes depending on the option you select above it To change the color of a particular item you select it and then adjust the Hue Saturation and or Luminosity Change the hue saturation and or luminosity by dragging the scroll box or clicking on one of the scroll arrows until the screen element is the desired color Hue p gt Saturation gt Luminosity e Hue Represents the item s basic color such as red orange or blue e Saturation Determines how dark or light the hue is A saturation level of zero scroll box positioned at the extreme left means that none of the selected hue will be used thus leaving the color white When the scroll box is at the extreme right the hue is at its maximum saturation e Luminosity Affects how bright the color is by adding more or less black When the scroll box is at the extreme left the color is black When the scroll box is at the extreme right the color is at its brightest with no black Change the color of each item in the list as needed until you are satisfied with the overall effect Choosing Reset returns the colors to what they were when you first opened the dialog box Select the next element whose colors you want to change and repeat steps 4 and 5 Choose OK to save the color configuration
232. en nennen 14 11 Rescaling Chromatogram Values eese ener rennen 14 13 Showing and Hiding Coordinates esee eene ener 14 14 Showing and Hiding Title Bars eeeeeeeseeeeeeerenerenenenneen ener enne 14 14 Showing and Hiding Axis Labels esee enne 14 14 Showing and Hiding Baselines Component Names and Peak Retention Times 14 14 Adding and Editing Chromatogram Labels eese 14 16 Adding Labels to Chromatograms seen nennen rennen ene 14 16 Editing Chromatogram Labels eese eene enne enne nee 14 16 Moving a Label to the Top of a Stack eene 14 19 Linking and Unlinking Labels to Data eeeeeeeeeeeeeeeneneneenen eene 14 19 Aligning Peaks in Two Chromatograms esee eene enne 14 20 Aligning Peaks By Time 5o epe rta te e pedo eR Ee ets 14 20 Aligning Peaks by Voltage sss 14 24 Calculating a New Chromatogram eese enne eene nennen nre nennen 14 28 Editing Calculated Parameters eese enne eene nennen 14 31 Saving the New Chromatogram sese een ren eene tenete 14 31 Table of Contents vii Volume Il Chapter 15 Reprocessing Files in Batch How Batch Reprocessing Works essent nennen rennen enne 15 2 Using Batch Reprocessing ea eerte bebe pr E uer ete desee wie an 15 3 Reprocessing a Sequence or I
233. ene eene 8 7 Understanding Component Parameters essent enne 8 9 Component Type Sisir nea esee ore trn e OR Pte ri rep eibi tei 8 10 Setting Up Search Windows eienen aaae rU DERE denen 8 13 Reference Compotients e genie Sein tig EHE GRE mantle scien 8 13 Internal Standard Components eseeeeseeseeeseeeeeeenee nennen nennen 8 14 Calibration Type eec deg Db ihe ced 8 15 Response oe ar e ie oderam ardet d RUE Iba 8 16 Selecting Fit Parametetr ooi rap eg tepR EHE eR Etpe 8 16 User Values EIMS roter ttti rente e three 8 19 Setting Component Defaults essent eene nennen enne en enne nete trennen 8 20 Entering Default Component Information esee eere nennen 8 21 Adding and Editing Components essent nee enne 8 28 Adding a Component 2g gne gae eoe E e pcd D Pata ions 8 30 Editing a Component eee droite i ete te mM tete e s Edge E 8 39 Loading and Merging Components From Files eene 8 40 Deleting Components kie anini reei ee UE AE eR Dn AG E 8 42 Changing Parameters for Multiple Components Simultaneously esses 8 43 Table of Contents iii Performing a Manual Calibration npin ener nennen nre ene 8 46 Excluding and Deleting Replicates eeesseeeeeeeeeeereen rennen enne 8 47 Deleting All Calibration Replicates sess eene 8 49 Chapter 9 Building a Report
234. entation about a method and copy and save the plot image for use in other applications Process Menu Lets you edit instrument timed events and baseline timed events optimize parameters such as noise and area thresholds and manually integrate peaks by redrawing the baseline Calibration Menu 10 6 Using the Graphic Method Editor Lets you perform component tasks such as creating or merging component lists from peak lists change component information and build or edit named and timed groups display and revise search windows and update calibration information Display Menu Lets you control the characteristics of the display including the plot scale and whether items such as the report header peak report or reference chromatogram appear on the screen Other Menu Closes the Graphic Method Editor and opens the Method Editor with the current method loaded and lets you start the optional LC spectral analysis application Status Bar The status bar appears at the bottom of the window This area shows the raw data file name the coordinates of the mouse cursor along the X and Y axes and how many points there are in the chromatogram In addition the status bar displays Help for the currently selected command and whether or not you have modified the file Editing Methods and Results Graphically 10 7 Using the Graphic Method Editor 10 8 Loading Files in the Graphic Method Editor You primarily work with two types of files
235. eplicates 8 1 Introduction to Calibration Parameters Introduction to Calibration Parameters 8 2 Calibration parameters identify and calibrate the components that TotalChrom analyzes Calibration parameters are divided into two groups e Global parameters which apply to the method as a whole e Component parameters which define the specific calibration treatment for each peak in the analysis The calibration section of the method includes a component list and parameters that determine how TotalChrom matches peaks with named components Calibration parameters which apply only to components being analyzed by the method include component names expected retention times and calibration data the responses produced by different component amounts The calibration section also includes parameters TotalChrom uses to calculate each component s calibration curve Every cycle in a sequence identifies the method whose calibration parameters TotalChrom uses for that particular run If the method calls for dual channel data acquisition each channel can either use the same method and calibration values or use a different method If the method calls for single channel data acquisition you only need one set of calibration parameters Always use the same data acquisition mode for your calibrations and analyses For example for dual channel analyses only use calibration values determined in dual channel calibrations Similarly for single cha
236. er programs during data analysis The entry points for the programs can be e After baseline subtraction e After peak detection or integration e After component identification e After calibration e After quantitation e After report generation e After replot generation You can also synchronize these programs in TotalChrom with the Analyze program which is the program responsible for data analysis Synchronization lets you prevent Analyze from continuing the stages of analysis until your user program has completed running For specific information on running System Suitability Fit Analysis or Summary as a user program see the corresponding chapter in this manual Running User Programs gt To run user programs in conjunction with analysis 1 Choose User Programs from the Process menu to open the Process dialog box with the User Programs tab selected Integration Baseline Timed Events Optional Reports Replot User Programs m Program Name and Options Delete All Command line RST LJ Execute after Annotated Replot Generation E Synchronize with data analysis Cms s Options are those for program 1 2 Select the name of the program to run during data analysis See your application manager for information about access to programs 3 Toremove files from the list use the Delete or Delete All command 4 In the Command Line text box enter the information you want to pass to the u
237. er Rotate Around The X Axis to change the amount by which the chromatograms are shifted to the right from each other Displaying Chromatograms 14 9 Controlling the Appearance of Chromatogram Windows 4 Move the slider under Rotate Around the Y Axis to change the degree of rotation for the chromatograms The image in the dialog box changes concurrently You can shift all chromatograms up to 45 degrees Chromatograms Overlay View of x E File Operation Options Window View Help 18 xl slale L1G ow Calf m ive a Stat 0 000 End 5 000 Offset 35 275 Scale 803508 7 5 When the 3 D effect suits your needs choose OK If you want to cancel the changes you have made choose Reset If you want to remove all rotation choose Default Hidden Lines The Suppress Hidden Lines check box in the 3 D Preview dialog box lets you view a 3 D overlay with either the topmost plot covering other plots or with all plots equally visible The effect will appear both onscreen and in printed output Select this check box to make the most recently opened plot opaque Only other plot lines areas that are outside the frontmost plot s area are visible Deselect this check box to make the most recently opened plot transparent so that all areas of all plots in the overlay window are visible 14 10 Displaying Information in Chromatograms Displaying Information in Chromatograms The following co
238. erface in the instrument section of the method These parameters include the sampling rate run time channel and relay timed events you want to occur during a run Timed events cause relays in the interface to switch triggering an outside event such as a valve switch on a chromatograph For more detailed information refer to Chapter 12 There are five steps to configuring a 900 Series interface e Choose a data acquisition port e Set A D configuration options e If necessary configure an autosampler e Save the configuration Each step is described in a separate procedure gt To choose a data acquisition port 1 In the Navigator choose Configuration from the Build menu to open the Configuration Editor 2 Select the 900 Series Interface you want to configure and choose Configure from the Instrument menu Configuring Instruments 3 Ifthe interface is not configured the Acquisition Port dialog box opens Acquisition Port 4 Click the marks to expand the tree and select the data acquisition port to which the interface is physically connected When a port is highlighted you can click Query Port For Type to see which type of interface is connected to it gt To set A D configuration options 1 Choose Continue The A D Analog to Digital Configuration dialog box appears and shows the selected instrument name A D Configuration 2 Entera new name in the Instrument Name text box if yo
239. erial Dilution x Serial dilution method teen Name of serial dilution file 2 Enter or select the Serial Dilution Method name If you enter the name you must include the complete path so that TotalChrom can find it If you select the name TotalChrom inserts the path 3 Choose OK An X appears in the Note column to indicate that serial dilution information exists for this row Appending New Cycles to a Sequence You can append new cycles to a sequence by using the Append commands on the Build menu Append New Cycles Lets you append cycles that include sample specific information After you choose the Append New Cycles command you complete the Editing the Sequence Spreadsheet Append New Cycles dialog box like you would for a new sequence This procedure is described in Building a Sequence Vial By Vial Append New Template Lets you append a structure of calibrations and samples in a single operation After you choose the Append New Template command you complete the Sequence Template dialog box like you would for a new sequence This procedure is described in Building a Sequence by Template Append Sequence File Lets you append the cycles from another sequence that is designed to use the same instrument After you choose the Append Sequence File command you select a sequence from the File Select dialog box You can also append cycles to a sequence from a text file See Appending Sequence
240. ers If you select Multiple Per Row the following columns appear instead of Method Inst Method Instrument Method The method containing the instrument parameters Proc Method Processing Method The method containing the processing parameters Calib Method Calibration Method The method containing component and calibration parameters Rpt Fmt File Report Format File The report format file for the first report to be printed for a row You can specify additional optional reports in the processing part of the method Data File If you select Same Name in the Global Parameters dialog box TotalChrom applies the same base name to both the raw and result files If you select Separate Names the following columns appear instead of Data File Raw Data File The file containing the raw data Result File The file containing the analysis results When the sequence is run TotalChrom appends a unique suffix to the base name to name the data file s Calib Rpt Calibration Report Whether a calibration report will be printed and if so the amount of detail that it will include Cal Level The name of the calibration level Update RT Retention Times Whether the calibration is set to update peak retention data or to retain the initial data Sample Amt The actual amount of the sample injected excluding the amount of internal standards Based on settings in the calibration method this value c
241. ers as they are defined in this section of the method gt To edit replot parameters 1 Choose Replot from the Process menu to open the Process dialog box with the Replot tab selected Integration Baseline Timed Events Optional Reports Replot User Programs m Plots Iv Gi at Generate second replot Number of pages fi Scale factor fi 000 m Orientation m Miscellaneous CC Portrait v Set plot limits to data limits Gradient overlay Landscape Start tine min poo Iv Draw baselines m Retention Labels End time min oo M Timed events C None Plot title Chromatogram Top of plot X axis label Time min Y axis label Response mV C Peak crests r Component Labels p Scaling Type p Scaling Parameters None Vertical scaling Offset mV o 000 C Expected time C Autozero offset Scale factor fi 000000 Actual time C Absolute scaling Full scale mV e0 000 te am Generate a full page replot of the chromatogram at the end of the run 2 To suppress printing of a full page plot after data analysis deselect the Generate A Separate Replot check box and skip to Step 8 If you deselect this option you can still enter parameter values that will affect a replot embedded in the report 7 12 Editing Replot Parameters 3 Inthe Number of Pages text box enter the number of pages on which you want the replot s to appear This optio
242. es how to set up your initial system configuration and change an existing configuration Chapter 4 Using the Navigator Explains each of the features that appear in the Navigator Chapter 5 Building a Method Provides an overview of the TotalChrom Method Editor and how to create and modify a method A method consists of instrument processing and calibration parameters which are described in subsequent chapters Chapter 6 Developing Instrument Parameters in the Method Describes how to set and change instrument parameters in a method These parameters affect how TotalChrom acquires and analyzes data by controlling settings for the chromatographic instruments configured on your system Chapter 7 Developing Processing Parameters in the Method Describes how to set and change processing parameters in the method Processing parameters control how peaks are detected and integrated how reports and plots are printed and which user programs will run at what point in the data analysis process Introduction and Overview 1 6 Using this Guide Chapter 8 Developing Calibration Parameters in the Method Describes how to set and change calibration parameters in a method Calibration parameters identify and calibrate the components being analyzed Chapter 9 Building a Report Format Explains how to use the Report Format Editor to create customized report formats These control which parameters are included in the reports that are printed following
243. es search windows to identify peaks refer to Chapter 8 Displaying and Printing Information Displaying and Printing Information The Report Header and Peak Report commands in the Display menu let you view the contents of each report on screen These commands display the report in a format different than when it is printed The Peak Report command displays the information for each peak detected in the run including component identification and quantitation If the selected report format contains the options to include named and timed groups in a printed report then those are displayed in the list instead of their constituent peaks Peak Report lets you quickly review the results for any peak that is not part of a group by clicking on that peak in the plot The Peak Report list then scrolls to highlight the data for that peak gt To display report information e Choose Peak Report or Report Header from the Display menu ja Graphic Method Editor C PenExe TcWS Wer6 2 0 Examples solvent mth of x Report Return Help 2 BIB 2 Software Version 6 2 0 0 0 404 Date 01 30 2001 1 25 24 PM NTS perator Sample Name SOLVE Sample Number Study SOLVENT SAMPLES AutoS ampler Rack Vial 0 0 Instrument Name Unknown Channel A Interface Serial UNKNOWN A D mV Range 1000 g x 5 5 258 5 2 R g 8 bi S 5 Ft fo n E T 1 41 p 1 i i 1 hi ho sx ig ies PTUS 1 1 I i amp 61
244. esee 19 2 Converting Files to Other Formats eese nee nrennenren ennemi 19 4 Chapter 20 Review and Approve What is Review and Approve sito bet e abet da DER er ie ea 20 2 About the Review and Approve Environment eese eere 20 3 The Review and Approve Process ccssssssecssesscneeeecsseeeessecaeesecsevsecnaeeeesaeeaeeseeaeeaeens 20 5 Assigning Job Type Permissions for Review and Approve seeeeene 20 6 ReportStatus uote leve eme ebaieaihieeema n 20 6 General Requirements for Status Changes eee eee 20 8 Review and Approve Levels esses ener enne nnne enne nennen nnne 20 9 Software Behavior Based on Levels eese 20 10 Printed Reports 2a IER n EE RED 20 12 Report with Signature Table 0 ec eeesesecsseeecsseceeesecseesecneeseesecnessecsaeeecaecaseseeaeeats 20 14 M in View inira biet e papa oti isis oui RE ERU ERE ise 20 15 File e RE 20 15 Plot WindOw i p ence e p eR e teme Hr Ir pee o eee be 20 16 Report WindOWw 2 nete bete rie e ep tere ye re E EE Ha de toes 20 16 Main Toolb t aon Beet a etri a ed ee ey RE ee tots 20 17 Menu B t s ien deu portait tees de en 20 17 Status Bar sess ees gie eem e tp RR TF RO RR peg 20 24 About the Properties Inspector Dialog eene 20 25 About the Options Dialog seserian Koea ne TAE EEE o e E aroa 20 27 Options Dialog Initial Scaling Tab eese 20 28 Opti
245. ess number to an initial value of one 1 Select the Instrument Control Parameters check box to include a summary of the instrument conditions used by a LINK controlled instrument in the report Select any Report Body Options you want to use To print only the system header information in the report deselect Print Main Report Body and go to step 5 Refer to the Status bar for a description of each Report Body Option Certain options are further described below e f you choose to include named or timed groups in the body of the report then the individual members of the group will not be reported The group amount will be based on the calibration of the group as a whole Conversely if groups have been defined but are not included in the report body the individual components and or peaks will be reported based on their individual calibrations e If you select Missing Components Missing Named Groups or Missing Timed Groups the peak index and quantities will be zero because no peaks will be found The rows will contain zeroes and will use the ex pected retention time Enter a value for Area Reject to represent the minimum peak area that you want included in the report This value is used for report generation only Select any Miscellaneous Options you want to use Refer to the Status bar for a description of each option Certain options are further described below e If you select either Expand Named Groups or Expand Timed Group
246. et TotalChrom configure the instrument automatically This method avoids problems which may arise because of the complexity of the AutoSystem and HP 6890 configurations You can use this option if the instrument s IPM has already been downloaded to the LINK e Choose Copy Inst Config to use the configuration data from a similar instrument A dialog box will appear that lists configured instruments from which you can copy configuration data You can then edit the configuration as needed e Configure the instrument manually by following steps 4 through 14 After configuration TotalChrom will download the Instrument Personality Module IPM for the instrument Under Options select whether or not you have PPC Programmable Pneumatic Control installed Selecting YES makes available the other PPC options in the dialog box Select Gas Leak Alarm if you want to be alerted of a gas leak within an instrument under PPC control Under Inlets select the Injector setting that matches your instrument for Channel A and or B If the instrument has valves select the valve type for each valve The PPC split vents will be configured automatically Under Detectors select PPC for detector A and or B if PPC is installed then select the Detector Mode and Output settings that match your instrument for Channel A and or B Under Carrier Pneumatics select the Pressure Units and other options Select a setting for Carrier A The available setting
247. et text box enter a value for the first channel being used This value specifies the voltage corresponding to the bottom of the plot window In the Full Scale value text box enter a value to specify the height of the real time plot In the Number Of Pages text box enter the number of pages screen widths over which you want to display the plot If you are using both channels repeat Steps 2 through 4 to set the options for Channel B Setting Control Options 6 Doany ofthe following e To save your work and close the dialog box choose OK e To save your work without closing the dialog box choose Apply e To close the dialog box and discard your changes since the last time you chose Apply choose Cancel Setting Control Options 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 TotalChrom opens the Instrument Control dialog box which contains tabs for each major control command gt To set control options parameters 1 Choose Control Options from the Instrument menu and choose a command from the cascaded menu The Instrument Control dialog box opens to the tab corresponding to the command that you selected 2 Select the tab for each control option that you want to complete or edit 3 Make any changes to the values in the dialog box and do any of the following e To save your work and cl
248. exit the program to return to the Navigator User Notes Menu Lets you create header footer and title text for the report Report Menu Lets you select the columns that you want to have in the report including custom expressions that generate values in a column Edit Menu Lets you move and delete columns Options Command Lets you specify a variety of reporting options such as the size of the system header and the components to include Using the Report Format Editor General Procedure for Creating a Report Format The following is the general procedure for creating a report format Specific procedures for the tasks referenced in this procedure are provided later in this chapter You can also create a new report format by editing an existing report file and renaming it with the Save As command gt To create a new report format file 1 Do one of the following e In the Navigator choose Report Format from the Build menu The Startup dialog box appears Startup r Select startup option Create new report C Load report stored on disk Load a recently edited file Select one of the displayed options and choose OK to open the Report Format Editor window e Ifthe Report Format Editor is already open choose New from the File menu The name lt untitled gt appears in the title bar of the Report Format Editor window and TotalChrom displays the default format Your defaults may look different from
249. ey are when you run the Sequence Editor from TotalChrom You can include switches on the command line to indicate how text should be incorporated into a sequence If there are no switches on the command line the B switch is assumed B build new sequence based on the input text file M merge input text file into existing sequence file of the same name A append input text file to existing sequence file of the same name Using Index Files You can add the quiet mode switch Q so that the Sequence Editor does not open during this process When you use the Q switch you must add the B M or A switch When you use the Q switch you cannot build a dual injection sequence or select an autosampler tray When you use the Q switch you may provide instrument information for the sequence file by adding the following line after all the cycle records in a text file UserData Instrument lt target instrument key The instrument entry must be the instrument key not the instrument name This value will overwrite the instrument key in the sequence file when you merge or append a text file to it Using Index Files As TotalChrom acquires data from a series of runs it creates a record of those runs in the form of an index file with the extension IDX The information in an index file is basically the same as in a sequence but with one important difference the index file contains the actual name of each file collected whereas a sequenc
250. f necessary change the number in the Rack text box If you are using a LINK controlled GC select the appropriate Injection Site In the Instrument Method text box enter or select the name of the method file that contains the instrument parameters that you want to use This information is required but you can enter the name of a method that does not yet exist as long as the path exists and you create the method before you run the sequence 11 19 Building a Sequence Vial by Vial gt To enter identification information for a dual injection sequence For a dual injection sequence you may enter different parameters for each channel 1 On the Identification tab of the Append New Cycles dialog box select an entry for the Type field Identification Files Quantitation Calibration Type Cal e iia of cycles fi Method k Mecs ver6 0 0 config user koontzsa DEFA Channel C Channel B Sample description Name r e Number pattern HHH Actual number Do Study pem Vial Do jJ Back in Close Add Type of sample to be added to the sequence The type that you select will be used for both channels If you want to specify different types for each channel you can edit the spreadsheet later If you use a type that is not a sample or a calibration type it must appear for both channels 2 If the sample is to be injected more than once enter the number of cycles i
251. face in the Configuration Editor 2 Choose Reset LINK from the Interface menu Any existing configuration data in the LINK will be erased and you must reconfigure the LINK Disconnecting an Instrument Before you make any physical changes to an instrument you should disconnect it from the system by choosing Disconnect from the Instrument menu Using Run Counters Run counters count the number of runs made on each channel of an instrument The current number of runs for each instrument is displayed in the Interface group box on the Configuration Editor screen The configuration printout includes these values in the instrument table of Configuration E ditor Eile Instrume s Interface User View Help Configure Disconnect Post Sequence Reset Run Counters Reset All Run Counters gt To reset a run counter 1 Select the Reset Run Counter or Reset All Run Counters command on the Instrument menu Configuration 3 15 Configuring Instruments 3 16 The following dialog box opens Reset Run Counters Srramme tib Reset Channel B counter Select the channel counter you wish to reset then choose Reset The following appears Configuration E ditor Choose Yes to reset the counter Configuring User Options Configuring User Options Fonts Configuration The User menu in the Configuration Editor lets you define the font style and size for plot labels set colors define plot prefere
252. ference then this check box will be selected when you select that component gt Toadd a named group to the component list 1 Select the Identification tab of the Components dialog box and select Named Group as the Component Type r Component Type C Peak Timed group 2 Inthe Name text box enter a name for this group 3 Select the components you want to include in the named group from the Group Members box The list includes all peak and timed group components contained in the open method To select multiple components hold down the Ctrl key and then click on each name 4 From the Internal Standard list select the component you want to use as the internal standard This list consists of all components in the open method that have already been designated as internal standards gt To add a timed group to the component list 1 Select the Identification tab of the Components dialog box and select Timed Group as the Component Type r Component Type 2 C Peak C Named group 2 Inthe Name text box enter the name you want to use for this timed group 8 32 Adding and Editing Components 3 In the Start Time text box enter the starting time you want to use TotalChrom only includes in the group those peaks whose crests occur after this time 4 Inthe End Time text box enter the ending time you want to use TotalChrom only includes in the group those peaks whose crests oc
253. formation in spreadsheet format Channel A and Channel B appear in separate windows When an instrument is capable of collecting only a single channel of data only one spreadsheet appears The spreadsheet window has the following features W Sequence Information Channel A Edit Bar Column Label Row Number Cell View Tab ah General Sample Description A Methods Building a Sequence 11 5 Using the Sequence Editor 11 6 Edit Bar Displays the full contents of the currently selected cell You can move the cursor to the edit bar and enter text there Text that you enter in the edit bar is mirrored in the cell and vice versa You cannot use the edit bar to edit cells that contain a drop down list Column Label Identifies the type of information in all cells in the column Column labels are displayed as headers across the top of the spreadsheet Columns are explained in Columns in the Spreadsheet Row Numbers Always the first column in a spreadsheet Because a spreadsheet can contain more rows than are visible in the window row numbers help you find your location in the spreadsheet Cell A box at the intersection of a row and a column A cell contains one item of data a text string an integer or a real number All the cells in a given column contain the same type of data A cell that is not applicable in the context of the current row is shown in black View Tab Displays the columns that are asso
254. g Rows To move rows in a spreadsheet you use the Cut and Paste commands from the Edit menu or the shortcut menu When you move rows TotalChrom cuts and pastes them in both the Channel A and Channel B spreadsheets simultaneously gt To move spreadsheet rows 1 Select the rows that you want to move 2 Choose Cut 3 Select the row above which you want to insert the rows If you do not select a row TotalChrom appends the rows that you cut to the end of the spreadsheet If you select the last row TotalChrom gives you the option to insert or append 4 Choose Paste You may paste the same selection as many times as needed while it remains on the clipboard 5 Check that the values in the rows that you have moved and the rows that follow are correct in their new context You can use the Smart Fill command to increment values in the Number Vial and Data File columns if necessary See Editing Column Values on page 11 37 Copying Rows Building a Sequence To duplicate existing rows you use the Copy and Paste commands from the Edit menu or the shortcut menu The Copy and Cut commands are available When you copy rows TotalChrom copies them in both the Channel A and Channel B spreadsheets simultaneously 11 35 Editing the Sequence Spreadsheet 11 36 gt To copy spreadsheet rows 1 2 Select the rows that you want to copy Choose Copy Select the row above which you want to insert the copied rows If y
255. g to set the rate at which the instrument samples its detectors e Select By Peak Width At Base and then enter the number of seconds in the text box With this option TotalChrom 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 TotalChrom calculates the optimum sampling rate for that peak width collecting at least 20 data points across the peak e Select By Sampling Rate and enter a rate in the text box With this option TotalChrom acquires data from the instrument using the number of data points per second that you explicitly set or the nearest available rate to that value Setting Data Channels If your power line frequency is 60 Hz you must enter a sampling rate as follows e for single and dual channel acquisition a rate that is evenly divisible into 100 For example 10 pts s is acceptable as entered however TotalChrom changes 12 pts s to 12 5 pts s If your power line frequency is 50 Hz you must enter a sampling rate as follows e for single channel acquisition a rate that is evenly divisible into 50 e for dual channel acquisition a rate that is evenly divisible into 25 If necessary TotalChrom will change your entry for sampling rate to conform to this requirement This is done to prevent the excessive baseline noise that may be produced with certain detector grounding configurations with older generic interfaces 5 I
256. grams Scaling the Voltage From Origin The Scale Voltage From Origin command on the Chromatogram pop up menu rescales the Y axis of the target chromatogram relative to a reference chromatogram gt To align peaks by scaling voltage from origin 1 Seta high voltage in both chromatograms 2 Right click in the target chromatogram and choose Scale Voltage From Origin The target chromatogram is scaled such that the low and high voltage values align with the low voltage and high voltage values in the reference chromatogram Scaling the Voltage Using Two Points To scale voltage using two points you mark baselines and peak crest points on each chromatogram and TotalChrom rescales the aligned chromatogram such that the baseline points and peak crests are at equivalent positions on the Y axis The Scale Voltage command on the Chromatogram pop up menu allows you to match the baselines of two chromatograms It affects the Y axis by changing the low voltage of the target chromatogram Because you are actually changing the low voltage and full scale values for the aligned chromatogram you can also perform this task through the Rescale command on the Options menu 14 26 Aligning Peaks in Two Chromatograms gt To align peaks by scaling voltage 1 Set a low and high voltage in both chromatograms Chromatograms Soly_001 raw of x Eile Operation Options Window View Help sem xs aale m e ve a R Solv_002 raw L
257. he Column Information dialog box OR Choose Delete Column from the Edit menu to open the Delete Column dialog box enter the number of the column that you want to delete and choose OK Replacing Editing Column Information Use the Replace command to modify the information that appears for any column in a report format file gt To edit existing column information 1 Click on the column that you want to change to open the Column Information dialog box Edit the information as necessary but do not change the column number or you will move the column Choose Replace Editing Report Columns Moving Columns You can change the position of columns in a report format file in two ways by using the Move Column command in the Edit menu or the Move button in the Column Information dialog box gt To move a column 1 Building a Report Format Click on the column you want to move to open the Column Information dialog box In the Column Number text box enter the new column number Choose Move to close the dialog box and reposition the columns OR Choose Move Column from the Edit menu to open the Move Column dialog box Move Column x Which column to move fi New column position tees New location for this column 1 to 8 Enter the number of the column you want to move in the Which Column To Move text box and enter the number where you want the column to appear in the New Column Position text
258. he Delete Timed Events dialog box Delete Baseline Events x Select the event s to be deleted 3 Select one or more events to delete and choose OK 10 24 Setting Processing Parameters TotalChrom deletes the events from the list and the chromatogram gt To reprocess peak data after adding or deleting baseline timed events 1 Choose Reprocess TotalChrom reprocesses the raw data by performing peak detection integration component identification and quantitation using the current method settings 2 Choose Return to close the baseline timed events display Editing Methods and Results Graphically 10 25 Setting Processing Parameters Setting Noise and Area Thresholds To ensure that TotalChrom detects small peaks but does not interpret baseline noise as peaks you need to calculate the baseline noise and set noise and area thresholds to ignore the baseline noise The Noise Area Threshold command in the Process menu lets you change the settings that exist in the method and view the result of the changes immediately gt To change the noise and area thresholds used in a method 1 Choose Noise Area Threshold from the Process menu The status bar message prompts you to outline the portion of the baseline that you want to use for calculating a new threshold level 2 Inthe working chromatogram drag to select the part of the baseline that you want to analyze TotalChrom only uses the starting and ending t
259. he Run menu Start Run Stop Run Cancel Run Pause Sequence Resume Sequence Clear Setup Stop Pump Take Control Release Control Attach Detach 3 Choose the Run command you want to use The CMD line in the Status box displays an indication that processing of the command is taking place Acquiring and Viewing Data 12 19 Controlling Data Acquisition 12 20 gt Tochoose a Run command for one or more instruments 1 Select the required command from the drop down Run menu in the Navigator A dialog box appears listing the available instruments The instruments that are available depend on which command you selected from the menu You may select multiple instruments from the Primary list only 2 Selectthe instrument s to which you want to send the command 3 Choose OK The CMD line in the Status box displays an indication that processing of the command is taking place Starting Data Acquisition The precise action of the Start Run command depends on the instrument configuration You must choose Start Run if you are using a LINK controlled autosampler This tells the autosampler when to start the injection process for the first sample of a sequence For other configurations each run can be initiated by a device that is external to TotalChrom such as a standalone autosampler or by pressing the chromatograph run button LINK Controlled Autosamplers If you are using a LINK co
260. he component identification information You can add the following types of components e Single peak components e Named group components e Timed group components Note the following about component types e Any peak component you add to the component list in a method can also act as a reference component or internal standard e You must have identified the single peak or timed group components before you can create a named group The members of a named group do not need to be located contiguously in the chromatogram they can appear anywhere e Peaks need not be identified to be included in a timed group Adding and Editing Components gt To add a peak component to the component list 1 Select the Identification tab of the Components dialog box and select Peak as the component type r Component Type 1 C Named group Timed group In the Name text box enter a name for the component In the Retention Time text box enter the expected retention time for the component In the Absolute Window text box enter the size of the absolute search window you want to use on either side of the expected retention time In the Relative Window text box enter a percentage of the expected retention time you want to add onto either side of the absolute search window Select Find Largest Peak In Window if you want TotalChrom to identify the largest peak based on height not area as the component rather than the one closest
261. he settings available for each option vary depending on the instrument you are using LC Configuration x Instrument name SMIRI Detector Options Jsutasampleny pUOTTS Voltage threshold o 00 Accessories Ean temp LOW z Wavelength res nm fi x Lamp ype Deuterium zi Syringe size 10 M H Vecode teen Enter the name you wish to give to this instrument To rename the instrument to something other than its default name enter the new name in the Instrument Name text box Select a setting for each option that is active for your instrument 3 13 Configuring Instruments If you are configuring an LC and you are using a 900 Series interface to communicate with an autosampler choose R V Decode rack vial decode to set autosampler options See the To Set A D Configuration Options procedure in Configuring a 900 Series Interface on page 3 4 Choose OK to return to the LINK Configuration dialog box gt To save the configuration 1 Choose Finish in the LINK Configuration dialog box TotalChrom creates a configuration file CFG for each instrument and downloads the IPM All IPMs available to you are installed during the TotalChrom installation process If TotalChrom cannot find an appropriate IPM consult your application manager When you first configure a LINK controlled instrument a dialog box similar to the following appears asking if you want to check communi
262. her the mouse or the Rescale Plot command choose Preserve View from the File menu before opening another file gt To expand the chromatogram using the mouse 1 Position the mouse cursor where you want the starting point of the expansion to be 2 Drag to select the part of the working chromatogram you want to enlarge ta Graphic Method C PenExe TcCS Wer6 1 0 Examples solvent mth Eile Process Calibration Display Other View Help tal 1B lela ze e x uj epe st CYCLO ISOBUT ETHYLA ETHYLB CAPenExe TcCSWer6 1 0 Examples SolvO01 raw 8873mn 722887mv 1200pts 10 18 Changing Display Options 3 Release the mouse button The working chromatogram expands and TotalChrom highlights the visible portion in the reference chromatogram ta Graphic Method Editor C PenExe TcCS Ver6 1 0 Examples solvent mth Elle Process Cali Display Other View Help xta BI e eje ALa xJ il vl su ISOBUT C PenExe TcCS Wer6 1 0 Examples Solv001 raw 5219 min 30 173 mv The left and right sides of the selection rectangle are equivalent to the starting and ending times in the Rescale Plot dialog box The height and bottom position of the selection rectangle are equivalent to the full scale and offset values in the Rescale Plot dialog box gt To return the chromatogram to a previous level of expansion e Position the mouse anywhere
263. hereafter the settings you choose for all three features will stay in effect until you change them Each of these commands acts as a toggle to show or hide any of these attributes select or deselect the command on the Options menu Displaying Chromatograms 14 15 Adding and Editing Chromatogram Labels Adding and Editing Chromatogram Labels One of the tasks that you can perform through the Chromatogram pop up menu is the adding of labels After you create a label you can move it edit its text and appearance move it to the top of a stack of labels and link or unlink the label to data in the chromatogram Adding Labels to Chromatograms You can add labels to chromatograms by using the Add Label command on the Chromatogram pop up menu After you create a label that shows the time into a data acquisition run you can customize it by entering text that you want the label to contain You can move labels delete them set the font and set the text colors gt To add a label to a chromatogram 1 Open the chromatogram file in which you want to add labels Files of this type have the extension raw or rst 2 Click the right mouse button where you want a label to appear The Chromatogram pop up menu appears 3 Select Add Label A label will appear that displays the time into the run for the position of the cursor in the chromatogram 4 To accept the label press Enter If you want to delete the label after you accept it right c
264. hod choose Save from the File menu The Documentation dialog box opens 4 Complete the Description tab in the Documentation dialog box and choose OK For a discussion about entering descriptive information about a file refer to Chapter 2 TotalChrom Basics The TotalChrom File Save As dialog box opens 5 Entera name for the method in the File Name text box and choose Save The dialog box closes and the new method name appears in the title bar Reviewing Method Parameters When you are finished working in the Method Editor choose Exit from the File menu Alternatively you can choose from the Other menu to go directly to another application Opening a Method Referenced in a Sequence File You can open an existing method directly or you can open it through a sequence in which it is used gt To open a method referenced in a sequence file l 2 In the Method Editor choose Open from the File menu In the TotalChrom File Open dialog box select Sequence Files seq from the Files Of Type list and select a sequence Under Method Source enter the number of the cycle that specifies the method you want to open If that cycle includes different methods for instrument processing and or component parameters TotalChrom loads the instrument method Reviewing Method Parameters You can review the parameters in the instrument processing and calibration sections of the method sequentially by using the Review comma
265. hods refer to Chapters 5 through 8 Sequence If you need to analyze a large number of samples or want to automate routine analyses the best choice is to set up your instrument using the Sequence option The sequence provides all of the information TotalChrom needs to acquire and analyze data from a complete set of samples The sequence can e Define when to carry out calibrations e Include unique descriptive and quantitative parameters for each sample e Specify different methods for different samples e Include instructions to run an application program at a specific point in the analytical process For detailed information on building sequences refer to Chapter 11 Building a Sequence Once you decide which Setup option is appropriate for the current analysis you can start the setup procedure Acquiring and Viewing Data 12 3 Setting Up Data Acquisition Using Quick Start gt To use the Quick Start setup type to acquire data 1 If you are setting up an LC and the interface status is Released choose Take Control from the Run menu 2 Select an instrument in the instrument selection panel and click the Setup button to open the Setup Instrument dialog box for that instrument 3 Select Quick Start as the Setup Type Setup Instrument instrument SEQUENCE C PenExe T cwSWer6 2 0 Examples C Take a different path From the default one i Inst Chan User fiti f Storm when read
266. hrough the point you selected In the target chromatogram right click where you want the high voltage to appear and choose Set High Voltage A dotted horizontal line appears through the point you selected In the target chromatogram right click where you want the Low Voltage to appear and choose Set Low Voltage A dotted horizontal line appears through the point you selected Aligning Peaks in Two Chromatograms Halo003 raw ioj x gt To return to the original chromatogram view e To return to the original chromatogram view right click in the reference chromatogram and then choose Clear You can also choose the Defaults button through the Rescale command on the Options menu to restore the chromatograms to their default settings Shifting the Voltage Scale The Shift Voltage command on the Chromatogram pop up menu shifts the voltage range of one chromatogram relative to another chromatogram You select a point on each chromatogram that must be at the same position on the Y axis For example this lets you compensate for different baseline signal levels between two chromatograms gt To align peaks by shifting the voltage 1 Seta high voltage in both chromatograms 2 Right click in the target chromatogram and choose Shift Voltage The target chromatogram is shifted such that the high voltage aligns with the high voltage in the reference chromatogram Displaying Chromatograms 14 25 Aligning Peaks in Two Chromato
267. icon and select an output printer Contact your application manager for information about default and other printers OR e To save a report to a file click the Folder icon to open the Output Selection dialog box Select the type of output file you want RST creates a RD file TC Publisher report file with the same name as the result file File creates a file where the report will be written Output Selection x Dutput File C IDX RST File Tta Dutput Printer HP CLJ 8500 PS HP DeskJet 540 Printer HP LaserJet 4000 Series PS HP LaserJet 5 Xerny NacuTech 9 PS nuk teen Select to choose an output printer When specifying printers for TC Publisher always use the UNC printer name When you choose OK in the Output Selection dialog box TotalChrom inserts the output information that you selected in the Output field on the Optional Reports tab 7 10 Selecting Optional Reports gt To specify plot settings 1 Click the Plot Settings button to open the Plot Settings dialog box Plot Settings x Plot number hd Generate this plot IV Set plot limits to full run Gtert tine min p 00 End time min 20 00 Scaling type Scaling parameters Scale factor fi 000 Vertical scaling C Autozero offset C Absolute scaling teen Plot to receive current plot settings 2 From the Plot Number list select the plot to which you want the cu
268. idual data files by name Batch Reprocessing also gives you five options for starting and ending processing For example you can choose to start reprocessing with peak detection and end with storage of new result files without generating a report or plot Or you can generate a duplicate set of reports without changing the integration This could be used to generate all the reports from a series of runs at a later time Batch Reprocessing is described in Chapter 15 Reprocessing Files in Batch Viewing Chromatographic Data TotalChrom provides two post run graphics functions Chromatograms and Fit Analysis which allow you to view your chromatographic data graphically and perform certain operations on the chromatogram itself The Chromatograms function lets you select multiple raw data files and display them in separate windows or overlaid in the same window You can also change the scaling expand and contract align and label the chromatograms and generate printed plots Chromatograms also lets you perform ratios and differences or add two raw chromatograms and store the result as a new raw data file This function is convenient for subtracting baseline bleed profiles from a stored raw chromatogram You can then re integrate the baseline subtracted raw data and generate new reports Introduction and Overview 1 5 TotalChrom Functions The Chromatograms function is described in Chapter 14 Displaying Chromatograms You acce
269. iguously A single peak component can be a member of more than one named group If you wish you may calibrate the components in a named group individually and report the results for individual components A timed group is a group of contiguous peaks whose retention times fall within a time window which you define TotalChrom can include a peak in a timed group even if the peak is not identified as a component In both named and timed groups each peak is detected and integrated individually TotalChrom calibrates the group independently of its members calibrations the group area and height are the sum of the individual peak areas and heights For more information on developing a component list in the method refer to Chapter 8 The procedure for creating and editing these groups in the Graphic Method Editor is similar to that for single peak components Working with Components gt Tocreate a named group 1 Choose Edit Components from the Calibration menu The Edit Components dialog box appears and shows the options for single peak components 2 Choose Named Group from the Type menu The dialog box changes to reflect the options for named groups ata Graphic Method Editor C PenExe TcCS WVer6 1 0 Examples solvent mth Type Re ldentify Retum Help Group 0 Retn time 0 000 Area Height Name ISTD Group members METHANOL ETHANOL ACETONE T Update calibration twe Amount pon lt iCS
270. ilibration time to use after the first run in the text box 5 To turn the pump off at the end of the run without recycling to initial conditions select Shutdown In Final Conditions Only set this option for a shutdown method which is run as the last cycle in a sequence Changing LC Pump Parameters Graphically As you enter values in the table the gradient curve changes to reflect the new values You can also change the values by dragging the point associated with each step In addition you can add and delete steps from the program by using the Duplicate and Delete buttons in a pop up menu In this section solvents A B and C represent the solvent names that you enter in the Pump Config tab gt To change pump parameters using the gradient curve 1 From the group of available solvents select the solvent whose parameters you want to change The corresponding curve appears for the solvent that you select The curve that you select has small square selection points at the ending time of each program step Developing Instrument Parameters in the Method 6 27 Setting Control Options 6 28 2 Select the point that represents the end of the step that you want to change and then do either of the following e To change the time duration of the step drag the point horizontally e To change the percentage of the total solvent composition drag the point vertically As you drag the point TotalChrom displays a dotted
271. ilter width in milliseconds which smoothes out the detector signal Higher values improve the signal to noise ratio but attenuate narrow peaks Depending on the detector type either set the PMT percentage FPD detector only or enter a gain adjustment value The PMT percentage is the percentage of the maximum photo multiplier tube voltage and sensitivity To make the detector autozero at the start of each run select the On check box for the Autozero option If the Value text box is available enter a value to specify an offset If the Polarity option is available select Positive or Negative If the Filament option is available select On or Off Under Gases specify the gas flow rates for the detector If the instrument 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 in the Attenuation list e In the Offset text box enter the amount by which to offset the analog output for an external recorder Repeat Steps 2 through 10 for the second detector Setting Control Options for LCs If you are using an LC the possible tabs in the Instrument Control dialog box are Autosampler Pump Config Pump Program Detectors Instrument Timed Events This section describes how to complete each tab Because instrument timed events are similar for both GCs and LCs the procedures are combined under
272. imes of your selection not the height Tu z ra AN Wa J Aull 3 Release the mouse button The Noise Area Threshold dialog box opens and TotalChrom draws the baseline drift and RMS baseline noise levels for the selected section Noise Area Threshold x Baseline drift rv min 40 741982 Baseline intercept mv 19 965090 RMS baseline noise pV 260 390975 Current NT 1 Current AT 5 Suggested AT 1302 Cancel Enter the noise threshold 1 to 999999 The Noise Area Thresholds dialog box has the following information and options 10 26 Setting Processing Parameters Baseline Drift The calculated drift slope for the best fit Baseline Intercept The calculated intercept at time 2 0 minutes for the best fit RMS Baseline Noise The calculated noise value root mean squared for the best fit Current NT The current noise threshold level Current AT The current area threshold level Suggested NT The suggested optimum noise threshold Suggested AT The suggested optimum area threshold 4 Make any changes to the values in the Suggested NT and Suggested AT text boxes and choose OK TotalChrom reprocesses the data and redraws the results of the integration based on the new noise and or area threshold levels Editing Methods and Results Graphically 10 27 Setting Processing Parameters 10 28 Setting a New Sampling Rate or Bunching Factor When you develop a method you
273. imizing Data Analyses With Graphic Editing Applications Graphic Method Editing Versus Reprocessing Results Using the Graphic Method Editor Using Reprocess Results Changing Display Options Setting Processing Parameters Working with Components Displaying and Printing Information 10 1 Optimizing Data Analyses With Graphic Editing Applications Optimizing Data Analyses With Graphic Editing Applications 10 2 Method parameters such as integration thresholds timed events and component retention times determine how TotalChrom analyzes raw data When you vary these parameters you can dramatically affect the outcome of an analysis However when you first create a method in the Method Editor it is difficult to estimate what values will provide the best data analysis Sometimes you need to perform an analysis before you can verify the results TotalChrom provides two applications that you can use to optimize the analysis graphically and interactively Graphic Method Editor Use this application to test and change the method by viewing and manipulating the chromatographic display of raw data after a run When you view the data in graphic form you can determine if TotalChrom is detecting peaks correctly placing baselines properly and if expected retention times and search windows for components are identifying peaks accurately If you discover that the analysis is inadequate or wrong you can change the method parameters while viewi
274. in Hands On you are modifying step 0 of the solvent program directly at the pump If you want the pump to return to the active method conditions when you exit Hands On you must repeat the Setup procedure 3 Tochange program settings select one of the following options Continue Resumes the solvent gradient from hold Hold Holds the solvent composition at the current state Advance Advances the solvent program to the next step Reset Resets the solvent composition to the initial conditions Setting LC Parameters The Program options are only available if you have a 200Q 410 pump configured for the instrument 4 Toclose one or more relay s for two seconds make the appropriate selection s under Active Relays El and E2 are not available for all instruments 5 To activate new pump parameters choose Set Pump 6 To start stop the pump choose Start Pump Stop Pump Purging a Pump You can purge an LC system pump remotely from the Purge tab in the LC Hands On dialog box You can change the setpoint then activate it by choosing Set Pump You can start and stop the pump at any time with the Start Pump Stop Pump command LC Hands On x Pump Purge Detector Autosampler r Setpoint r Actual us Set Pump Elow Time min 0 00 C 10024 A Pressure Psi 20 Start Pump Flow mL min 0 00 C 100zB B Comp A 100 0 C 100zC C i uH C 100D D XC 00 C Current Method XD 0 0
275. in how you align peaks by time and voltage The first chromatogram or reference chromatogram is the one to which you want to align peaks The second chromatogram or target chromatogram is the one in which peaks will be shifted Aligning Peaks By Time You can align peaks by time using three procedures e Shifting the time scale e Scaling the time from origin e Scaling time by using two time points as constants Before you can shift the time scale or scale time from origin you must set the end time in the two chromatograms to be aligned Before you can scale time you must set the start and end times in the two chromatograms that you want to compare gt To set start and end times 1 In the reference chromatogram right click where you want the end time to appear and choose Set End Time on the Chromatogram pop up menu A dotted vertical line appears through the point you selected 2 Inthe reference chromatogram right click where you want the start time to appear and choose Set Start Time A dotted vertical line appears through the point you selected 3 In the target chromatogram right click where you want the end time to appear and choose Set End Time A dotted vertical line appears through the point you selected 4 In the target chromatogram right click where you want the start time to appear and choose Set Start Time A dotted vertical line appears through the point you selected Aligning Peaks in Two Chro
276. in testing B 2 printing method and reports B 18 reports B 4 result file list creating for B 16 running automatically B 20 testing definition B 2 window B 8 T T See tangential skim timed event Take Control command 12 24 tangential skim timed event 18 42 tangential skims 18 27 18 42 target chromatograms 14 20 TCR file 20 6 TCR File Warning 20 32 TCSTRUCTURE HLP file 19 3 template appending to sequence 11 49 building a sequence by 11 13 for instrument notes 6 4 6 5 selecting for report 7 9 tests running validation C 14 text files building sequence from 11 52 commands for loading components 8 40 converting files to 19 2 creating comma delimited B 14 creating from report 9 16 16 24 example validation run C 17 format for sequence 11 52 loading sequence information from 11 57 11 58 merging sequence information from 11 58 three dimensional chromatograms 14 8 thresholds 10 26 18 8 18 9 18 15 18 16 Tile Horizontally command 14 7 Tile Vertically command 14 7 time delaying between run start and data analysis 6 9 scaling 14 22 shifting scale 14 21 start stop 14 13 time from origin scaling 14 22 time slice definition A 2 timed events adding 7 8 adding or editing 6 36 changing time or value of 6 37 deleting 6 37 7 8 deleting baseline 10 24 deleting instrument 10 35 descriptions 7 6 editing 7 8 printing 7 14 programming 6 36 selecting 7 6 setting baseline 10 22 setting instrument 10 33 types area threshold 18 15
277. ine which part of the chromatogram and hence the run you will see in the window In the Offset column enter the minimum value that you want to use as the offset in the Y axis The offset is the signal level that appears at the bottom of the chromatogram window as the Y axis minimum The Y axis maximum value is equal to the offset plus the full scale value In the Full Scale column select the cell for the file that you want to change and enter the desired height in mV of the chromatogram The Autoscale button sets the X axis scale to the full run time and the Y axis scale such that the largest peak is full scale The Defaults button sets the X axis scale back to the full run time and the Y axis scale back to the real time plot parameters in the method Choose OK 14 13 Displaying Information in Chromatograms 14 14 Showing and Hiding Coordinates The default display in the status bar shows the Start and End times for each chromatogram However you can change these fields to show the exact position of the mouse cursor on the X axis and Y axis in minutes and mV respectively as you move around in the window gt To show the coordinates of the mouse cursor e Choose Show Coordinates from the Options menu The coordinates appear in the status bar The numbers change dynamically as you move the mouse in the selected window Showing and Hiding Title Bars If more than two chromatograms are open you might want to hid
278. ing to the instrument Detaching TotalChrom is detaching the instrument Seizing The instrument is being seized for control by TotalChrom Links only Releasing The instrument is being released from control by TotalChrom Links only Setting Up The instrument is setting up Pausing The current sequence is being paused Unpausing The current sequence is being unpaused at current row Resuming The current sequence is being resumed from the specified row Clearing Setup The current setup is being cleared Starting Run A run is starting on the instrument Cancelling Run The current run is being canceled and the data is being discarded Stopping Run The current run is stopping and the data is being saved Starting Monitor The instrument is starting in monitor mode Stopping Monitor Monitor mode is stopping on the instrument Stopping Pump The pump is being stopped LC only Binding The instrument is being bound to the user Unbinding The instrument is being unbound from a user Acquiring and Viewing Data 12 41 Understanding Status Messages 12 42 Instrument Messages Line 5 This line displays the status of LINK controlled GC s or of the pump for LINK controlled LC systems For a LINK Controlled GC Equil The GC is equilibrating Hold The GC temperature program is in a hold state Not Ready The GC is not ready Off The GC is off Oven Off
279. ion Use the Derivatization dialog box to program the derivatization operation The options in this dialog box change slightly depending on whether you choose air or liquid as the mixing mode In addition to selecting the mixing mode you also need to use the Entry Table to set values for each reagent you want to transfer to the sample vials For each reagent complete the corresponding row in the Entry Table specifying the location of the reagent vial the volume to transfer and so on When you run the sequence specifying this instrument method the Autosampler transfers mixes and reacts the volumes in every sample vial identified in the sequence Creating Derivatization and Dilution Programs Series 200 Autosamplers Only gt Tocreate a derivatization program 1 Select Deriv under Derivatization Dilution and choose the Program command button to open the Derivatization dialog box m Parameters Mixing mode Ciquid C Air Number of Reagents E Sample volume uL o Mix speed in Medium x Air mix volume po z Mix speed out Medium m r Entry Table Reag Vial Volume JL Mix Cycles Reaction Tim 1 0 0 0 0 00 1 0 0 0 0 00 1 0 0 0 00 1 0 0 0 1 0 0 0 Select liquid mixing mode 2 Select Liquid or Air as the Mixing Mode 3 Inthe Sample Volume text box enter the volume of liquid in the sample vials This volume is the amount of liquid present before the Autosampler transfers
280. ions apply to Auto and Time modes TotalChrom collects apex spectra for the entire run In the End Time text box enter the time at which you want to stop collecting spectra If you later edit the detector program so that the total Detector Time is less than the end time for spectral acquisition TotalChrom reduces the amount for spectral acquisition However if you lengthen the detector program TotalChrom does not increase the spectral acquisition end time To turn the lamp off at the end of the run select Lamp OFF At End Of Run To have the system shutdown at the end of a sequence select this option and then use this method in the last row of the sequence You must also select Shutdown In Final Conditions in the Pump Program tab Setting Control Options Setting 785 Detector Parameters You should periodically perform a wavelength calibration procedure before you set up this type of detector for data acquisition gt To set 785 detector parameters 1 Select the Detectors tab of the Instrument Control dialog box Instrument Control n U 2 Enter a value in whole numbers in the Wavelength box 3 Choose a Rise Time from the list This is the length of time it takes for a step change 4 Enter a value in the Zero Offset box This is the amount the recorder pen is offset from zero 5 Setthe duration of the detector program in the Detector Time box The Program Time displays the duration of the pump sol
281. ironments From Within the Sequence Editor Building a Sequence from a Text File Using Index Files Printing Sequence Information 11 1 How a Sequence Works How a Sequence Works A sequence controls the acquisition and analysis of chromatographic data produced by a series of injections in TotalChrom TotalChrom displays sequence information in a spreadsheet format which consists of one or more columns and rows Columns are the vertical elements of the spreadsheet and rows are the horizontal elements The columns contain the parameters that control the acquisition processing and reporting of the data A row can either specify an analysis or specify an application that TotalChrom will run A row that specifies an analysis is also referred to as a cycle Each cycle contains all the information TotalChrom needs to acquire and analyze data produced by one or possibly two injections With some instruments cycles may contain information that controls two simultaneous injections These are called dual injections A cycle can specify a calibration or an analysis of an unknown sample If the cycle specifies a calibration TotalChrom uses the data from that run to update the calibration data in the method If the cycle indicates the analysis of an unknown sample TotalChrom processes the data from the run using the previously calibrated method to generate quantitative results How TotalChrom Uses A Sequence A sequence enables TotalCh
282. is file is saved in the future 3 If auditing is enabled and you want to enable electronic signature select the Start Electronic Signature check box This will cause the Electronic Signature dialog box to appear every time this file is saved in the future 4 Choose OK TotalChrom Basics 2 9 Using Audit Trail Using Audit Trail The audit trail feature creates a record of the changes made to a file Entries in the audit trail are created e interactively by the user when saving a file e non interactively by TotalChrom when an audited file is updated as a result of background processing such as when a method is updated with a new set of calibration replicates as a result of batch reprocessing You enable auditing on the Description tab in the Documentation dialog box Auditing for a result file is automatically enabled if any of the methods used to create it have auditing enabled Entering Audit Trail Information 2 10 If you previously enabled auditing for a file the Audit Trail dialog box appears every time you save the file or select Save As to save it under a new name The Audit Trail dialog box also appears when you switch between the Method Editor and the Graphic Method Editor even though you may not be saving a file This dialog box cannot be opened manually by any menu command or button Your application manager may have set up the system so that you must select a reason in the Audit Trail dialog box before you
283. is guide Choose The terms choose and select indicate actions that you perform Choose represents carrying out an action associated with a command or command button When you are likely to use the mouse to choose an action mouse specific terms are used such as click right click and double click When you are likely to use the keyboard to choose an action the specific key is mentioned such as Enter or Tab Select The term select refers to highlighting an object or item or moving the cursor 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 box option you activate the option but the function is not carried out until you choose the OK button which closes the dialog box and sometimes completes another operation Enter or select When you use the File Select or File Open dialog box 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 text box 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 Locate and select When you must browse for a file or other entity the term locate and select is used For example in the Sequence Editor certain spreadsheet columns contain cells that you edit by sel
284. is information through the parameters in the Component Defaults and the Components dialog boxes These dialog boxes contain essentially the same parameters parameters that specify how TotalChrom matches components to a peak or peaks on the Identification tab and parameters that affect calibration on the Calibration tab The default parameter values apply to every new component added to the list You can change the values associated with each component individually by choosing the Edit or Add Component command in the Components menu This section describes some of the parameters and concepts you need to know when completing the parameters in the components dialog boxes The procedures for completing the information follow the descriptions starting with Setting Component Defaults on page 8 20 Developing Calibration Parameters in the Method 8 9 Understanding Component Parameters Component Types You can define three types of components in the method peak single peak components named groups and timed groups Single Peak Components The single peak component is the simplest and most common component type This setting identifies a component as a single peak in the run TotalChrom performs a calibration by relating an amount to a single peak response at each level except when you calibrate by reference or a constant calibration factor Components EIEVIGUS 8 10 Understanding Component Parameters
285. is the base file name you enter in the Setup Instrument dialog box plus the MTH extension For a detailed explanation of the Method Editor commands that are available from Setup refer to Chapters 6 and 7 When you use the Quick Method Editor with Quick Start default values are provided for all parameters You need to alter these values so that they are appropriate for your analysis If you set up an instrument using the Method option you can also use Quick Method to modify an existing method gt To use the Quick Method editor 1 Click the Quick Method button Build Buick Method _j Vial List The applicable dialog boxes open in succession 2 Ineach dialog box select the options and enter values that are appropriate for the analysis you are performing and choose OK Acquiring and Viewing Data 12 15 Setting Up Data Acquisition 12 16 When you close the last dialog box the Quick Method Editor summary screen appears showing the principal parameters you set Choose Save from the File menu to save the new method 4 Choose Exit from the File menu to return to the Setup Instrument dialog box in the Navigator Although you can switch to other applications when the Quick Method Editor window is open do not try to re access the Navigator until you close the Quick Method editor Building a Vial List If you are setting up a LINK controlled instrument with an autosampler you must specify the samples to be inj
286. isplay features in TotalChrom r Qu Review Publish or Chromatograms Provides access to additional applications you have installed on your system The commands that appear on the Apps menu will vary depending on your system configuration No Navigator buttons correspond to the Apps menu Apps Menu 4 6 Navigator Tasks and Other Application Tasks Admin Menu Lets you change passwords and access system configuration and administration functions See the Application Manager s Guide for information about commands in this menu No Navigator buttons correspond to the Admin menu Navigator Tasks and Other Application Tasks The Navigator is both an application itself and the main point from which you start other TotalChrom applications Some of the buttons and commands in the Navigator window perform Navigator tasks others start other TotalChrom applications This section differentiates these two aspects of the Navigator providing a table for each Each table visually maps a task to the command that invokes it and directs you to the area of the documentation that describes the task Performing Navigator Tasks To perform this task Use this button or For more information command See Select an instrument E Chapter 2 Instruments Set up instruments for Chapter 12 data analysis View instrument status Chapter 12 Series 200 LC Pump No Method ACQ No Data VF Not Ready CMD None View Status Using The Naviga
287. ith other commands on the Format menu Hiding and Unhiding Columns The Hide Unhide Columns command lets you select which columns to display in a spreadsheet view Columns that are hidden or unhidden are always the same for Channels A and B Editing the Sequence Spreadsheet gt To hide and unhide spreadsheet columns 1 Choose the Hide Unhide Columns command from the Format menu or from the toolbar Hide Unhide Columns Lx r Columns Shown i aT i 4098 ee Study name 3 Name 4 Note 5 Number 7 8 Vial Method 3 Apt Fmt File 10 Data 11 Calib Rpt 12 CalLevel 13 Update RT 14 Sample Amt 15 Int Std Amt 16 Sample Vol 17 DilFactor 18 Multiplier 19 Diwisor E Cancel List of columns shown in spreadsheet 2 Select the column names that you want to hide or unhide and move them to the other list by clicking the appropriate arrow button 3 Choose OK to close the dialog box and redisplay the spreadsheets TotalChrom will save information about which columns are displayed To use the shortcut menu follow one of these steps e To hide columns immediately select the columns that you want to hide and choose the Hide Column command from the shortcut menu e To unhide columns you need not select any columns Choose the Unhide Column command from the shortcut menu and follow the procedure for using the Hide Unhide Columns dialog box Formatting View Tabs
288. itinin renta iskisa ronseis ieina te saaksite eene enne 6 11 Setting Control Options for LCS cece ecsseeecesecseeeecneeeecseeeesaecseesecsesseeeaeeeeaeeaseaeeneeaes 6 20 Setting Instrument Timed Event essere enne enne nennen 6 35 Creating Derivatization and Dilution Programs Series 200 Autosamplers Only 6 37 Setting up a Derivatization eeseseseeeeeesee esee teeth entente tene tant tette SeN Ea RUSE NES 6 37 Setting pa Dilutions eR ERREUR PRA edna I be Pu EE orte EES 6 39 Chapter 7 Developing Processing Parameters in the Method Introduction to Processing Parameters c cccsccesceesseeeeeesceeeceeeceeceseceaeceaecaecaeecaeeeaeeeseeeneees 7 2 Entering Peak Detection and Integration Parameters cescceecceeeceeeceseceeeeneeceeeeaeeeneeeeeees 7 4 Entering Baseline Timed Events eese eene ener enne innen enne 7 6 Selecting Optional Reports einen d egeta e eem teet 7 9 Editing Replot Parameters esses enne nennen nnne enne 7 12 About Scaling Types icr tee ER et tei te RE de oerte ip teg erani eee 7 14 Running User Programs iss aora tnt Do et m ERO Ge IDE boda 7 16 Chapter 8 Developing Calibration Parameters in the Method Introduction to Calibration Parameters eese rennen ener 8 2 Understanding Global Calibration Parameters esee 8 4 Editing Global Calibration Information eese e
289. ive to other columns on the page For a column type that is not currently in the report the default value is the next available column number For a column type that already appears in the report the default is the existing column number If you assign the new column the same number as an existing column TotalChrom automatically shifts the columns to insert it Enter a number to specify the Column Width in characters Editing Report Columns 9 8 If Digits is available type the number of digits you want to display after the decimal point Enter text for the top line of the column name in the Column Label text box A column label can consist of one or two lines of alphanumeric characters The Column Label text box is the upper line If the column label exceeds the number of characters in the Column Width text box the column will expand to the label width 7 Enter text for the bottom line of the column name in the Second Label text box The default format uses the second line for units Select Calculate Total For This Column to include a column total This option is only available for columns that have numeric values Choose Insert Add The new column appears in the report format There are two ways to delete a column from a report format from the Column Information dialog box or by using the Delete Column command in the Edit menu gt To delete a column Click on the column you want to delete and choose Delete in t
290. k Area Pt to Pt 1 0 1 0 Area Height 420120 00 33427 20 BEB R tquared DIETE Pohto PohtFIt No FitCoemokat Response 5 4 Using the Method Editor Method Editor Commands File Instrument Process Components Setup Other View Window Help elal sl S alake Al The Method Editor contains the following menus and commands File Menu Lets you create open save and print method files import the method parameters saved in other files enter and review documentation about a method review method parameters and exit the Method Editor Instrument Menu Lets you define and edit various instrument parameters for a method enter file header information set the scale for the real time plot and define control options for the chosen instrument Process Menu Lets you define and edit processing parameters such as peak detection and integration identify different report formats to use set up replot characteristics and set up user programs Components Menu Lets you set default parameters perform various tasks with components and load and merge the components from text result or other method files Setup Command Lets you switch to the Setup dialog box in the Navigator Other Menu Lets you switch to other TotalChrom applications such as the Graphic Method Editor or the Sequence Editor without returning to the Navigator In addition to showing Help text for each command and field that yo
291. keep them unique Your application manager may have set up your system to append a timestamp to all files 5 Optionally enter or select the Baseline File that you want subtracted from the raw data collected from this cycle 6 If you specified a Baseline file name enter the name of the Modified Data File to be generated TotalChrom creates a modified file by subtracting the baseline file from the raw data file for this cycle If you create a modified data file TotalChrom analyzes the data in this file rather than that in the original raw data file You can collect a data file and use it for baseline subtraction in the same sequence For the first injection enter a file name in the Data File column and leave the Baseline File column empty For the second and subsequent injections specify the Data File file name as the Baseline File 7 If you want to change the current output port settings for this sample select new ports from the Report Device and Plot Device lists 8 If necessary repeat this procedure for the second channel Building a Sequence 11 23 Building a Sequence Vial by Vial Specifying Quantitation Values You complete the Quantitation tab in the Append New Cycles dialog box to set the parameters that relate to sample amounts On this tab you also set the conversion factors that TotalChrom uses to calculate adjusted component amounts from raw amounts gt To enter quantitation information 1 Select the Q
292. l Identification command 10 49 Manual Integration command 10 32 manual integration timed event 18 42 manually drawn baselines 10 32 mathematical operations in reports 9 10 16 19 memory segmentation in interfaces A 7 menu bar 20 17 Merge command 8 40 Merge From Method command 16 10 Merge From Peak List command 10 36 Merge From Result File command 16 10 Merge Text File command 11 58 merging components from files 8 40 messages status See status messages method acquiring data with 12 6 creating 5 6 definition 5 2 18 2 modifying downloaded 13 13 modifying with Quick Method 12 15 preparing IVM C 6 C 12 printing 5 8 referenced in sequence opening 5 7 reviewing parameters 5 7 suitability creating new B 9 modifying B 11 reusing B 11 Method Edit command 11 51 Method Editor commands 5 5 menus 5 5 overview 5 2 windows 5 3 Method Summary window 5 3 Modify Active Sequence command 13 16 Modify Downloaded Method command 13 13 monitor mode 12 30 mouse cursor coordinates 14 14 Move Column command 9 9 16 19 Move command 15 12 Move To Top command 14 17 14 19 N N See negative peak detection timed event Name command 6 2 6 3 Named Group command 10 43 10 44 named group components adding to component list 8 32 creating and editing 10 43 10 44 definition 10 42 setting defaults for new 8 23 Navigator buttons and commands 4 4 tasks overview of 4 7 window 4 3 needle reset by autosampler 13 12 negative amount values 18 74 negati
293. l Options Setting Series 200 DAD Parameters With this detector spectra are collected for the full data run time gt To set the Series 200 DAD detector parameters 1 Select the Detectors tab of the Instrument Control dialog box Instrument Control eee 2 Under Chromatogram Acquisition edit the default monitoring wavelength bandwidth and reference wavelength for each channel as necessary The bandwidth is the spectral window around the wavelength setpoint 3 Under Spectral Acquisition select the mode you want to use for collecting spectra Select Time if you want to collect spectra at regular time intervals 4 If you selected Time above select the interval from the Spectra Period list This interval for spectral acquisition is independent of the sampling rate for chromatogram acquisition Developing Instrument Parameters in the Method 6 35 Setting Control Options 6 36 Setting Instrument Timed Events Use the Instrument Timed Events tab of the Instrument Control dialog box to select one or more timed events from a predefined list and enter the time at which you want the event to take place The events available depend on which instrument you have selected For a 900 Series Interface you can choose events to set relays 1 through 7 on or off Another event RVPRT instructs the interface to read rack and vial information from the attached autosampler at a specified time For information abo
294. l channel acquisition a rate that is evenly divisible into 100 For example 10 pts s is acceptable as entered however TotalChrom changes 12 pts s to 12 5 pts s If your power line frequency is 50 Hz you must enter a sampling rate as follows e for single channel acquisition a rate that is evenly divisible into 50 e for dual channel acquisition a rate that is evenly divisible into 25 If necessary TotalChrom will change your entry for sampling rate to conform to this requirement This is done to prevent the excessive baseline noise that may be produced with certain detector grounding configurations with older generic interfaces 4 Choose OK TotalChrom reprocesses the data and redraws the chromatogram using the new values Changing Peak Separation and Exponential Skim Criteria Peak separation indicates whether a peak is fully resolved from the peaks on either side of it or if it partially overlaps one or both of the other peaks TotalChrom uses two criteria to determine if peaks are separated width ratio and valley to peak ratio TotalChrom uses three criteria to define whether or not to use an exponential skim line to calculate the area of peaks eluting on the trailing edge of a parent peak peak height ratio adjusted height ratio and valley height ratio The Peak Separation Expo Skim command in the Process menu lets you set and modify each of these parameters For more information on each of these options refer to Ch
295. l number still do so after renumbering even if they are not adjacent 7 Editing the Sequence Spreadsheet If there are calibration samples in the sequence and you want to use the same vial number for each occurrence of a particular calibration level select the All Calibrations From One Vial Set check box The vial number associated with the first occurrence of a level will be used wherever that level appears Choose OK Using Smart Fill to Rename Data Files Building a Sequence Many editing operations apply only to the cell you have selected After you insert copy move or delete rows in a spreadsheet it is a good practice to check the accuracy of values in other rows You use the Smart Fill command to rename data files in the same column gt To rename data files l Select all or part of the data files columns Raw Result Data or Modified in the channel for which you want to make changes Select the Smart Fill command from the Change menu or the shortcut menu Starting row fi Ending row 2 Directory Base file name par Starting number fi teen First row to be changed 1 to 2 If you change your mind about the rows to which a change should apply change the value for the Starting Row and or Ending Row If necessary enter or select the full path name of the directory in which to store or search for these files in the Directory text box You need not enter a path name and in normal usage yo
296. l rows will be entered in the sequence based on your entries in the Samples Between Calibrations and Number of Samples text boxes For example if you have four calibration levels and 12 samples and you indicate that you want four samples between calibrations the calibration standards will appear in the rows 1 to 4 9 to 12 and 17 to 20 6 From the First Injection list select the type of calibration that you want to use This defines the type of calibration that TotalChrom will perform on the first injection of each standard level within a set of standards in the sequence Cal Replace 7 Cal Replace Cal verage Cal Bracket Overlapped Cal Bracket NonO verlapped Cal Grand Avg Cal Replace This replaces existing calibration data in the method with new data from the run 11 14 Building a Sequence 10 11 Building a Sequence by Template Cal Average This averages the new calibration data with the existing data in the method Cal Bracket Overlapped A type of bracketed calibration in which the final set of calibrations for one group of samples also acts as the first set of calibrations for the next group Cal Bracket Non Overlapped A type of bracketed calibration in which each group of samples is analyzed with its own set of calibrations Standards are duplicated between sample groups The bracketed calibration types involve using standards both before and after a group of samples to derive the c
297. lains the parameters in the Global Information dialog box The procedures for completing the dialog box follow Volume Units Specifies the units you want to use for sample volume in the analysis These units are for reference only in the method and in reports and do not affect the calculations that TotalChrom performs Quantitation Units Specifies the units used for amounts or concentrations for calibration standards and sample quantitations These units are for reference only in the method and in reports and do not affect the calculations that TotalChrom performs 8 4 Understanding Global Calibration Parameters Sample Volume Specifies the normal sample volume for the calibration standards If the actual sample volume you enter for the calibration cycles in the sequence differs from this value TotalChrom corrects the calibration amount values prior to calibration The term sample volume is used to distinguish this parameter from injection volume which is used for a LINK controlled autosampler Injection volume controls the volume of sample injected into the chromatograph whereas sample volume is simply a correction factor applied to the quantitative results Void Time Specifies the elution time of an unretained peak TotalChrom uses this value to calculate k and relative retention values as follows p peak retention time void time void time peak retention time void time relative retention
298. le runs 12 7 Setting Up Data Acquisition 12 8 11 12 13 14 If Single Run Data Buffering is not selected the interface memory will be divided into segments large enough to store the data from a single run This enables the interface to acquire data from multiple runs even if the Navigator window is closed or the computer is turned off For details refer to Appendix A How Interfaces Collect Data Select Suppress Processing if you do not want to process the data immediately after it is collected This automatically suppresses the data analysis process including the printing of reports and plots and the creation of a result file You may want to select Suppress Processing if you plan to use your computer for another task and do not want to be interrupted by data processing at the end of each run Since data processing is a compute intensive task it can cause your computer to be unresponsive for several seconds as the various data analysis functions are carried out If you suppress processing you can use Batch Reprocessing later to obtain results from the analyses Select Suppress Reports Plots if you do not want to print a report and plot If you do not select this option TotalChrom will automatically print a report and plot at the end of a run To run a program after TotalChrom downloads the method to the interface select Run A User Program After Setup Enter or select the name including the path of
299. lect the one you want to modify from the list and choose OK The method is displayed in the Method Editor window If it is the active method the term Modify Active is displayed in the title bar of the window Modify Active D PENEXE TCCS VER6 0 0 EXAMPLES GASOLINE mth nf x File Instrument Process Components Setup Other View Window Help Al oala Sia ejas alir N Method Summary Instrument Name 950 Sampling Rate 0 402 pts s Experiment Time 120 00 min Voltage Range 1 V Delay Time 0 00 min Channel DA Run Time 120 00 min Replot Pages 1 User Programs 0 Scale Factor 1 000000 Report Files 0 Offset 0 000 mY 25 00 uv Scale 60 000 mv Timed Events 0 Components 16 Volume Units units Unidentified Peaks Named Groups 0 Sample Volume 1 000 Global Calibration Facta Timed Groups 0 Quant Units ng Reject Outliers Calibration EXTD Void Time 0 000 min Outlier Tolerance jWabmED 7 Modifying a Downloaded Method Although you can switch to other applications when you are modifying a downloaded method you cannot re access the Navigator until you close the Modify Active Method Editor window 4 Inthe Method Editor choose from the Instrument Process and Components menus to modify the parameters associated with those menus 5 Save your changes after modifying the method Notice that the Save As command is not available because you cannot save the changes as a new
300. length calibration for a 785 detector and select instruments for display on the primary tab in the Instrument panel Run Button and Menu Using The Navigator The Run button lets you control a data acquisition run It opens the Run pop up menu which is the same as the Run menu The Run commands also let you control single or multiple runs from within TotalChrom and take actions that affect LINK controlled instruments ns RUN 4 5 Navigator Buttons and Commands View Buttons and Menu The Details and Real Time Plot buttons have corresponding commands on the View menu Use these buttons to view detailed information about an instrument during a run and to display a real time plot as an instrument is collecting data Real Time Plot Details The Status and Error Messages commands on the View menu display instrument status and error information Reprocess Buttons and Menu The Results Batch and Summary buttons have corresponding commands on the Reprocess menu Use these buttons to access the Results Batch and Summary Report applications which pertain to data reprocessing functions hill A Results Batch Summary Display Buttons and Menu The Chromatograms Spectra Review or Publish buttons have corresponding commands on the Display menu Use these buttons to access the Chromatograms application the optional LC spectral analysis application and the TC Publisher application These applications pertain to post run d
301. lhng IVM o Sept hotte catia a dep caine Hebr ap M imet bestes C 3 Testing Unipolar and Bipolar Interfaces esee eene C 4 Validation Procedures di eure dicere tete e etre ee RR E EEY C 6 Pr panmeg the Method una been nies Seas BUD DA e nA C 6 Setting Up the Sequence ient toe dete eret ete etienne dee C 12 Running the Test ence a ie rere eet sere e pt tec eden C 14 Example Validation Report skein agna e ERROR RENTUR ER R ER Pi NEE C 15 Validation Specifications ecce tei d rti te p e tco d dieit i ntt C 17 TThe Result File 5 ettet roit N a RES I EP TEES IEEE C 17 The IVM Text File nee eR pe bete EE Rr pO C 17 Troubleshooting iore eie D A ae need oe e Mere ed C 18 How Calculations Are Performed esses C 19 Appendix D Serial Dilution Mixing Volume Rules for Liquid Mixing esses D 4 Glossary Index Table of Contents xiii xiv Chapter 1 Introduction and Overview This chapter provides a general overview of the TotalChrom software and how it is typically used in a laboratory It also describes the contents of the TotalChrom User s Guide discusses conventions used throughout the manual and describes the TotalChrom online help To learn about Go to page TotalChrom TotalChrom Functions Using This Guide The Help System 1 1 TotalChrom TotalChrom TotalChrom is a hardware and software system developed by PerkinElmer to perform the foll
302. lick in it and choose Delete Editing Chromatogram Labels After you create a label you can move it with the mouse edit its text delete it define colors and set the font and other characteristics by using the Labels pop up menu Using the Labels Pop up Menu When you right click in a label the Labels pop up menu opens Delete Edit Text Set Text Color Set Beckaround ol Set Font Drayiborde Move To Top v Link Position to Data 14 16 Adding and Editing Chromatogram Labels The Labels pop up menu has the following commands Gom a Deletes a selected label Edit Text Redisplays the label in an edit box allowing you to enter any text Set Text Color Displays the standard color selection dialog box allowing you to select a color for the label text and border Set Font Displays a dialog box that allows you to select typeface style size and an angle of rotation Move To Top When labels overlap this causes the currently selected label to move to the top of a stack of labels Link Position To Data When you select this option the label will keep the same relative position in terms of the time and intensity axes When you do rot select it the label maintains the same absolute position in the window when you rescale the chromatogram Moving a Label In addition to the tasks that you can perform through the Labels pop up menu you can move a label by using the mouse gt To move a label e Select
303. locity to which the carrier is being changed The initial setting is the pressure flow velocity of the carrier at the start of the run or throughout the run When the Oven program tab is selected this column displays the temperature for the oven Hold column Represents the period for which the pressure flow velocity is held before starting the next ramp 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 You can also adjust the Setpoint Temp and Hold fields by dragging the corresponding points on the curve to the desired position gt To set parameters for carriers configured as a PPC zone 1 Select the Carrier tab of the Instrument Control dialog box Instrument Control x Oven Inlets Carrier Detectors Instrument Timed Events m Program time min A Press H2 20 00 bh oO Oven time 2900 Data end time z00 5 0 100 150 200 250 300 Column Length m ER 00 Rate Setpoint Hold Initial oo 14 0 999 00 Diameter um pa Vacuum comp Off M r Split Control Mode Ratio n 1 2o 0 EowimL mm poo Flow pressure option for Carrer If PPC is disabled for the channel selected in the grid then the Carrier Control drop down list is disabled but the control displays the setting i e Pressure or Flow
304. lot gt To stop a run for the selected instrument e Click the Run button in the Navigator and choose Stop Run from the pop up menu Canceling a Run The Cancel Run command in the Run menu resets the interface to start the run again and discards all data collected up to that point Acquiring and Viewing Data 12 21 Controlling Data Acquisition 12 22 gt To cancel a run for the selected instrument e Click the Run button in the Navigator and choose Cancel Run from the pop up menu When you cancel a run the interface both the 900 Series and LINK will go to the Not Ready state This allows you to correct whatever problem caused you to cancel the run and then restart the instrument To restart an instrument with a LINK controlled autosampler simply choose the Start Run command For a LINK controlled instrument with manual injection starting the next run will automatically restart the instrument and data acquisition To restart an instrument connected to a 900 Series Interface press and hold the Stop button on the front of the interface and press the Start button simultaneously This will set the 900 Series Interface back to the Ready state and you can start the run in the usual way Pausing and Resuming Data Acquisition You can temporarily halt a sequence by choosing Pause Sequence in the Run menu Since Pause Sequence stops data acquisition after the current injection cycle it is only effective in a multi injection
305. ls the vertical position of a chromatogram in the window and is the amount that the bottom of the window is offset from the 0 zero point on the Y axis of the window Multiplier This is the factor by which the data values in plot 2 are multiplied before the addition subtraction or division operation Choose OK TotalChrom calculates the results and displays the new chromatogram in a separate window The operation performed is reflected in the title bar by a or sign between the file names If you save this as a new raw data file that name appears in the title bar and you can process the data in the same way as any other raw data file Calculating a New Chromatogram Editing Calculated Parameters After you create a new chromatogram using the New Calculation Plot command the Edit Calculation Plot command on the Operation menu becomes available To edit the new chromatogram make sure that both source chromatogram files are open If you want to use another file for plot 1 or plot 2 you must open this file gt To edit a newly calculated chromatogram 1 Make the new chromatogram active by clicking inside it 2 Choose Edit Calculation Plot on the Operation menu The Edit Calculation Plot dialog box appears reflecting the values you entered to create this chromatogram 3 Change whichever parameters are necessary including the plots you are using to achieve the results that you want to see in the new chromatogram 4
306. lues in the table or by dragging points on the curve with the mouse You can enter 10 rows or steps in the pump program Step 0 is always the pre run equilibration for which you enter Time Flow and Solvent values The table has the following columns Time The duration of each program step Flow The flow rate during each program step A B C Solvents The percentage of each solvent at the end of each program step D Solvent The percentage of this solvent at the end of each program step TotalChrom ensures that the sum of all solvents used is 100 Setting Control Options Curve The type of gradient curve to use for this program step The types of curve are step 0 linear 1 convex 1 1 to 9 9 and concave 1 1 to 9 9 for increasing solvent percentage The magnitude of the number determines the degree of curvature Developing Instrument Parameters in the Method 6 25 Setting Control Options gt To set pump control parameters 1 Select the Pump Program tab of the Instrument Control dialog box Instrument Control x Autosampler Pump Config Pump Program Detectors Instrument Timed Events GA CB GE Program time 35 00 Detector time Enable solvent saver Shutdown in final conditions Saver equil time min fa 0 Cancel Apply Type of gradient curve to use for this program step convex step linear concave 9 9 9 9 The Program Time field displays the sum
307. lumns labeled Instrument Process and Calibration This allows you to use a different method for acquisition analysis and component information Under Raw Data And Result Files select Same Name or Separate Names When you select Same Name the same base name will be used for both raw and result data files When you select Separate Name you may use different base names for the raw and result data files Choose OK When you are building a new sequence TotalChrom opens the next dialog box e If you selected From Template on the Build Parameters tab TotalChrom opens the Sequence Template dialog box For dual injection sequences you must complete the Sequence Template dialog box for both channels Refer to Building a Sequence by Template on page 11 13 e Ifyou selected Vial by Vial on the Build Parameters tab TotalChrom opens the Append New Cycles dialog box Refer to Building a Sequence Vial by Vial on page 11 17 Building a Sequence by Template e f you select By Worklist on the Build Parameters tab TotalChrom opens the Sequence Worklist dialog box Refer to the Connect documentation for information Building a Sequence by Template Building a Sequence Using a template simplifies the process of creating a routine sequence The template lets you define a structure of calibrations and samples in a single operation The template holds no sample specific information such as sample name you must provide that inf
308. ly the pressure and flow values for inclusion in the instrument s Ready logic You must set the actual pressure and flow rate on the instrument itself gt To set parameters for carriers 1 Select the Carrier tab of the Instrument Control dialog box 2 Enter the pressure or flow rate for carrier A and B in the corresponding initial setpoint cell Enter 0 0 if you do not want the actual pressure or flow setting to prevent the instrument from becoming ready Setting GC Valves You can use the Instrument Timed Events tab of the Instrument Control dialog box to enter the initial settings for any valves installed on the instrument gt To set the valves 1 Select the Instrument Timed Events tab of the Instrument Control dialog box The Valves group box reflects your system configuration Instrument Control a NONE BONE Change sean fe Sonar Sic nra eiu u Setting Control Options 2 Under Valves set the Initial Setting buttons to On or Off for each valve You can set split control by Timed Event For example you can set the split flow to 0 by Timed Events rather than by the SPLI and SPL2 settings Setting GC Detector Parameters You can use the Detectors tab of the Instrument Control dialog box to control the temperature of the detector the sensitivity of detection and the magnitude of any optional analog output from the GC gt To set detector parameters for
309. m assigns it a three digit cycle number starting at 001 and increases the sample number by increments of one The cycle number is added to the base names of the raw data and result files that are created during data acquisition In the Name text box enter the name of the sample to be injected In the Number Pattern text box enter an alphanumeric pattern to define the basic form of the sample number Use characters to indicate the position and length of a numeric string within the sample number Numeric digits can be located anywhere in the sample number The following are valid patterns ABC 2 ABC THHHHE ABCIHHHHEXYZ Use only one set of pound signs A pattern such as ABC DEF will give sample numbers of the form ABCO1DEF because only the first set of characters is replaced by a number In the Actual Number text box enter the value that you want TotalChrom to use in the sample number The default value is the next available number and it will be increased by an increment of one for each new sample in the sequence In the Study text box enter the name of the study to which this sample belongs In the Vial text box enter the vial number from which you want a LINK controlled autosampler to take the injection If you do not have a LINK controlled autosampler this number is informational only The default value is the next available number and it will be increased by an increment of one each time you choose Add I
310. matograms gt To return to the original chromatogram view e To return to the original chromatogram view right click in the reference chromatogram and then choose Clear You can also choose the Defaults button through the Rescale command on the Options menu to restore the chromatograms to their default settings Shifting the Time Scale The Shift Time command shifts the time of one chromatogram relative to another You select a point on each chromatogram that you want to be at the same position on the X axis For example if you know that two peaks appearing at different retention times represent the same component you can shift one to cause both to appear at the same time gt To align peaks by shifting the start time on the X axis 1 Set an end time in both chromatograms Chromatograms Halo_002 1raw of x File Operation Options Window View Help gala He elea m 2e a Mi Halo_001 raw For Help press F1 Start 0 000 End 2 998 Offset 37 036 Scale 915 552 7 Displaying Chromatograms 14 21 Aligning Peaks in Two Chromatograms 2 Right click in the target chromatogram and choose Shift Time The peak in the target chromatogram is shifted along the X axis to align with the peak in the reference chromatogram Chromatograms Halo_004_raw of x File Operation Options Window View Help gem Lia ra efe m 2 r af M Halo_003 raw 4 Halo_004 raw For Help press F1 Start
311. matograms appear on your screen Stack Stacks chromatograms horizontally across the window Each window is displayed at the full screen width but you can view a limited number of chromatograms at a time depending on the resolution of your monitor TotalChrom automatically sets the appearance to Stack when you open 11 or more files in a single operation Cascade Arranges the windows so that they cascade from the upper left to the lower right corner of the screen Tile Horizontally Displays windows horizontally across the screen The first three files will appear at full screen width as in stacked mode If you have more than three files open TotalChrom will divide the screen into two or more columns always making the X axis longer than or equal to the Y axis Tile Vertically Displays up to three chromatograms at full window height side by side If more than three files are open the window is divided into two or more rows of equal width which makes the Y axis longer than or equal to the X axis Automatically Sizing Chromatograms The Auto Size command on the Window menu automatically resizes each window when you change the size of the Chromatograms window or when you open or close a new file The Auto Size command functions as a toggle that you turn on or off it is selected by default and has a check mark next to it If you deselect Auto Size the individual windows do not change when you enlarge or reduce the Chromatogram
312. me to the list for every unidentified peak in the chromatogram These component Working with Components names take the form peak n where n is the index number of the peak TotalChrom bases the index number on the order that it occurs in the run The new component names appear on the chromatogram When you merge or load from component lists TotalChrom creates default component names You can use the Edit Components command to enter new names gt To review and revise component names 1 Choose Edit Components from the Calibration menu to open the Edit Components dialog box atu Graphic Method Editor C PenExe TcCS Ver6 1 0 Examples solvent mth Type Redentify Retum Help 21X Peak 1 Retn time 0 397 Area 322728550 Height 577858 92 M Ref M ISTD Name Reference E ISTD Absolute window s pm Relative window pm Iv Find largest peak in window T Update calibration Reset RT Level a is BENT Calibration type Giver Replace ag Prev Delete L ISOBUT ETHYLA CYCLO CAPenExeXT CCS Ver 1 0 NExamples NS olvOOT raw 9 949 min 620 215 mv 1200 pts Use Next Prev or Retum to accept changes Click on another peak to cancel changes 2 Inthe Name box rename each component as necessary 3 Choose Next or Prev to process the change and to select the next or previous
313. menu bar lets you select the instrument to which it applies afterwards The changes made to the Hands On dialog boxes during a run are NOT made to the method stored in the raw file The icon that appears in the Hands On button in the Navigator changes based on the instrument that is selected The first icon shown below represents a 900 Series Interface The second icon represents a LINK controlled gas chromatograph and the third icon showing a schematic drawing of a pump represents a LINK controlled liquid chromatograph E H w Hands n Hands n Hands On Setting Relays for a 900 Series Interface Setting Relays for a 900 Series Interface With a 900 Series Interface the Hands On dialog box contains a series of relay options which you can turn on or off It also has an option to read the rack and or vial number from an autosampler if one is attached You may access Hands On for a 900 Series Interface when it is in the Ready state gt To change relay settings for a 900 Series Interface 1 Select the interface in the Instrument panel then click the Hands On button in the Navigator Hands n OR Choose Hands On from the Instrument menu then select the interface The Interface Hands On dialog box appears showing the current relay settings When you first set up a method all relays are set to OFF as the default setting iu E Se i CON OFF 2 em gop Beattie 3 CON gam Fasi 4 eu gu A 9 5 CON
314. meters 7 4 18 6 procedures 18 6 18 23 relationship to timed events 18 15 height ratio definition 18 28 heights calculating 18 44 integration parameters 7 4 integration definition 18 3 list definition 10 36 retention times calculating 18 44 compensating for shifts in 8 13 hiding or showing 14 14 separation criteria changing 10 30 definition 10 30 overview 18 14 Index width for acquired data 6 7 peak detection timed event 18 16 peak end detection timed event 18 20 Peak or Component Properties 78 Peak Report command 10 51 10 52 Peak Separation Expo Skim command 10 30 10 31 Peak Table 20 92 peaks aligning by scaling time 14 22 by scaling voltage 14 26 overview 14 20 scaling time from origin 14 22 scaling voltage from origin 14 26 shifting time axis 14 20 14 21 shifting voltage axis 14 24 shifting voltage scale 14 25 child and parent 18 28 creating and editing timed groups of 10 45 detecting and integrating 10 22 finding end of 18 13 forcing daughter 18 22 identifying 10 39 10 49 identifying as correct run component 10 47 integrating 18 24 18 26 locating top of 18 12 merging list with component list 10 36 naming unidentified 10 36 optimum number of 18 6 overlapped 18 14 preventing undetected 18 38 quantifying unidentified 18 78 re identifying 10 41 relationship to search window 8 13 selecting for identification 10 36 separated 10 31 18 14 shifting 14 20 Peltier Tray temperature 6 23 plot See also chromatogram
315. method 6 Close the Method Editor window to return to the Navigator The Status box will display different messages based on the instrument you are using While are you modifying the method the instrument state will be Paused Working with Instruments Interactively 13 15 Modifying a Sequence During a Run Modifying a Sequence During a Run The Modify Active Sequence command in the Navigator lets you change sequence information while a run is in progress The Active Sequence command is available from the Modify button and from the Instrument menu once you set up and bind an instrument Modify Active Sequence pauses the current sequence and opens a limited version of the Sequence Editor TotalChrom does not resume the sequence until after you have finished editing it If you have multiple instruments set up and bound Modify Active Sequence works like other functions in TotalChrom the button applies to the instrument currently selected in the Navigator Choosing the command from the menu lets you select which instrument you want to use afterward If you change the sequence either before or after a run the interface will change to Not Ready until you finish editing the sequence You can edit the rows representing future or past runs and append or insert as many rows as you wish Changes affect only future injections Because you can modify completed rows you cannot use the sequence file as documentation for a series of runs
316. mmand 10 33 10 34 10 35 Instrument Status window 12 37 instruments See also instrument breaking communication with 12 24 configuration options for A 4 configuring 3 4 3 8 controlling when released 12 24 re establishing communication with 12 24 releasing control of 12 23 selecting 2 15 viewing detailed information about 12 34 viewing detailed status of 12 32 Integration command 7 4 integration parameters 7 4 interface function of A 2 memory types A 7 performance validating for 900 Series interface C 2 status messages 12 40 Interface Validation Module calculations overview C 19 error conditions in C 18 gain errors in C 20 installing C 3 IVM file extension C 17 IVM EXE file C 3 IVM MTH file C 2 IVM RPT file C 2 IVM SEQ file C2 C 12 linearity errors in C 20 overview C 2 preparing methods with C 6 report sample C 16 running tests in C 14 sequences setting up C 12 C 13 standard deviation gain errors C 22 test methods C 10 test plots C 19 text report file C 2 validation procedures C 6 validation specifications C 17 internal standard amounts correcting 18 54 18 69 overview 18 52 calibration 8 5 17 8 18 50 components defining 8 14 IPMs See instrument personality modules ISTD See internal standard IVM See Interface Validation Module L labels absolute positioning of 14 19 adding 14 4 14 16 configuring 7 13 14 16 14 18 deleting 14 17 displaying hidden 14 19 editing 14 16 14 17 linking to data 14 19 moving
317. mmands on the Options menu allow you to control what types of information appear in each window Instructions for using these commands follow this list Command Rescale Expand All Plots Show Coordinates Show Title Bars Show Axes Show Baselines Show Components Show Retention Times Action Lets you change the start time end time offset and full scale by a specific amount for multiple files at one time instead of by changing them individually within each window Expands the display of individual chromatograms or expands all chromatograms simultaneously by the same amount Shows and hides the coordinates of the cursor in the active chromatogram This command does not apply to overlaid chromatograms Shows and hides the title bars of all open chromatograms Shows and hides the X and Y axes coordinates of all open chromatograms For result files displays and hides the baselines for each chromatogram For result files displays and hides the component names for each chromatogram For result files displays and hides the peak retention times for each chromatogram Expanding Chromatograms You can expand or zoom the display of individual chromatograms or expand all chromatograms simultaneously by the same amount by using the Expand All Plots command on the Options menu This command works whether your windows are cascaded stacked or tiled TotalChrom does not save expansions when you exit the
318. must be between 2 and 40 characters 4 Enter a value in the first empty cell in the Amt column You do not need to enter an amount of more than zero when you set defaults Do this only when you add components to the list The value displayed in the Area Height column is grayed out because it is not relevant for default components TotalChrom adds a new row to the table after you complete the columns for the current level 5 Repeat Steps 2 to 4 to add additional levels 8 26 Setting Component Defaults Setting User Value and LIMS Defaults You can use the User Values LIMS tab to e Specify a number of default constants associated with a default component type e Setup a default for SOL LIMS reporting if you have Connect You can specify default constants and then use these values in custom expressions which you create in the Report Format Editor For example you can multiply the peak area or the peak concentration or other value by a constant factor for each individual component You are more likely however to enter constants as you add each component rather than entering them as defaults gt To set default user values for components 1 Select the User Values LIMS tab of the Component Defaults dialog box Component Defaults x Identification Calibration User Values LIMS User label fl m User Values 2 ox omo o9o ommo kn du lw Send results for this component to
319. n Disable negative peak detection Inhibit end of peak detection Allow end of peak detection Turn on non forced common baseline Turn off non forced common baseline Force the end of current peak Force start of new peak Force baseline to current point Entering Baseline Timed Events Force horizontal forward baseline DE Deremate oe ertet MR Siar manoa merasa wmo _ End manual integration window M Turn on valley to valley baselines Fromottaesnvateybesines Proce an eonenna if eewwsewwasm X mwsewmenam OO i Smoon rems 5 wwmareor S4 Force retention time of current peak to be RT the event time Locate peak retention time at the LM maximum data point Force a baseline at any point in data file JU Developing Processing Parameters in the Method 7 7 Entering Baseline Timed Events gt To add timed events 1 Choose Baseline Timed Events from the Process menu to open the Process dialog box with the Baseline Timed Events tab selected Integration Baseline Timed Events Optional Reports Replat User Programs Time min p 000 Add Event Set Bunching Factor BF m Deee Replace Yalue le Clear List m Defined Events Time Event Value Code Level dl Set Bunching Factor 1 5 000 iy Set Noise Threshold 1 NT Correct actual times of all baseline events based on actual RT of nearest reference peak
320. n the Of Cycles text box When you are creating a new sequence start by adding data for the first injection cycle Cycle 1 As you add each cycle TotalChrom assigns it a three digit cycle number starting at 001 and increases the sample number by increments of one The cycle number is added to the base names of the raw data and result files that are created during data acquisition 3 In the Instrument Method text box enter or select the name of the method file that contains the instrument parameters that you want to use You can enter the name of a method that does not yet exist as long as you create it before you run the sequence 4 Select Channel A or Channel B 11 20 Building a Sequence Vial by Vial 5 In the Name text box enter the name of the sample to be injected 6 Inthe Number Pattern text box enter an alphanumeric pattern to define the basic form of the sample number Use characters to indicate the position and length of a numeric string within the sample number Numeric digits can be located anywhere in the sample number The following are valid patterns ABC 2 ABC THHHHE ABCIHHHEXYZ Use only one set of pound signs A pattern such as ABC DEF will give sample numbers of the form ABCO1DEF because only the first set of characters are incremented 7 Inthe Actual Number text box enter the value that you want TotalChrom to use in the sample number The default value is the next available n
321. n Graphic Method Editor eese 10 9 Using R process Results 2 2 trt ROREM eco d 10 10 Understanding the Reprocess Results Window eese 10 11 Loading Files in Reprocess Results eese enne 10 12 Saving Files in Reprocess Results eese eene nre 10 13 Changing Display Options eseeeeseeeeseeeeeeen eene ennemi nee nr enne nne 10 14 Changing the Plot Display orem Rh 10 14 Changing the Plot Scale cheeses ett det e tee eate 10 14 Expanding Chromatograms eese eren eene nre nren etre enne netten 10 15 Manipulating the Reference Chromatogram esee 10 19 Hiding or Showing the Reference Chromatogram eeeeeeeeeee 10 19 Setting Processing P r meters 5 iot ei RAPERE RR REPE OPERE 10 20 Setting Baseline Timed Events esee eene nennen ener 10 20 Setting Noise and Area Threshold enne 10 24 Setting a New Sampling Rate or Bunching Factor eere 10 26 Changing Peak Separation and Exponential Skim Criteria esses 10 28 Drawing the Baseline Manually eese enne eterne 10 30 Setting Instrument Timed Events Graphic Method Editor Only 10 31 Working with Components serrer ori e Seese nnen nennt ener enne nnenne nnne ennt ennt 10 34 Using the Calibration Commands in the Graphic Method Editor
322. n enables you to display more detail than if you print the replot on a single page This option is only available if you select Generate A Separate Replot 4 To print two plots with different scale factors on the same page select Generate Second Plot and then enter a Scale Factor for the second plot All other replot parameters are shared between the two plots 5 Under Orientation select Portrait or Landscape Portrait Prints the plots so that the X axis spans the width of the page Landscape Prints the plots so that the X axis spans the length of the page 6 Under Retention Labels select a label position option Labels do not overlap if you place them at the top of the plot If they are close enough to overlap some labels will be omitted All labels at the tops of peaks are shown even if they overlap 7 Under Component Labels select an option to specify how you want component names to appear on the replot None Suppresses all component names on the replot Expected Time Includes the names of all expected components on the replot whether or not a corresponding peak is present The component name appears at the expected retention time for the component Actual Time Positions component names under the corresponding peak at its actual retention time If no peak corresponds to an expected component the component name does not appear on the replot 8 Under Miscellaneous do one of the following e To print
323. n the Delay Time text box enter the number of minutes that you want to elapse between the start of the run and when peak detection starts 6 Inthe Run Time text box enter the number of minutes that you want the interface to collect data Note that TotalChrom will not allow the delay time to be greater than the run time 7 Choose OK Developing Instrument Parameters in the Method 6 9 Setting the Real Time Plot Scale Setting the Real Time Plot Scale The Real Time Plot Scale command in the Instrument menu lets you set the scaling parameters that appear in the Real Time Plot window When you acquire raw data TotalChrom uses the scaling parameters in the instrument section to draw the real time plot To view this plot during data acquisition click the Real Time Plot button in the Navigator 6 10 gt To set real time plot parameters 1 Choose Real Time Plot Scale from the Instrument menu to open the Data Acquisition dialog box with the Real Time Plot tab selected Data Acquisition x Data Channels Real Time Plot Channel Offset mV Full scale mV 000 000 Number of pages fi teca Signal level at the Y axis minimum 1 000 000 to 10000 000 The Real Time Plot Scale tab shows the settings for Channels A and B Depending on the type of instrument that you have chosen the units for the plots will be either millivolts mV or milli absorbance units mAU In the Offs
324. n the instrument method column GPCCal Average and GPCCAL Replace Used with the optional TurboSEC application In TotalChrom these function like sample types See the TurboSEC documentation for more information General Procedure for Building a Sequence Building a Sequence The following is the general procedure for creating a new sequence Specific procedures for the dialog boxes referenced in this procedure are provided later in this chapter You can also create a new sequence by editing an existing sequence file and renaming it with the Save As command 11 9 Using the Sequence Editor gt To create a new sequence 1 Do one of the following e In the Navigator choose Sequence from the Build menu or click the Sequence button select Create New Sequence in the Startup dialog box and choose OK Your application manager may have disabled the display of the Startup dialog box e Ifthe Sequence Editor is already open choose New from the File menu 2 Complete the dialog boxes that are displayed Global Parameters and either Sequence Template or Append New Cycles or Sequence Worklist Instructions for completing these dialog boxes appear later in this chapter Instructions for the Sequence Worklist dialog box are in the Connect documentation 3 When the spreadsheet windows for Channels A and B open you can edit data and change the appearance of the spreadsheet Refer to Editing the Sequence Spreadsheet on page 11
325. nable the Fixed Mode option where the injection volume is equal to the loop volume select a Loop Size value less than 50 uL 5 To operate in Fixed Mode set the value of the Fixed Mode list to On This option forces the Injection volume to be equal to the loop volume Fixed mode is useful if you are working with small sample sizes or applications that require high precision You can only use Fixed Mode when the Loop Size value is less than 50 uL Developing Instrument Parameters in the Method 6 21 Setting Control Options 6 22 10 11 12 In the Excess Volume text box enter the amount of sample that you want withdrawn from the vial in addition to the injection volume This option prevents evaporation and contamination by isolating the actual plug of sample to be injected as it is transported to the injection loop This option is only available if Fixed Mode is set to Off In the Air Cushion text box enter the amount of air that you want to insert between the sample and flush solutions to prevent the two solutions from mixing From the Sample Syringe Size list select a syringe volume From the Sample Speed list select the speed at which you want the sample pump to fill the injection loop Slower speeds provide more reproducible injection volumes particularly for viscous samples From the Needle Level select the appropriate percentage This value sets the height at which the sampling needle extracts the sample
326. name in the list 4 Choose Return when you are done Editing Methods and Results Graphically 10 37 Working with Components Editing Component Information The Edit Components command in the Calibration menu of the Graphic Method Editor lets you e Assign a component name to a previously unidentified peak e Change the association between peaks and components re identify peaks e Update the calibration level and amount for a component e Define or specify components as reference components or internal standards e Define and modify single peak named group and timed groups components e Display or change search windows gt To open the Edit Components dialog box e Choose Edit Components from the Calibration menu to open the Edit Components dialog box ta Graphic Method Editor C PenExe TcCS WVer6 1 0 Examples solvent mth Type Re ldentify Retum Help 21x Peak 1 Retn time 0 397 Area 3227285 50 Height 577858 92 Iv Ref M ISTD Name d Q z 5 E 2658 59 R g 8 9 MES mom Y 5 5 3 Refeence id ISTD Absolute window s 5 00 Relative window 2 5 00 Iv Find largest peak in window T Update calibration Reset RT Hn Level Y Amount 0 0001 Calibration type i GL Oirizubeg Prev Delete JN ip mEI T sees Pu i d 44 3 i j 4 E BOW a2 98 E E 1 eo P 5 Eos CAPen
327. nces such as whether or not to display the reference chromatogram in the Graphic Method Editor define a set of often used paths for quick access to files select the reporting program to review your data and set a Project Directory User options apply only to the local TotalChrom workstation The Fonts dialog box lets you choose the typeface style and size of text that will appear in different TotalChrom functions such as reports the user interface and displayed and printed plots The different TotalChrom functions are listed in the Select Font For selection box Typefaces font styles and font sizes are limited by the capability of the target printer or plotter For example only printers and plotters that can scale fonts produce labels that match non default requested sizes Wherever possible TotalChrom uses default printer fonts gt To select a font 1 Choose Fonts from the User menu Fonts Lx Font Font Style Size T n OK arial Regular fio a ES ES Cancel Courier Italic 1 ee T Courier New Bold 12 Apply ol Fixedsys ZI Beda H ha m Sample AaBbYyZz Select Font For Report Print normal b 2 Select where you want to use the font in the Select Font For selection box 3 Select a font style and size of text 4 Choose OK Choose Apply to make the changes and select other fonts without closing the dialog box 3 17 Configuring User Options Colors The Colors dialog bo
328. nd in the File menu This command opens each of the method dialog boxes in succession allowing you to easily review and edit parameters gt To review all of the parameters in a method 1 2 Building a Method Choose Review from the File menu For all dialogs boxes other than the Instrument Name dialog after reviewing or making any changes in each dialog box choose Next to go to the next dialog box in the series or Back to go to the previous one 5 7 Printing Method Parameters Printing Method Parameters 5 8 You can print either the specific parameters from a method file or the summary information for a method by using the File menu Print Print Preview or Print Summary commands Two print related dialog boxes will appear when you select Print one for method parameter options and one for standard Windows printing options gt To print the parameters from the method 1l Choose Print from the File menu to open the Print Options dialog box CU ES I Instrument Parameters I Processing Parameters I Calibration Parameters M Level Lists I Replicate Lists zu 2 Selectthe data you want to print and choose OK 3 Make any changes in the Print dialog box and choose OK gt To print summary information for a method 1 Choose Print Summary from the File menu to open the Print dialog box 2 Make any changes in the Print dialog box and choose OK Importing Method Parameters Importing Method Parame
329. ndex File eese eene 15 4 Reprocessing Sequentially Named Data Files serene 15 8 Reprocessing an Individual Data File essent 15 10 Using the Control Buttons During Interactive Reprocessing eseeeeeeee 15 12 Chapter 16 Summarizing Component Data Using Summary 5 5 Aot o qiie rela o RD re te He e iR RR 16 2 Summarizing Results iro tete Died erf ar eene Henr Het adler 16 3 Developing the Result FUE List nite ed tp e Re EE E ntt 16 4 Creating Editing a Component List Manually eese 16 9 Selecting a Summary Report Format essere eene nenne 16 11 Printing a Summary Report eese eene entren nennen trennen 16 11 Using the Summary Report Format Editor esee 16 12 Summary Report D t p eene gare dense ca ied 16 12 Menus nd Commands uote ent eg ee pdt H 16 13 General Procedure for Creating a Summary Report Format esses 16 13 Creating Title Header and Footer Text esee eene 16 15 Editing Report Columns e esei naea nee nee nenne neen nennen ne enne 16 16 Creating a Custom Expression eesseeseeseeeeeeeeen eene enne enne rennen innen enne 16 19 Editing Summary Report Options essent 16 23 Printing Summary Report Format Information eese 16 24 Automating Summary Reports eiernes tenerent eene etre
330. ndow to return to the Setup Instrument dialog box Controlling Data Acquisition Controlling Data Acquisition You control data acquisition by using the commands in the Navigator Run menu which appears as both a drop down menu in the menu bar and as a pop up menu from the Run button The procedures for using the Run commands are fundamentally the same for both menus but the dialog boxes displayed depend on how you choose the command e If you choose the command from the menu bar you must then select the instrument you want to control e Ifyou click the Run button the command affects the instrument currently selected in the Navigator The procedures appearing later in this section to explain specific Run commands assume you are using the Run button s pop up menu The Run menu includes commands that affect single runs as well as an entire sequence It also includes commands that affect the status of 900 Series Interfaces and LINK controlled instruments You may also control data acquisition from within the Real Time Plot window This enables you to perform an action while simultaneously viewing the incoming data for the instrument you select For more information on viewing the real time data refer to Viewing Real Time Plots on page 12 26 gt To choose a Run command for the active instrument 1 Select the instrument from the instrument selection panel in the Navigator 2 Click the Run button in the Navigator This displays t
331. nel shows up to eight configured instruments to which you have access Instrument Selection Clarus 1 Selecting an instrument in the Navigator sets the entire Navigator to reflect the status of that instrument The Status button shows current data for the instrument and if you start a TotalChrom application it will open with that instrument as the focus For example if you click the Real Time Plot button any plots that appear will reflect activity at the selected instrument TotalChrom Basics 2 15 Using TotalChrom Toolbars and Status Bars Using TotalChrom Toolbars and Status Bars 2 16 Many TotalChrom applications have 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 button as well as a definition in the status bar at the lower edge of the window A status bar appears at the bottom of many TotalChrom windows and dialog boxes The status bar 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 In dialog boxes it displays field lengths and allowable values that you can enter for the selected field The status bar is displayed in dialog boxes and is displayed by default in application windows Some applications let you hide the main status bar by choosing the Status Bar command on the View menu Chapter 3 Configuring TotalChrom This chap
332. ng the chromatogram and see the effects of the change immediately Reprocess Results Use this application to change a result file and view the outcome instantaneously in order to find the optimal parameters for a particular analysis You can use Reprocess Results to fine tune parameters for a specific run even after you have optimized the parameters in a method to produce satisfactory analyses in the Graphic Method Editor The primary difference between Reprocess Results and the Graphic Method Editor is that with Reprocess Results you only change the result file not the method The method you are modifying in Reprocess Results is not the method file itself but a copy embedded in the result file when TotalChrom generated it Graphic Method Editing Versus Reprocessing Results Graphic Method Editing Versus Reprocessing Results To edit a method in the Graphic Method Editor you specify a raw data file representing a chromatogram of the analysis you want to optimize TotalChrom processes the raw data with the method and displays the chromatogram showing the resulting integration and peak identification You can change the parameters in the processing and calibration sections of the method until the parameters produce the results you want At this point you can save the optimized analysis of the raw data in a result file and save the modified method file under the same name or give it a new name With the Graphic Method Editor you can als
333. nge for overnight runs Day of year at set up does not change for overnight runs Month of setup does not change for overnight runs Using Common Dialog Boxes The format of the date related items when resolved is numeric with the year given as four digits The Separator selection defines what character is to be inserted between tokens added to the token string Note that the separator is only added when another token is chosen This is in case the user wants to add some literal text to the string The separators the user may select from are _ underscore the default space hyphen plus equals and none The Clear button erases the current token string The Raw Data File name is shown in its tokenized form as it is constructed The label on that field is changed appropriately with the file type being defined After adding a token the cursor remains at the end of the field This is done to make it easy to add literal text to the name if you wish to do so For this reason the file number suffix will not be shown in this dialog The suffix token is appended only after clicking OK and return to the Default Paths Base Names Default Paths Base Names E xi Data paths Raw data path CAPenE xe TcWS WerB 3 0 Examples Result files path C APenE xe T cw Werb 3 0 Examples Use instrument default paths instead of these paths This user is required to use the default path or su
334. nit Set 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 Actual The current actual flow Ready Whether or not the split flow zone is ready Pump Program LC only Time The duration of the pump program step in minutes Flow The solvent flow rate during the pump program step in mL min A The percentage of solvent A at the end of the pump program step B The percentage of solvent B at the end of the pump program step C The percentage of solvent C at the end of the pump program step D The percentage of solvent D at the end of the pump program step Curve The type of curve used for the pump program step Pump Status Current state of the pump ON or OFF Pump Time During a run the elapsed time into the current pump program step Outside a run the length of time the pump has been ready equilibrated Understanding Status Messages Understanding Status Messages Use the Status command in the Navigator to view the general status of all instruments currently configured on your system gt To view the status of all instruments on your system 1 In the Navigator choose Status from the View menu or click the Status button The Instrument Status window opens listing each instrument configured on your system its location and its current status Instrument 5 ow
335. nnel analyses only use calibration values determined in single channel calibrations You develop and modify calibration parameters using the commands in the Components menu in the Method Editor Global Information command Lets you define global component values for all components or unidentified peaks in the method Also gives you access to functions needed for use with Connect Defaults command Lets you set the default values that TotalChrom provides when you add new components to a method New Component command Lets you add a new component to the method This includes entering component identification information and setting the calibration parameters you want to use Also gives you access to functions needed for use with Connect Edit Component command Lets you edit the currently selected component Calibrate command Lets you update the calibration information in the method using response values from result files Introduction to Calibration Parameters Change Component Info command Lets you change component identification parameters for a range of components Change Calibration Info command Lets you change calibration quantitation parameters for a range of components Delete Component command From the Component List window lets you delete an individual component from the component list Delete All Components command From the Component List window lets you delete all components levels and
336. normalization factor This represents the normalization percentage if you want to report results as normalized concentrations 10 If necessary repeat this procedure to set the sample values for the second channel Building a Sequence 11 25 Building a Sequence Vial by Vial Specifying Calibration Parameters You complete the Calibration tab of the Append New Cycles dialog box only if you selected one of the calibration options from the Type list on the Identification tab gt To enter calibration information 1 Select the Calibration tab of the Append New Cycles dialog box and select Channel A or Channel B Append New Cycles 2 Select a Calibration Level The choices come from the calibration method indicated on the Files tab 3 Select the Calib Report Length option that you want to use Short Provides a summary of the current calibration status for each component Long Includes the amount and response data for components in the run None Provides no calibration report 11 26 Editing the Sequence Spreadsheet 4 Selectan option from the Update RTs Retention Times list Yes Updates the expected retention times for components in the method using the actual retention times obtained during the calibration run No Does not update the expected retention times for components in the method The list in the Update RT column of the spreadsheet has a third option Replace but because you
337. ntly Edited File Activates the selection box where you can select and open a file with which you recently worked Clear MRU List Clear the list of the most recently used files Using Common Dialog Boxes File Open and File Select Dialog Boxes The File Open dialog box allows you to open an existing file in order to edit it rename it or use it as a template to create a new file similar to the existing file This dialog box opens when you choose Open from the File menu In many TotalChrom dialog boxes there is a folder icon next to an edit box that requires a filename or path Clicking the icon opens a File Select Path Select or Program Selection dialog box Sequence D PenE xe T CS Wer6 0 0 Examples G asoline seq Default Data Path D PENEXE TCCS WERG 0 0 EX4MPLES The File Select dialog box allows you to select a file such as a method file that TotalChrom will use during its operation for later use This dialog box opens when you click the folder icon next to an edit box that requires a filename TotalChrom File Open 2 x Look in C3 Examples J e ek E3 lAcaClient Interface Info E GASOLINE MTH E svs QUAT MTH p EI HS40TEST MTH TEST1 MTH amp j IvM MTH 2 TEST2 MTH NOISE MTH i TESTPLOT MTH 2 SOLVENT MTH E TurboMatrix 1 mtl SYS BIN MTH H Files of type Method Files mth Cancel Quick paths C PenExe TcwS Wer6 3 0 Examples 7 Header lt lt Method 5 File Header Inf
338. ntrolled autosampler you may want to set up the instrument before you have finished preparing the samples and placing them in the autosampler This allows the instrument to equilibrate If you did not select the option Start Run When Ready in the Setup Instrument dialog box the instrument will remain in the Ready state until you choose Start Run Alternatively if you have everything already prepared you can check Start Run When Ready in the Setup Instrument dialog box and the Start Run command will be issued automatically as soon as all parts of the instrument become ready 900 Series Interfaces For a 900 Series Interface the Start Run command causes the interface to begin collecting data immediately Normally you will only want the interface to begin collecting data when a sample has been injected at the chromatograph Therefore the usual procedure is to use a relay from the chromatograph or autosampler to trigger the start input on the 900 Series Interface rather than choose the Start Run command from within TotalChrom Controlling Data Acquisition LINK Controlled LC Pump Modules Without Autosamplers If you are using a LINK controlled LC pump module without an associated autosampler the Start Run command will begin the pump program starting with the equilibration step If the pump is off when you choose Start Run the pump will first be turned on The normal procedure is to inject the sample and press the run button on the pump whi
339. o change column width with the mouse 1 Position the cursor over the right border of the column header whose size you want to change it will become a sizing cursor Drag the cell border to the right or left to increase or decrease its size All other columns retain their size If you want to apply changed column widths to the other channel choose the Synchronize Column Widths command from the Format menu If you use the Column Width command you can select either the number of characters you want columns to contain or you can configure the width to correspond with the longest entry in each column gt To change column width with the Column Width command 1 2 Select the columns that you want to resize Choose Column Width from the Format menu or the shortcut menu Column Width x Column width E Fitto contents IV Set other channel to the same width teca Enter width of column in characters 1 to 255 If you want the selected columns to contain a specific number of characters enter a value between 1 and 255 in the Column Width text box TotalChrom limits the number of characters that you may use in many columns but you may make such columns wider if you wish Or if you want the column widths to correspond to the longest entry in each column select the Fit To Contents check box This selection overrides any value in the Column Width text box If you want the column widths to be the same for bo
340. o edit instrument timed events graphically but these events have no effect on the data being reprocessed When you reprocess results however TotalChrom draws a chromatogram based on the result file you select and the raw data file that TotalChrom analyzed to produce the result file Again you can test different parameters to view the results When you produce an optimal analysis of the raw data you can save the new results in the result file or save them as a new file Thus the goal of reprocessing results is to improve the results of a single analysis When you close the Reprocess Results window after changing the result file TotalChrom asks if you want to save the modified result file because you are not saving changes to the method itself The first two sections of this chapter explain how to open and get started with the Graphic Method Editor and Reprocess Results applications The rest of the chapter explains how to perform the different tasks With the exception of calibration and component tasks in the Graphic Method Editor the procedures for both applications are identical Thus the common tasks are combined and most figures use the Graphic Method Editor as a representative example Editing Methods and Results Graphically 10 3 Using the Graphic Method Editor Using the Graphic Method Editor You can open the Graphic Method Editor from either the Navigator or the Method Editor gt To open the Graphic Method Editor 1 Do one
341. ocessing batch controlling files during 15 12 xiii definition 15 1 index or sequence files 15 4 Rescale 115 Rescale command 12 28 12 29 14 11 14 13 14 21 14 25 Rescale Plot command 10 16 Reset LINK command 3 15 Reset Run Counters command 3 15 response methods of plotting 17 8 options overview 8 16 ratios definition 8 5 8 14 values definition 17 6 solving for 17 11 result file list for Suitability calculations building B 16 editing B 17 printing B 18 for Summary report creating by base file name 16 4 creating from sequence file 16 6 creating or editing manually 16 8 overview 16 4 result files definition 18 2 summarizing in report 16 2 results sending to SQL LIMS 8 19 Resume command 15 13 Resume Sequence command 12 22 retention time 8 14 14 15 18 13 retention time data updating 18 55 retention time timed event 18 22 Return command 10 23 10 34 10 39 10 51 10 52 Review and Approve levels 20 10 Review command 5 7 RST See result files RT See retention time timed event Run counters resetting 3 15 resetting all 3 15 run logs 6 7 runs canceling 12 21 canceling reprocessing 15 13 stopping 12 21 S S See start new peak timed event sample identifying in sequence 11 18 notes 11 45 numbers defining 11 15 11 19 11 21 incrementing 11 38 volume parameter definition 8 5 Sample Fill In 11 44 Sample Note command 11 45 sampling needle adjusting 13 12 sampling rate setting 6 7 6 8 10 28 Sampling Rate
342. oded yellow columns must have the same value blue columns can have different values For the special case of a dual injection sequence all parameters can differ for the two channels except the instrument method For a description of the columns in the Sequence spreadsheet see page 11 6 Using the Sequence Editor Using the Sequence Editor You use the Sequence Editor to create new sequences and to modify existing sequences You can create new sequences by e Building a new sequence using a template e Building a new sequence vial by vial e Building a new sequence from an existing sequence file by editing and renaming it e Building a new sequence from a text file e Building a new sequence from a SQL LIMS worklist if you have Connect refer to the Connect documentation for information You can modify existing sequences by changing adding or deleting data Menus and Commands in the Sequence Editor You can choose commands from the Sequence Editor menu bar from a shortcut menu that you display whenever you want it or from the toolbar The Sequence Editor contains the following menus File Menu Allows you to create open save and print sequence files preview a sequence file before you print it enter and review documentation about a sequence and exit the Sequence Editor Edit Menu Lets you edit rows in your sequence file such as by cutting copying pasting and deleting them You can also copy and pas
343. of the instrument You can open only one Details window at a time There are three commands in the Details window Select command Opens the Select Instrument dialog box Next command Displays information about the next active instrument Previous command Displays information about the previous active instrument Text appearing in black on your screen represents information that is changing dynamically as the instrument status changes Text appearing in gray represents information that does not apply to this setup gt To view detailed status and run information e Jn the Navigator click the Details button to open the Details window for the currently selected instrument or choose Details from the View menu Details OR Choose Details in the Real Time Plot window The Details window opens showing the status of the currently selected instrument The contents of the Details screen are different for 900 Series Interfaces LINK controlled GCs and LINK Controlled LCs Viewing Data and Instrument Information N AutoSystem XL GC Details Lol Instrument View Help gt v al Sample Name A Sample Number A Raw Data File Ch A C PenExe TcWS Ver6 2 0 Examples AutoSystem XL GC A 001 raw Sequence File CPenExelTCWSlVer amp 2 DExamplesiSeries 200 LC Pump_ _ seq 1 ir EET urr Starting Row SeqRow 1 Vial Number 1 Instrument Method C PenExe TcVVSiVer6 2 0 Examples Gasoline mth Run Time 120 00 min
344. ollowing example cells in the columns Study Method Rpt Fmt File and ISTD Amt are selected Starting row fil Ending row n Apply to other channel also Study name 2600 Data x Inst Method D PenExe T cw SNVerb Rpt Fmt File D PenExe TcWS Web Int Std Amt 1 000000 Values entered for these columns will be used for both channels regardless of the state of the eckbox above First row to be changed 1 to 1 If you change your mind about the rows to which a change should apply change the value for Starting Row and or Ending Row If the columns you selected are all blue and you want both channels to reflect your changes select the Apply To Other Channel Also check box When an asterisk appears to the left of a column name it is a yellow column changes you make to it will always be entered into both channels For each column type enter or select the value that you want each cell to contain Note that this operation applies only to the cells you have selected It puts the exact value you enter in the dialog box into each of the selected cells of that column type Editing the Sequence Spreadsheet Editing Rows Use commands from the Edit menu or the shortcut menu to perform the following edits to spreadsheet rows e Moving rows e Copying rows e Inserting rows e Appending a row Edit menu only e Deleting rows These functions encompass the entire row including hidden columns Movin
345. om File Open dialog box Locate and select the method file that you want to open and choose Open The title bar changes to show the method name that you selected Using the Graphic Method Editor gt To specify a new report format file 1 Choose New Report Format from the File menu to open the TotalChrom File Open dialog box 2 Locate and select a report format file and choose Open The report format file that you specify primarily determines which printing format TotalChrom uses for output Some aspects of the report format such as the type and order of the data columns affect how the Peak Report appears when you display report information above the chromatogram For information on how to use the reporting features in the Graphic Method Editor refer to the sections Editing Methods and Results Graphically 10 9 Using the Graphic Method Editor Displaying and Printing Information on page 10 49 and Printing a Report or Replot on page 10 51 Saving Files in Graphic Method Editor When you work in the Graphic Method Editor you can save a modified method and you can save the optimized analysis of raw data in a result file e To save a method either choose Save from the File menu to save the method with the same name or choose Save As to rename it e To save a result file either choose Save Result File As to rename it or choose Save Result File With Time Stamp to use the original name with a time stamp added
346. omatogram command 10 20 exponential skim calculating 18 31 criteria listed 10 30 18 28 forcing 18 42 overview 18 28 18 31 preventing 18 42 requirements 10 31 timed event 18 42 external standard calibration 17 8 18 49 definition 8 5 F file formats for Lotus 1 2 3 16 24 for Microsoft Excel 16 24 File Open dialog 34 File Open dialog box 2 3 Index File Select dialog box 2 3 File Level Type list 8 47 files See also text files converting into alternate formats 19 5 converting to ASCII text 19 2 entering descriptive information in 2 8 reprocessing 15 3 Fill Down command 11 43 17 15 Fit Analysis automating as user program 17 18 menus and commands 17 4 overview 17 2 fit parameters overview 17 8 selecting 8 16 flush cycle activating by autosampler 13 12 Foley Dorsey B 23 font attributes 14 18 font changing in sequence 11 32 Fonts command 3 17 fonts selecting 3 17 footer report 9 5 16 16 For Amount command 17 11 For Response command 17 12 From Base Name command 16 4 From Sequence command 16 4 16 6 G gain errors C 20 gas chromatograph autosampler parameters 6 12 carrier parameters 6 15 configuration options setting 3 11 controls adjusting after setup 13 5 oven coolants 6 13 oven temperature 6 13 6 14 status viewing detailed 12 32 valves 6 18 global calibration parameters editing 8 7 options 8 5 overview 8 4 Global Information command 8 7 Global Parameters command 11 49 12 18
347. on reference component can be any component in the method other than an internal standard and it is distinct from any time reference peak specified for identification purposes Developing Calibration Parameters in the Method 8 15 Understanding Component Parameters 8 16 Use Curve Creates a calibration curve based on the data collected from standard samples The actual curve for each component depends on the values in a number of parameters If you specify an external standard calibration the curve then shows the relationship between amount and response area or height values If you specify an internal standard calibration the curve then shows the relationship between amount ratios and response ratios between the component and its designated internal standard component Response The Area and Height Response options on the Calibration tab specify whether TotalChrom calibrates and quantitates each component using peak area or peak height values You can change the option if you want to use a different response mode for different components Selecting Fit Parameters If you select Use curve as the Calibration Type in one of the components dialog boxes the Curve fit type Scaling Weighting and Purity parameters become active These parameters determine exactly how the software constructs the curve from the data points Calibration Type C Use calibration factor C Ava calibration factor C Calibrate by reference Cur
348. on reference component s calibration type is Use Calibration Factor or a first order curve FORCED THRU THE ORIGIN The permitted range will be the standard TotalChrom floating point range positive numbers only The default value will be 1 0000 Understanding Component Parameters Origin TotalChrom provides three alternatives for defining how you want to treat the origin in calculating a calibration curve The origin is the point 0 0 The options under Origin Treatment are Force The intercept is always zero in the calculation With this option the curve is forced to pass through the origin Include The origin is added to the calculation but does not appear in the calibration level list None If you deselect both of these options the software does not factor the origin into the calibration User Values LIMS The User Values LIMS tab provides additional settings you can use when setting up and editing components User Values You can define up to five numeric constants for each component You can then include these values in custom expressions within the Report Format Editor Setting up these values enables TotalChrom to perform such calculations as molar concentration percentage recovery or BTU content LIMS If you have Connect you can send results for a particular component to SQL LIMS For information refer to the Connect documentation Developing Calibration Parameters in the Method 8 19 Setting Com
349. on the use of reference peaks for component identification Use First Peak In Run As RRT Reference Use the first integrated peak to calculate relative retention values for all other peaks in the run Use This Component As RRT Reference Use the peak selected from the list below to calculate relative retention values for all other peaks in the run Editing Global Calibration Information Editing Global Calibration Information gt To edit global calibration parameters 1 Choose Global Information from the Component menu to open the Global Information dialog box Global Information LIMS Results Volume units rc r Unidentified Peak Quantitation Quantitation units a 7 Calibration factor fi 000000e 06 Sample Volume ul fico C Always use calibration factor Use nearest component eme A ooo Use nearest reference r Calibration Extemal standard RAT Calculation Intemal standard Use first peak in run as RRT reference T iRoed cules CUTE cancun C Use this component as RAT reference Allowed deviation x Boo LED z r Sample Amount Options I Correct amounts for calibration standards Iv Convert unknown samples to concentration units Gen The units for volume entries for display purposes only There are two tabs in the Global Information dialog box Global Information Use this tab to set parameters that apply to all components in the method or to
350. onal information To learn about Go to page Using the Report Format Editor Creating Title Header and Footer Text Editing Report Columns Creating a Custom Expression Editing Report Format Options Printing Report Format Files 9 1 Using the Report Format Editor Using the Report Format Editor 9 2 After TotalChrom analyzes a raw data file it saves the analysis as a result rst file and reports the results of that analysis using the format file s listed in the sequence file If you have identified additional report format files in the processing section of the method you can generate up to six different secondary reports If you do not include the name of a report format file in the sequence or method TotalChrom will not print a report In addition to specifying which information you want to include from the data analysis the report format file also defines how the information appears on the page You can also use a report format file to format information for use in other applications For example you can create a file for importing results to SOL LIMS and you can save a report as a comma separated ASCII file Menus and Commands The Report Format Editor window is available by choosing Report Format from the Navigator Build menu It includes the following menus and commands File Menu Allows you to create open and save files enter and review documentation about a report format print report formats and
351. ones 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 Temp Init Set Setpoint temperature for detectors A and B Actual Current temperature of the detectors A and B Ready Whether or not the temperature zone is ready Carrier Pressure Flow Init Set The initial carrier setpoint for channels A and B Actual The current actual carrier pressure flow of channels A and B Units Units configured for the carrier Ready Whether or not the carrier zone is ready Acquiring and Viewing Data 12 35 Viewing Data and Instrument Information 12 36 Detector Flow Init Set The setpoint detector flow two flows can be associated with each detector Actual The current actual detector flow of detectors A and B Ready Whether or not the detector flow zone is ready Auxiliary Pressure 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 Actual The current actual pressure flow of auxiliary zones 1 through 4 Units Units configured for the carrier Ready Whether or not the pressure flow is ready for the auxiliary zones Split Flow I
352. ons Dialog Peaks Components Tab esee 20 30 Report Print Options Dralog cscs 5a aee dni nb ea aeS E 20 31 Busy TCR File Warning Dialog ssesesercesesosesersecosenerensssevevsncnetsesenesenenenpevsnenes 20 32 Prnt All Repotts oc eau eed metit Et ete e Eten 20 33 Selecting Data for Review una nb bem Re RR Rua ORI OR And 20 34 TotalChrom File Open Dialog eese nenne nennen ener 20 34 Eie tist Wandow iuitepe nete tote fte eate 20 35 File List Window Show Hide Dialog eene 20 38 File List Window Properties Dialog eene 20 40 Brrr EOg etate Ie NO QUEE RU E eot IR neris 20 41 Plot Window 5 2 osa obe eere eerte rt deu ien teer PR 20 42 Graphic Objects uoi rh RR I PEU e RE A 20 42 Sien Toolbar eiim hr bre EE EEEE SEE E E EE a oi 20 43 Report Windows 5 eee etie Ree R eee 20 44 Viewing Chrorat gramis asi eere ed ete tete RED Aero c eR nee feet 20 45 About the Plot WindOw eie a erit a crit et t e ee e eee end 20 45 Graphic Objects aide ette aided di eet be ri ED Pere 20 45 About the Plot 5 0 io negone teet tte eed ette teres 20 46 Viewing Chromatograms Plot Window eese 20 47 User L belzz42 uie ert ea eh ee ea ee tense ie ec ct i eerie 20 50 Multiple Chromatogram Layouts eseeeeeeeeeeeeeeeeeere nennen eene nennen rennen 20 51 Scaling the Chromatogram via a Zoom Box seen 20 54 Scaling the Chroma
353. open the result file TotalChrom also opens the corresponding raw data file in order to plot the chromatogram Although you can modify method parameters in Reprocess Results you are only modifying a copy of the method embedded in the result file not the method itself If you save the changes you make to a result file in Reprocess Results that new file will contain the modified method parameters To maintain the current view and the current scaling parameters choose Preserve View from the File menu before choosing Open gt To open a new result file in the Reprocess Results window 1 Choose Open from the File menu to open the File Open dialog box 2 Locate and select the result file that you want to open and choose Open You can select an index file instead as described under Using Reprocess Results starting on page 10 10 TotalChrom opens the selected result file and the associated raw data file TotalChrom performs peak detection integration and component identification using the method parameters embedded in the result file and finally displays the processed chromatogram Editing Methods and Results Graphically 10 13 Using Reprocess Results gt To specify a new report format file 1 Choose New Report Format from the File menu 2 Locate and select a report format file and choose Open To learn how to use Reprocess reporting features refer to 10 14 Using Reprocess Results Displaying and Printing Information
354. opy Levels From Method File selected if you want to copy calibration levels 3 Leave Copy Replicates From Method File selected if you want to copy replicate injection information 4 Choose OK to open the file selection dialog box showing method files Loading and Merging Components From Files 5 Select the file whose component list you want to load into the current method file and then choose OK The component information contained in the selected file appears in the component list The new information overwrites existing data in the component list The procedure for merging components is similar to loading including the option to include calibration information from method files gt To merge components from a result text or method file 1 Choose Merge Text File Merge Result File or Merge Method File from the Components menu 2 Select the file with the component information you want to merge including the levels and replicates from the calibration section of the method if you are merging a method file 3 Choose OK Developing Calibration Parameters in the Method 8 41 Deleting Components Deleting Components You can delete a component from the component list by using the Delete command or the Delete key gt To delete a component from the component list 1 Inthe Component List window select the component you want to delete 2 Choose Delete Component from the Components menu The selected component an
355. or If you want to define custom colors refer to your Microsoft Paint documentation gt To set the text color 1 Click the right mouse button in the label whose text color you want to set 2 Choose Set Text Color from the Labels pop up menu 3 In the Color dialog box select one of the Basic Colors or choose the Define Custom Colors selection box 4 Choose OK Setting the Font The Set Font command on the Labels pop up menu allows you to select the font style size effects color script and the angle of rotation for a label Some fonts cannot be rotated If you choose a font that cannot be rotated the sample in the Font dialog box will move but will not rotate Choose a different font if you want to rotate a label Adding and Editing Chromatogram Labels gt To set the font and other attributes 1 4 Click the right mouse button in the label whose font or other characteristics you want to edit Choose the Set Font command from the Labels pop up menu In the Font dialog box select the font and other attributes that you want the label to contain If you want to change the angle of rotation move the slider at the bottom of the Font dialog box The angle of the label will be displayed under Sample You can rotate the angle between 90 degrees and 90 degrees Choose OK Moving a Label to the Top of a Stack Labels can become hidden behind other labels when multiple labels occur at or near the same location
356. or click the Run button and choose Take Control from the pop up menu Re establishing Communication with an Instrument TotalChrom can lose communication with an instrument for a variety of reasons including by request Refer to Breaking Communication with an Instrument The Attach command allows you to re establish communication gt To re establish communication e Jn the Navigator click the Run button and choose Attach from the pop up menu TotalChrom attempts to re establish communication with the instrument If communication is established the interface status changes from Detached to some other state depending on what state it was in previously and what caused it to become detached Breaking Communication with an Instrument If you want to break communication with an instrument you use the Detach command in the Run menu There are two principal reasons for breaking communication with an instrument e Anerror has occurred e You do not want the Navigator to upload or process data while you perform another task Choosing Detach prevents TotalChrom from spending time attempting to communicate with the instrument Breaking communications between TotalChrom and an interface generally does not interfere with any data acquisition task that the interface is performing The one exception to this is if the interface is being run in single run data buffering mode because the run may produce more data than the interface can stor
357. or data acquisition A holmium oxide filter must be installed for the wavelength calibration process gt To check wavelength calibration 1 Choose Bind from the Instrument menu then select the instrument that you want to bind 2 Choose Wavelength Calibration from the Navigator Instrument menu to open the Wavelength Calibration dialog box Wavelength Calibration x sp ose Select Instrument 0 3 0 25 0 2 0 1 0 1 Absorbance Units 0 0 0 00 wo to to w w CO CO CO CO CO CO CO CO CO CO CO CO CO CO CO to w Ch Ch Ch Ch Ch Ch Ch Ch Ch CO CO CO CO CO CO CO O O OC c o C I3 t R O O Q O m amp amp O 6 6 OQ O t c6 I Oc Wavelength nanometers Select the instrumet to calibrate 3 Choose Start to initiate the calibration process The progress of the calibration is shown below the instrument name and a plot of the sample data is drawn in the bottom half of the screen When the calibration is complete TotalChrom prints a plot of the sample data 4 Choose Close Remove the holmium oxide filter before beginning data acquisition Working with Instruments Interactively 13 19 13 20 Chapter 14 Displaying Chromatograms This chapter explains how to use the Chromatograms application in TotalChrom A chromatogram or plot is the graphical representation of chromatographic data that is displayed when you use this application The terms chromatogram and plot are
358. ormation The File Open and File Select dialog boxes contain the same elements TotalChrom will open the appropriate dialog box depending on the task you are performing gt To open or select an existing file 1 In the File Name text box either enter or select the name of the file TotalChrom Basics 2 3 Using Common Dialog Boxes The Multiple File Open dialog lets you open more than one file at a time by using the Shift and Control keys when selecting files Use the Quick Paths selection box to quickly select an often used path You set up these paths in the Configuration application see Quick Paths in Chapter 3 for information 2 To select a different type of file scroll to the file type you want in the Files Of Type list The list of file types includes all of the available file types that the current application can recognize For example the Sequence Editor allows you to open SEQ and IDX files 3 Toggle the Header button to view file header information 4 Choose Open or Select Path Select Dialog Box The Path Select dialog box opens when you click the folder icon next to an edit box that requires a path This allows you to select an existing folder and file TotalChrom Path Select 1 A34 xl Select a path CiPenExelTcWSWWer6 3 0lExamples EC Ver 3 0 5 C3 TCWS Links QO Temp ema Quick Paths C PenExe TcwS Ver6 3 0 Examples z Use the Quick Paths selection box to quickly
359. ormation in the spreadsheet The Sequence Template dialog box opens when you build a new sequence and select From Template as the Build option in the Global Parameters dialog box You also use this dialog box when you use a template to add samples to an existing sequence with the Append New Template command Study Method Cha ChB Base file name ChA JC PenExe TcwS Wer6 ChB C PenExe TcewS Wer6 r Calibration T Include calibration standards T Assign sample numbers to calibrations First injection CatReplace kd Replicate injections CalAverage z Injections per calibration 1 Samples between calibrations 0 r Samples Sample number pattem tttttt Number of samples 10 Starting number 1 Injections per sample 1 Autosampler Initial vial number fi Injection Site Z T Allicatibrations from one vial set Cus Study name gt To enter Sequence Template information 1 If you want to identify the analysis being performed in the optional Study text box enter any combination of alphanumeric characters 2 In the Method text box enter or select the name of the Method that you want to use for Channel A 3 Enter a Base File Name for Channel A You can include the full data path here add it in the spreadsheet after you complete this dialog box or enter or change it during setup The base file name itself may contain 80 characters 11 13 Building a Sequence by Template Do not end a bas
360. orting of a particular set of data the status and security of that data must be changed to prevent any further modification The United States FDA regulations for the review and approval of electronic records are described in the general GLP and GMP regulations the Predicate Rules upon which 21 CFR Part 11 is based These regulations require that any relevant records or data in paper form or electronic are reviewed by one or more authorized individuals other than the one who was responsible for the generation of those records and that the reviewer s sign and date that record with an indication of the meaning of that signature for example Reviewed By Once data have been reviewed it can be submitted for final review by another individual or submitted for approval and or final approval by a similar process of signings including a date and meaning of the signature Such review and approval e signatures are applied to TCR TotalChrom Report files Introduction and Overview 1 6 TotalChrom Functions The function of Review and Approve is associated with the review and approval of the reporting of data rather than the data itself This consists of a combination of information from the existing TotalChrom file types listed below e The Raw data for the sample necessary to redraw plot images required for the report e The Result data used for the report e The Method used to generate that result file as embedded in the TotalCh
361. ose Cancels the Append New Cycles dialog box without applying data entered since the last Add Identifying the Sample You complete the Identification tab in the Append New Cycles dialog box to specify sample data and the instrument method to be used in a sequence The Identification tab differs for single and dual injection sequences refer to the procedure for the appropriate type of sequence Do not confuse dual injection with dual channel The former involves the injection of two different samples simultaneously whereas the latter involves the use of two detectors to monitor the separation of a single sample gt To enter identification information for a single injection sequence 1 On the Identification tab of the Append New Cycles dialog box select an entry for the Type field from the list Append New Cycles x Identification Fies Quantitation Calibration m Sample Iype of cycles Do Name ji eal Number pattern HHH Actual number po Study azz Vial n Back Injection site Method Jk Stecs ver6 0 0 config user koontzsa DEFA Type of sample to be added to the sequence Building a Sequence 10 Building a Sequence Vial by Vial If the sample is to be injected more than once enter the number of cycles in the Of Cycles text box When you are creating a new sequence start by adding data for the first injection cycle Cycle 1 As you add each cycle TotalChro
362. ose the Edit Components dialog box Working with Components gt Tocreate and edit a timed group 1 With the Edit Components dialog box open choose Timed Group from the Type menu The Edit Components dialog box changes to reflect the options for timed groups If the method has any existing timed groups the name of the first timed group appears in the Name text box and the values for other options are displayed The search time window for the group appears in the plot window 2 Choose New to create a new timed group A group window marker that spans the entire run appears in the plot window You define the size of this window by entering the Group Start and End Times The following example shows a new timed group window ta Graphic Method Editor C PenExe TcCS WVer6 1 0 Examples solvent mth Type Reldentify Retum Help e Group 1 Retn time 5 000 Area 30133610 00 Height 5149945 93 Name New Group Q z 5 E 28658 59 R g 8 9 FFF fg 5 g Reference z ISTD ba Group start time min 0 00 Group end time min 10 00 H T Update calibration Level E Amount 0 0001 Calibration type C Average Replace CAPen xe TcCS Ver 1 0 Examples SolvO01 raw 9744mn 242045mV 1200pts Use Next Prev or Return to accept changes Click on another peak to cancel changes 7A Editing Methods and Results Graphically 10 45
363. ose the dialog box choose OK e To save your work without closing the dialog box choose Apply e To close the dialog box and discard your changes since the last time you chose Apply choose Cancel The following sections describe how to complete each of the tabs in the Instrument Control dialog box The tasks for GCs and LCs are grouped in separate sections However because instrument timed events are similar for all instruments these procedures are combined in Setting Instrument Timed Events on page 6 36 Setting Control Options for GCs If you are using a LINK controlled GC the possible tabs in the Instrument Control dialog box are e Autosampler e Oven Inlets e Carrier e Detectors Developing Instrument Parameters in the Method 6 11 Setting Control Options e Instrument Timed Events For a complete definition of each GC parameter refer to the operating manual that came with the specific instrument Setting GC Autosampler Parameters gt To set autosampler parameters for gas chromatographs 1 Select the Autosampler tab of the Instrument Control dialog box Instrument Control x Autosampler Oven Inlets Carrier Detectors Instrument Timed Events r Injection Source C Manual C r Sample Injection Syringe capacity uL Sample pumps Injection volume pL 0 Viscosity delay Jala Injection speed Normal Wash waste vial set r Washes Pre injection solvent washes Pre injection s
364. ou are auditing Viewing the Audit Trail The Audit Trail tab in the Documentation dialog box displays a history of changes made to the audited file including an indication that electronic signature was verified Gf it is enabled It appears when you choose Audit Trail from the File menu You cannot edit the information in this tab gt To view the Audit Trail 1 TotalChrom Basics Choose Audit Trail from the File menu Description Audit Trail 01 02 2001 3 32 10 PM 01 02 2001 3 12 38 PM manager Changed total time from 1 20 000000 to 20 00000 Changed sample rate from 0 401506 to 1 562500 Changed detector configuration from Channel A to Changed injection source from Manual to Autosar gt Reason for Changes 2 11 Using Audit Trail 2 Select an audit trail record from the list on the left and review its details on the right 3 When you are finished viewing the information choose OK Printing the Audit Trail TotalChrom applications display a print options dialog box when you choose Print from the File menu This dialog box includes an option to print the Audit Trail for the current file 2 12 Using Electronic Signature Using Electronic Signature The electronic signature feature forces a user who saves a file to enter the TotalChrom password that corresponds to the logged on user The electronic signature feature of TotalChrom is provided to assist in satisfying th
365. ou do not select a row TotalChrom appends the rows that you copied to the end of the spreadsheet If you select the last row TotalChrom gives you the option to insert or append Choose Paste You may paste the same selection as many times as needed while it remains on the clipboard Check that the values in the rows that you have copied and the rows that follow are correct in their new context You can use the Smart Fill command to increment values in the Number Vial and Data File columns if necessary See Editing Column Values on page 11 37 Inserting Rows To insert new rows identical to rows you select you use the Insert command from the Edit menu or the shortcut menu The new rows are inserted above the rows you select When you insert rows TotalChrom inserts them in both the Channel A and Channel B spreadsheets simultaneously gt To insert new rows in the spreadsheet 1 2 Select the rows that you want to duplicate Choose Insert Check that the values in the rows that you have inserted and the rows that follow are correct You can use the Smart Fill command to increment values in the Number Vial and Data File columns if necessary See Editing Column Values on page 11 37 Editing the Sequence Spreadsheet Appending a Row When you append a row TotalChrom adds it to the end of both the Channel A and Channel B spreadsheets simultaneously gt To append a row to the end of the spreadsheet 1
366. owing tasks Introduction and Overview Control supported chromatographs through serial communications Acquire analog or digital chromatography data from chromatographs Analyze raw data and report results Control the acquisition and analysis of data from large batches of samples Work interactively with instruments to change instrument or interface settings before during or after a run Store raw data and the calculated results Create methods that define acquisition and analysis parameters Optimize analysis parameters graphically and use the improved parameters to reprocess raw data Compare chromatograms subtract add and calculate the ratio of chromatograms and manipulate calibration curves Interface with other software applications 1 2 TotalChrom Functions TotalChrom Functions The following sections provide a brief overview of the major functions in TotalChrom Acquiring Data You use the TotalChrom Navigator to collect store and analyze chromatographic data from analog or digital interfaces The Status function in the Navigator displays a summary screen that shows the status of all 900 Series Interfaces and any chromatographs controlled through LINK Interfaces currently connected to and accessible by the system You can download an acquisition sequence through the Setup function to prepare an interface or instrument for collecting data You can also view one or more real time chromatograms or analyze the information
367. own window gt To open one or more files 1 Choose Open from the File menu 2 Toopenraw data files select the files that you want to open in the Multiple File Open dialog box then choose Open 3 Toopen individual result files select Result Files rst in the Files Of Type list select the files that you want to work with and choose Open Replacing a File With Another File The Replace command lets you replace an open file with another file The new file assumes the same scaling and position in the window as the file that you replace Replacing files can be helpful if you want to compare a series of files against a standard file gt To replace one file with another 1 Select the file that you want to replace 2 Choose Replace from the File menu 3 In the File Open dialog box select the file that you want to open in place of the current file 4 Choose Open Displaying Chromatograms 14 5 Using the Chromatograms Application Printing Chromatograms and Their Scaling Information The Print command lets you print a copy of the chromatograms for all open files Chromatograms will be printed in stack mode You can choose whether a summary of the start time end time and the low voltage and high voltage values for each chromatogram is printed gt To print an overlay view 1 Select the Overlay View window before you choose the Print command 2 Choose Print from the File menu Printer System Printer H
368. ox If you do not check this box sample numbers for all calibration rows will remain as they appeared before you used the Smart Fill command Choose OK Using Smart Fill to Increment Vial Numbers Many editing operations apply only to the cell you have selected After you insert copy move or delete rows in a spreadsheet it is a good practice to check the accuracy of values in other rows For example if you change a vial number the values in the remaining Vial cells retain their original values You use the Smart Fill command to increment vial numbers in the same column gt To increment vial numbers 1 If this is a dual injection sequence select all or part of the Vial column in the channel for which you want to make changes For a single injection sequence changes will apply to both channels Select the Smart Fill command from the Change menu or the shortcut menu Smart Fill x Starting row f Ending row 2 Initial vial number fi Iv Maintain replicates All calibrations from one vial set taa First row to be changed 1 to 2 If you change your mind about the rows to which a change should apply change the value for the Starting Row and or Ending Row Enter a new Initial Vial Number If you want the renumbered vials to be synchronized with current vial numbers select the Maintain Replicates check box The Maintain Replicates option ensures that rows that previously specified the same via
369. ox e With this option TotalChrom 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 TotalChrom calculates the optimum sampling rate for that peak width collecting at least 20 data points across the peak e Select By Sampling Rate and then enter or select a rate With this option TotalChrom acquires data from the instrument using the number of data points per second that you explicitly set or the nearest available rate to that value 5 Under Data Storage do one of the following e Select Store All Data From Run to store all the data from a run TotalChrom collects and stores data for a run based on your instrument conditions This option is useful if you don t know the run time because you haven t entered the GC oven program or LC solvent program e 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 text box enter the number of minutes that you want to elapse between the start of the run and when data analysis starts A value entered here does not affect the measurement of peak retention time In the Run Time text box enter the number of minutes for which you want the interface to collect data Note that TotalChrom will not allow the delay time to be greater than the run time The number of data points value is calculated as follows Data Points RT x
370. p press F1 Start 0 000 End 2 988 Offset 37 036 Scale 915 552 7 2 Right click in the target chromatogram and choose Scale Time The peak in the target chromatogram is scaled such that it aligns with the peak in the reference chromatogram Chromatograms Halo_004 1raw lolx Eile Operation Options Window View Help clala 1 7 asit fes m ele a Halo_003 raw M For Help press F1 Start 0 000 End 2 988 Offset 37 036 Scale 915 552 7 Displaying Chromatograms 14 23 Aligning Peaks in Two Chromatograms 14 24 Aligning Peaks by Voltage You can align peaks by voltage using three procedures e Shifting the voltage scale e Scaling the voltage from origin e Scaling the chromatogram by matching baselines Before you can shift the voltage scale or the voltage from origin you must set the high voltage value in the two chromatograms to be aligned Before you can scale voltage you must set the low voltage and high voltage values in the two chromatograms that you want to compare gt To set low voltage and high voltage values 1 In the reference chromatogram right click where you want the high voltage value to appear and choose Set High Voltage on the Chromatogram pop up menu A dotted horizontal line appears through the point you selected In the reference chromatogram right click where you want the low voltage to appear and choose Set Low Voltage A dotted horizontal line appears t
371. pen the Chromatograms application 1 In the Navigator choose Chromatograms from the Display menu or choose the Chromatograms button Chromatograms 2 Inthe Chromatograms window choose Open from the File menu select the files you want to work with then choose Open To close one chromatogram 1 In the Chromatograms window select the chromatogram that you want to close 2 Choose Close from the File menu or click the Close box on the chromatogram window Using the Chromatograms Application gt To close all chromatograms e Choose Close All from the File menu gt To close the Chromatograms application e Choose Exit from the File menu or click the Close box Menus and Commands The Chromatograms application includes the following menus and commands File Menu Allows you to open replace close save print and copy one or more chromatograms for use in other applications This menu also provides access to the most recently used raw and result files It allows you to exit the Chromatograms program and return to the Navigator Operation Menu Lets you create a new chromatogram by performing a mathematical calculation on two existing chromatograms You can then edit the way that the new chromatogram is generated Options Menu Lets you change the scale of one or more chromatograms create a 3 D view of chromatograms in overlaid mode expand all chromatograms simultaneously by expanding one and show or hide mous
372. performing a serial dilution Series 200 LC only Monitor The instrument is in Monitor mode Not Ready The instrument is not ready Acquiring and Viewing Data 12 39 Understanding Status Messages 12 40 Acquisition Related Messages Line 2 Backlogged Data from one or more completed runs still reside in the interface Monitor The instrument is running in monitor mode from the Real Time Plot window No Data No data is available from the interface Other Data Acquire is collecting other data e g spectra instrument run log Sampling A run is in progress and the interface is collecting data Interface Related Messages Line 3 Canceling The instrument is in the process of responding to a Cancel Run command Injected A LINK controlled autosampler has made an injection and TotalChrom is waiting to receive the first data points from the run This can occur when a slow sampling rate a few points per second is used Inst NRDY The instrument is not yet ready to perform the run because it is not equilibrated at the set conditions Monitor The instrument is running in monitor mode from the Real Time Plot window Not Ready The interface is not ready to accept data Other Data Acquire is collecting other data e g spectra instrument run log Overflow The run has produced more data than the interface can store This can only occur if the interface has been set up in singl
373. ponent Defaults Setting Component Defaults 8 20 This section describes the Component Defaults dialog box and the procedures for setting up defaults For detailed information on the specific parameters in the Component Defaults dialog box refer to Understanding Component Parameters on page 8 9 The Defaults command in the Components menu lets you set the default values that the software provides when you add new components to a method Customizing component defaults is useful in the following situations e You want to add to a method or series of methods a large number of components whose parameters are the same e You want to add to a method a large number of components that share an internal standard or retention reference You generally use the component defaults function in conjunction with the Components dialog box which you use for adding new components For example if you want to add 100 components that have the same calibration settings set the common parameters in the Default Components dialog box Then when you add each component using the Components dialog box you only need to specify the unique parameters such as the component names and retention times For information on adding new components refer to Adding and Editing Components on page 8 28 Setting Component Defaults Entering Default Component Information The following is the general procedure for entering component default information gt To enter
374. ports 1 Choose Optional Reports from the Process menu to open the Process dialog box with the Optional Reports tab selected Integration Baseline Timed Events Optional Reports Regi User Programs r Report format or template files S e Plot Settings p Options for selected report pups Copies T Append to evisting result Keep temporary files Set the current selection 2 Locate and select the file that you want to use You can choose the Select from List button to display a list of reports associated with the current job type or Browse all available file types for example a TC Publisher method is tpm TotalChrom inserts the path and filename of the file that you selected in the report format field 3 Toremove files from the list use the Delete or Delete All command 4 If you want to generate a plot to include in a TC Publisher report choose the Plot Settings Command and select the settings for it in the Plot Settings dialog box The Plot settings do not apply to RPT file reports This is described in the following procedure To include plots in a TC Publisher report you must also select the Keep Temporary Files check box Developing Processing Parameters in the Method 7 9 Selecting Optional Reports 5 Under Options For Selected Report select the form of output you want and complete the Output Selection dialog box e To print a report click the Printer
375. processing modes 18 In the Post Method Cycles text box enter the number of flush cycles that you want after each method is completed in a sequence 19 Under Peltier Tray Control set the Temperature of the tray 20 In the list select a tolerance percentage to control when the system Peltier Tray becomes ready The autosampler will not come ready unless the Peltier tray temperature is within the range of the temperature that you set plus or minus the value in the tolerance section Configuring Pump Information The Pump Config tab of the Instrument Control dialog box lets you enter labels for solvents and set other pump configuration parameters such as the Ready Time and the pressure units The solvent labels you create appear in the Method Summary window and on the Pump Program tab gt To set pump configuration parameters 1 Select the Pump Config tab of the Instrument Control dialog box Instrument Control x Autosampler Pump Config Pump Program Detectors Instrument Timed Events r Pump Operation Ready time min 60 Pressure units PSI bd Standby time min 15 Max pressure 6200 Standby flow mL min 0 10 Min pressure r Solvent Names Soveta fA SoventB BC SoventC Fo SoventD Cancel Apply Time in Ready state after which pump shuts down 15 to 999 Developing Instrument Parameters in the Method 6 23 Setting Control Options 6 2
376. properly The B identifiers are used only with processing parameters in dual channel runs and with sample parameters in dual injection runs Building a Sequence 11 53 Building a Sequence from a Text File Identifier Corresponding Parameter 11 54 VOLUME A VOLUME B DIL A DIL B RPT B Number Number Number Number Number Number Number Number Number Number Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Text Actual sample volume for Channel A Multiplier for Channel A Building a Sequence from a Text File Baseline file name for Channel A Calibration report for Channel A samem Tee SOLMS Sale Dior Cue Building a Sequence 11 55 Building a Sequence from a Text File 11 56 Sixth user defined value for Channel B Eighth user defined value for Channel B Following are the syntax rules for listing the parameters in a cycle They are listed in the order indicated by line 2 They are separated by commas Spaces after commas are allowed but not required When a cycle does not have a value to correspond to a parameter identified on line 2 use two commas in succession to indicate its position You may use blank spaces between the commas but they are not required If the position of the missing parameter is at either end of the line a second comma is not required If the missing parameter is numeric the system will enter 0 in the se
377. ps soia e AU UO IRE nto ir Re eee ER ERA 13 9 Detector ACUOnS inen teen ent or ig b o ER AI de e A da 13 10 Autosampler Actions esie sienien edere ea tuos ie e ce Mete eee ap Rete s ei 13 11 Modifying a Downloaded Method esee eene 13 13 Modifying a Sequence During a Run eee nennen nennen nennen 13 16 785 Detector Wavelength Calibration eese nenne rennen enne 13 19 Chapter 14 Displaying Chromatograms Using the Chromatograms Application eeeseeeeseeeeenerenenn rennen enne nennen 14 2 Menus and Commands ise ee eaaet dee ees Cetus 14 3 Using the Chromatogram Pop up Menu seen ener nennen 14 4 Opening Chromatogram Files ees sesesecssesecseeeecneeeeceaeeeesaecaeesecneeseceaeeeesaecatesesaeeeeens 14 5 Replacing a File With Another File esee eene 14 5 Printing Chromatograms and Their Scaling Information eee 14 6 Using Images in Other Applications eese eene 14 6 Controlling the Appearance of Chromatogram Windows eee 14 7 Automatically Sizing Chromatograms eese eene 14 7 Displaying Chromatograms in Overlay View eese 14 7 Viewing Chromatograms Three Dimensionally eene 14 8 Displaying Information in Chromatograms esee eene nnne nre 14 11 Expanding Chromatograms eese eee enne nenn
378. quence If the missing parameter is text a blank will be entered Text parameters must be enclosed in quotes If a text parameter includes a quote such as DIET LITE STUDY use additional quotes around the quoted portion U DTET LITE STUDY Do not enclose number parameters in quotes Omitting quotes from text parameters or enclosing numeric parameters in quotes will not generate an error message a default value or a blank for text parameters will be used instead Building a Sequence from a Text File e The only permitted values for Type A and Type B are any of the types that you can select in the Sequence Editor Invalid combinations of Types within a single channel or between channels will produce an error when the text file is loaded If you omit the Type parameter TotalChrom will use a Sample type regardless of any other parameters that you include such as calibration level name The following is an example of a properly formatted text file 3 TYPE A SAMPLE A AMOUNT A VOLUME A INST RAW A RESULT A PROC A SAMP A Sample WASTEWATER 5 2 WATER PONDOO1 PONDOO1 WATER WATER Sample WASTEWATER 1 1 WATER POND002 POND002 WATER WATER Sample WASTEWATER 1 1 WATER POND003 POND003 WATER WATER Loading a Text File into a Sequence You use the Load Text File command on the Build menu to transfer the information from an existing text file to c
379. r more details refer to Appendix A How Interfaces Collect Data Select Suppress Processing if you do not want to process the data for post sequence runs immediately after they are collected This automatically suppresses the data analysis process including the printing of reports and plots and the creation of a result file You may want to select Suppress Processing if you plan to use your computer for another task and do not want to be interrupted by data processing at the end of each run Since data processing is a computer intensive task it can cause your computer to be unresponsive for several seconds as the various data analysis functions are carried out Setting Up Data Acquisition If you suppress processing you can use Batch Reprocessing later to obtain results from the analyses 9 Select Suppress Reports Plots if you do not want to print a report and plot for post sequence runs If you do not select this option TotalChrom will automatically print a report and plot at the end of a run 10 Choose OK in the Setup Instrument dialog box to initialize the instrument Using Quick Method The Quick Method button in the Setup Instrument dialog box opens a limited version of the Method Editor Use this editor to build a method when you use the Quick Start Setup type You can access only the instrument and processing parameters except the instrument name you cannot access calibration parameters The Quick Method name
380. r more information about how TotalChrom handles overlapping windows during component identification refer to Overlapping Windows in Chapter 18 Discussion of Data Analysis To compensate for these shifts in peak retention times you can use reference components As with any other peak component a reference component has an Developing Calibration Parameters in the Method 8 13 Understanding Component Parameters 6 14 expected retention time and a search window However a reference component is usually readily identifiable either because it is well separated from other peaks or because it is always the largest peak in that region of the chromatogram When you establish a reference component TotalChrom uses the ratio of the actual retention time of the reference peak to the expected time in order to calculate adjusted expected retention times for the components associated with the reference component The complete equation for the adjustment calculation is D ref void adj comp exp comp T ref T where Ton is the adjusted expected retention time for a component Tact ref is the actual retention time of the reference component from the run Tepig is the expected retention time of the reference component as defined in the method T oid is the Void Time if you have entered one in the Global Information dialog box Tota is the expected retention time of the component as defined in the method You can define one or more components
381. ram The detector program can have up to nine rows or steps with the following parameters Time The duration of the current step Wavelength A nm and B nm The wavelength selected to monitor Channels A and B Bandwidth BW A and BW B The bandwidth or total wavelength range around the nominal selected wavelength for Channels A and B Setting Control Options gt To set LC 235 detector parameters 1 Select the Detectors tab of the Instrument Control dialog box The Program Time displays the duration of the pump solvent gradient program which you set in the Pump Program tab The Detector Time displays the current duration of the detector program Instrument Control x Autosampler Pump Config Pump Program nstrument Timed E vents Min wavelength nm 210 Spectral threshold Trace 4 LA nm B nm AWB nm BWB m 255 280 5 5 Program time 35 00 o Detector time 15 00 Spectral Acquisition Mode Off S Start time min 0 10 Sampling period s 0 4 E End time min E oo Lamp OFF at end of run Cancel Apply 2 Inthe Min Wavelength text box enter the starting wavelength for peak purity measurements Peak Purity is available as a report option in the Report Format Editor 3 From the Spectral Threshold list select the peak size required to trigger a spectral scan in Auto or Apex spectral acquisition modes 4 Inthe Time column of the
382. ram display to reflect the new values Drawing the Baseline Manually The Manual Integration command in the Process menu allows you to set timed events that indicate the baseline that you want to use beneath specific peaks These manual integration timed events become part of the method just like ordinary baseline timed events and TotalChrom does not erase them if you reprocess the data later with the same method The UF events override the normal peak detection process If you manually draw in a baseline for a peak that TotalChrom did not previously detect TotalChrom integrates the peak However if you draw a segment of the baseline underneath a cluster of peaks TotalChrom will end the current cluster and draw new peaks as directed by the timed events gt To redraw a baseline 1 Toggle Manual Integration from the Process menu The status bar message at the bottom of the window prompts you to draw a baseline under a new or existing peak 2 To draw a new baseline drag the mouse from the required baseline starting point to the ending point As you drag TotalChrom creates a line between the starting point and the current mouse location 22M 10 32 Setting Processing Parameters When you release the mouse button the TotalChrom draws the new baseline on the plot and adds the UF and UF timed events to the chromatogram You can underline more than one peak at a time and include peaks that were not marked previousl
383. ration enables the use of the settings defined for the instrument in Configuration In the Method text box enter or select the name of the method file to be set up when the sequence is completed In the Data Path text box enter or select the path where you want to store post sequence data files In the Base File Name text box enter a file name or set a tokenized name by clicking the button The default Base File Name is typically set in System Configuration Allowable changes to the contents of these fields via typing or folder button depend on the permissions set in System Configuration Your application manager may have set up Default base names in System Configuration Your application manager may have set up your system to automatically append a date time stamp to all files Enter the Starting File Number you want to be appended to the base file name for the first post sequence run If necessary TotalChrom will add leading zeros to your entry to generate the three digit cycle number For example the entry 2 will become 002 Select Single Run Data Buffering if you do not want to store data from multiple post sequence runs in the interface If Single Run Data Buffering is not selected the interface memory will be divided into segments large enough to store the data from a single run This enables the interface to acquire data from multiple runs even if the Navigator window is closed or the computer is turned off Fo
384. reate a sequence file gt To load sequence information from a text file 1 2 Choose Load Text File from the Build menu Select the text file that you want to open and click Open The information from the text file becomes a sequence file If the text file does not match the parameters in the sequence file you get a message that says No Field Identifiers Were Specified or Unknown Field Identifier Another error is Invalid Type In Text File This means that you have either misspelled a Type parameter or have used an invalid combination of Types You need to fix the text file before TotalChrom can generate a sequence Appending Sequence Information from a Text File Building a Sequence You use the Append Text File command on the Build menu to append sequence information from a text file to the end of a sequence file gt To append information from a text file 1 2 3 Open the sequence file that you want to change Choose Append Text File from the Build menu Enter or select a text file name and choose Open This appends sequence information from the selected text file to the current sequence file 11 57 Building a Sequence from a Text File 11 58 Merging Sequence Information from a Text File The Merge Text File command on the Build menu merges sequence information from a text file with the current information in a sequence file If the two files have different values for the same parameter the text file v
385. refer to Chapter 11 Building a Sequence gt To build a vial list 1 Click the Vial List button Acquiring and Viewing Data 12 17 Setting Up Data Acquisition 12 18 If you are using a LINK controlled LC autosampler or you want to generate a vial list for dual simultaneous injections on the same instrument choose Global Parameters from the Change menu Otherwise continue with step 4 The Global Parameters dialog box opens Global Parameters x Build Parameters Configuration Logon Name em 850 SRG Tray Build sument Eom tempate wen Enter name or initials up to 10 characters If you are using a LINK controlled LC autosampler select the tray type installed in the autosampler from the Tray drop down list on the Build Parameters tab To generate a vial list for dual simultaneous injections select Dual as the injection type on the Configuration tab and choose OK Select the first cell in the Vial column in the spreadsheet Enter the vial number for the first sample to be analyzed Continue entering vial numbers for each row to be included in the current set of runs Add delete and move rows as necessary using the commands in the Edit menu Choose Save from the File menu to save your changes The vial list is saved as a sequence using the base file name you entered in the Setup Instrument dialog box plus the SEQ extension Close the Vial List wi
386. responding target vials Creating Derivatization and Dilution Programs Series 200 Autosamplers Only The Entry Table to program this operation looks like this First Vial Volume Mix Cycles Equil Time esr T win E The following table shows what the Autosampler does in each cycle when you run the sequence containing this method uo fof so fof s d fo Sequence Cycle Autosampler Actions Cycle Autosampler Actions Vial 41 Transfers 100 uL from the diluent tank to target vial 41 Transfers 50 uL of sample to target vial 41 Transfers 25 uL of internal standard to target vial 41 Injects vial 41 Vial 42 Transfers 100 uL from the diluent tank to target vial 42 Transfers 50 uL of sample to target vial 42 Transfers 25 uL of internal standard to target vial 42 Injects vial 42 Vial 60 Transfers 100 uL from the diluent tank to target vial 60 Transfers 50 uL of sample to target vial 60 Transfers 25 uL of internal standard to target vial 60 Injects vial 60 Developing Instrument Parameters in the Method 6 41 Creating Derivatization and Dilution Programs Series 200 Autosamplers Only 6 42 gt To create a dilution program Select Dilution under Derivatization Dilution and choose the Program command button to open the Dilution dialog box m Parameters Mixing mode Liquid C Air Number of Reagents fi Sample volume uL o Mix speed in Medium x Air mix volume 2400 Z Mix speed out Medium 7 r Ent
387. rmation on how to create new calibration levels refer to the next section Developing Calibration Parameters in the Method 8 25 Setting Component Defaults Adding Default Calibration Levels To determine unknown component amounts TotalChrom compares the component s response peak area or height to the response of a known amount of the same component in a single standard sample To improve the accuracy you can choose to inject more than one standard sample where each sample contains the same component but in different amounts These varying samples are called calibration levels The response produced by the component at each calibration level plotted against the level amount defines the points on which the component s calibration curve is based Some notes about calibration levels e You can only add calibration levels with the Avg Calibration Factor and Use Curve calibration types e Acomponent can have up to 100 calibration levels but the level names for all components in a standard sample must be the same e Use unique level names for different levels e Ensure that two different levels do not have the same amount unless the component is an internal standard component gt To add new calibration levels 1 Choose Avg Calibration Factor or Use Curve as the Calibration Type 2 Under Response select whether to use Area or Height 3 Enter a level name or number in the first empty cell in the Level column The level name
388. rom RST file e The Report Format files used for all reports generated during processing as specified in the Sequence as Optional Reports in the Method or as selected during processing in Batch or Graphic Editing In addition to the above the TCR contains a Signatures Table associated with each report effectively the same as each RPT file defined within the TCR file The signatures are applied to each report independently within the TCR file The Review and Approve function is described in Chapter 20 Review and Approve Introduction and Overview 1 7 Using this Guide Using this Guide This TotalChrom User s Guide is a step by step guide for using the TotalChrom Chromatography System It explains how to create a chromatographic method acquire data format and print reports build a sequence file and how to reprocess data using interactive graphics or a batch mode It also guides you through the post run capabilities of TotalChrom which include comparing chromatograms calculating ratios and differences and creating peak summary reports Chapter Topics Chapters in the TotalChrom User s Guide cover the following topics Chapter 1 Introduction and Overview of TotalChrom Describes the major features of the TotalChrom system and the conventions and terminology that appear in the documentation Chapter 2 TotalChrom Basics Explains the common elements of TotalChrom applications Chapter 3 Configuring TotalChrom Describ
389. rom to acquire data by providing all the information the program needs for a series of injections You can collect and analyze data automatically by using an autosampler which can be connected to either a 900 Series Interface or a LINK Interface Refer to the manual for your 900 Series Interface for information on connecting autosamplers to achieve various degrees of automation When you set up an instrument to run a sequence TotalChrom downloads the parameters from the instrument section of the method or methods to the interface you are using Without these parameters the interface cannot begin to acquire data nor can a LINK controlled instrument be run TotalChrom uses the remaining parameters from the sequence and its referenced methods when it uploads the data acquired from each run from the interface and processes it How a Sequence Works The Information in a Sequence Building a Sequence A sequence file contains two types of information also referred to as parameters e Values that identify a particular analytical sample also known as sample parameters e Information that affects how TotalChrom processes and stores data from a sample also known as processing parameters The main distinction between the two types of parameters is that some can have different values for the two channels A and B others must have the same values for both channels To indicate this the columns in the Sequence Editor spreadsheet are color c
390. rrent settings to apply 3 To generate the plot selected above using the options set in this dialog select Generate This Plot 4 To plot all data that TotalChrom collects during the run Select Set Plot Limits To Full Run If you clear this option TotalChrom only plots the data in the range that you define in the Start Time and End Time text boxes 5 Under Scaling Type select whether to use Vertical Autozero or Absolute Scaling These options and the necessary Scale Factors are defined in Editing Replot Parameters 6 Inthe Scale Factor text box enter the corresponding factor for the Scaling Type you chose in the previous step 7 Choose OK to save the settings and return to the Optional Reports tab Developing Processing Parameters in the Method 7 11 Editing Replot Parameters Editing Replot Parameters The Replot command in the Process menu lets you specify how the replot appears when you print it The settings include paper orientation what portion of the plot you want to print labeling information and scaling parameters You can produce replots in two different ways e You can print one or two chromatograms on one or more pages in portrait or landscape format e You can embed a portrait formatted replot within a report where both appear on a single page Although you select the embedded replot option in the Report Format Editor See Chapter 9 Building a Report Format TotalChrom uses the paramet
391. rument panel then click the Hands On button in the Navigator Hands n OR Choose Hands On from the Instrument menu then select the LC The LC Hands On dialog box appears The tabs and settings available depend on the type of equipment you are using Each tab is described separately below Working with Instruments Interactively 13 7 Setting LC Parameters 13 8 Pump Actions You can control pump actions from the Pump tab in the LC Hands On dialog box You can change any of the available values then activate them by choosing Set Pump You can start and stop the pump at any time with the Start Pump Stop Pump command The LC Hands On pump parameters displayed are the previous runs settings the composition currently in the column They are displayed until a new run is started then the new runs parameters are displayed LC Hands On x Pump Purge Detector Autosampler Elow mL min Pressure psi Poe e Co Cd Set pump New solvent flow rate 0 01 to 10 00 r Solvent composition XA A SGHVETEIBUE ret aig Oleg Ole gt To perform pump actions 1 To change the flow enter a different value in the New text box The current pressure appears below the flow rate 2 To change the solvent composition enter new percentages for solvents A B or C Only solvent A will be available for a binary solvent pump By changing the solvent composition
392. run 1 Choose Start Monitor from the Run menu The signal from the instrument is plotted on the screen If you are viewing the plot for a 900 Series Interface the interface switches to sampling mode The initial scaling of the monitor plot uses the real time plot parameters from the active method During monitor mode the Details window will display the current elapsed time as usual but the plot will not stop when the elapsed time reaches the Run Time set in the active method 2 Choose Stop Monitor to stop plotting the detector signal and to restore the instrument to its previous state Although the data points acquired during monitor mode are not saved in a raw data file on disk they are stored in the interface memory If the interface memory is segmented set up for multiple runs to be stored it is possible for the active memory segment to fill up during monitor mode If this occurs monitor mode will stop automatically Acquiring and Viewing Data 12 31 Viewing Data and Instrument Information Viewing Data and Instrument Information 12 32 The Details button and command in the Navigator open a window that lets you see the run information and instrument status for each instrument The Details menu command in the Real Time Plot window opens the same window The information that appears in the Details window varies depending on the type of instrument TotalChrom updates the information as necessary to reflect the current state
393. ry Table First Vial Volume uL Mix Cycles Equil Time Diluent 1 Tank 2 0 Diluent 2 1 3 0 Diluent 3 6 0 Diluent 4 3 0 Diluent 5 5 0 Cancel Enter the number of the source vial 1 225 Select Liquid or Air as the Mixing Mode In the Sample Volume text box enter the volume of liquid in the sample vials This volume is the amount of liquid present before the Autosampler transfers any liquid to the sample vial If the sample vials contain different volumes enter the smallest volume of the vial series If you are using air mix mode select from the Air Mix Volume list the volume of air you want delivered through the flush syringe for each mixing cycle Select a speed from the Mix Speed In list For liquid mixing this setting controls how fast the syringe draws up a sample from the vial for mixing For air mixing this setting controls how fast the syringe draws up air Select a speed from the Mix Speed Out list For liquid mixing this setting controls how fast the syringe dispenses the sample back into the vial for mixing For air mixing this setting controls how fast the syringe injects air into the sample vial Creating Derivatization and Dilution Programs Series 200 Autosamplers Only 7 Inthe First Vial column enter the vial position of the first source vial in the series that you want to use in the dilution For the dilution operation the Autosampler always dispenses dil
394. ry function to generate reports based on multiple result files Chapter 17 Performing a Fit Analysis Explains how to use the Fit Analysis function to plot calibration curves for components identified in the calibration section of the method Chapter 18 Discussion of Data Analysis Explains how TotalChrom uses the parameters defined in the method to produce an analysis of the raw data Chapter 19 Converting Files to Other Formats Explains how to use the Convert program that comes with TotalChrom to convert files to different formats Chapter 20 Review and Approve Explains how the Review and Approve environment provides a single interface to examine chromatographic data results and reports If electronic signoff and routing of the data is required the environment supports the use of electronic signatures and multiple levels of authority Appendix A How Interfaces Collect Data Explains how the 600 Series LINK Interface and 900 Series Interface collect and store data Appendix B System Suitability Testing Describes how to use the System Suitability program to assess the performance of a chromatographic system Appendix C Interface Validation Explains how to use the Interface Validation Module software which is an add on program to TotalChrom You use this module to characterize the performance of 900 Series Interfaces Appendix D Serial Dilution Explains how to use Serial Dilution which is a separate application for use with th
395. s To learn about Go to page Using Common Dialog Boxes Entering Descriptive Information About a File Using Audit Trail Using Electronic Signature Selecting an Instrument Using TotalChrom Toolbars and Status Bars 2 1 Using Common Dialog Boxes Using Common Dialog Boxes Many TotalChrom applications have the following dialog boxes in common 2 2 Startup File Select File Open Path Select Program Selection Tokenized File Names This section describes these dialog boxes and includes instructions for using them Startup Dialog Box Some TotalChrom applications such as the Sequence Editor display a Startup dialog box when you enter the application This dialog box allows you to choose the way in which you begin your work with the application Your application manager can set whether or not the Startup dialog box appears r Select startup option Create new method C Load method stored on disk Clear MRU List less mth C re xeXT cw SXVerb 3 UNE xamples C PenExe T cw S Wer6 3 NE xamplesNT urboM atrix 1 mth C PenExe T cw S WerB 3 0 Examples BLRUB mth Load a recently edited File When you select a Startup option TotalChrom does one of the following Create New File Opens appropriate dialog boxes that you complete to create a new file Load File Stored On Disk Displays the File Open dialog box where you can locate and select an existing file Load Rece
396. s 8 18 The Purity field is enabled whenever the grid is enabled that is when the calibration type is Use curve or Avg calibration factor The Purity field is disabled and will not be visible when the Calibration Type is Use calibration factor or Calibrate by reference In both of these cases the internal value stored for the component will be reset to 100 You cannot set a purity value for an Internal Standard component since it is always 100 Calibrate by Reference This is for use only with components that are calibrated by reference Components x Identification Calibration User Values LIMS Calibration Type C Use calibration factor yg calibration factor Benlicates Cal reference METHANE Scaling E Weighing v Cal reference factor 1 0000 Level Amt Area Vs _ level1 1 000000 1 260330e 06 Edit Component Cancel Apply Calculate amounts using the factor for the associated calibration reference component When you select Calibrate by reference the Cal Reference Factor entry field replaces the Purity field shown when the calibration type is Use curve or Avg calibration factor The Cal reference factor value is the factor that is modified to act AFTER the raw adjusted amount has been calculated in the usual way In other words Cal Reference Factor acts as an additional multiplier on the raw amount The factor can only be used if the calibrati
397. s Entering Baseline Timed Events 7 6 Baseline timed events alter the way TotalChrom detects and integrates peaks during the run You can use baseline timed events to help maintain consistent results when peak characteristics and baseline characteristics change Although you can set timed events in the processing section of the method you can also add them directly to the chromatogram by using the Graphic Method Editor Using the Graphic Method Editor helps you see how adding one or more baseline timed events affects the run For more information about the Graphic Method Editor refer to Chapter 10 Editing Methods and Results Graphically You select events in TotalChrom by choosing the Baseline Timed Events command in the Process menu You then select different events by clicking on a graphical representation of the event on the Baseline Timed Events tab The following table provides a brief description of each timed event The code column indicates the corresponding baseline timed event code that appears on the chromatogram in the Graphic Method Editor For technical information about these events refer to the sections How Timed Events Affect Peak Detection and How Timed Events Affect Integration in Chapter 18 Discussion of Data Analysis Set bunch factor to value Set noise threshold to value 1 999999 Set area threshold to value Enable peak detection Disable peak detection Enable negative peak detectio
398. s TotalChrom will include a supplementary report following the main report This report includes the individual component and or peak results These results are always based on the individual calibration of 9 15 Editing Report Format Options 9 16 the group members For timed group members this may be one of the options for calibrating unidentified peaks If you want the individual members of a group to use the overall group calibration select the Calibrate By Reference option for the individual components in the method file and identify the group itself as their calibration reference e Jf you select Print Baseline Timed Event Table and the method is set so that events track reference peaks then both method time and adjusted time will be included in the report e Select Create ASCII Delimited File if you want to create a file that contains a version of the report that is readable by another application These files are saved with the file extensions TXO through TX6 in the same directory as the result files TXO is the base report and TX1 through TX6 are the optional reports from the processing section of the method The report name is taken from the name of the result RST file e Select Create AIA Metafile to create a special data file in the standard format defined by the Analytical Data Exchange Protocol for Chromatographic Data ASTM E 1947 98 to transfer chromatography data between data systems These files are sav
399. s display changing 10 16 labels changing 17 7 options configuring 3 20 origins changing 12 30 parameters changing 12 28 redrawing 10 17 xi rescaling 10 16 scale absolute 7 16 methods of calculating 17 6 settings for reports 7 11 Plot command 3 20 Plot Settings dialog box 7 11 Plot Title Properties 20 65 plot window 42 45 Plot Window Properties 20 59 point index definition 18 6 point to point fit 18 70 Post sequence options 12 13 Post sequence Options 3 8 post analysis programs definition 18 4 preliminary baselines adjusting 18 24 Preserve View command 10 8 10 13 Previous command 12 32 Previous Component command 17 4 Print Method command 10 54 Print Options 20 31 Print Report command 10 53 Print Summary command 5 8 Printed Reports 20 12 printing audit trail 2 12 calibration data 17 16 chromatograms 14 6 configuration information 3 25 method information 5 8 10 54 options for plots 3 20 7 12 options for reports 9 13 replots 10 53 report format file content 9 17 reports 10 53 run logs 6 7 selecting optional reports for 7 9 sequence information 11 60 suitability method and reports B 18 summary report 16 4 16 11 16 25 summary report format file content 16 24 PRN file extension 16 24 Process dialog box 7 2 7 8 7 9 Process Number 9 15 processing parameters xii definition 5 2 entering in method 7 2 for dual channel instruments 7 2 overview 7 2 setting 10 22 Process Time programs 11 46 program parameter
400. s 13 8 Program Selection dialog box 2 5 programs See user programs Project Directory 3 23 property inspector 20 25 pump parameters adjusting after setup 13 8 changing 6 27 setting configuration 6 23 setting control 6 26 programs creating 6 24 deleting or duplicating steps in 6 29 6 30 purging 13 9 solvent gradient programs creating 6 24 starting and stopping 12 23 purging pumps 13 9 Q quantitating component parameters 8 9 unidentified peaks 18 78 quantitation units parameter definition 8 4 quantitation overview 18 68 Quick Method 12 15 quick paths 3 21 Quick Start acquiring data with 12 4 overview 12 2 reprocessing data acquired with 15 4 R ratios adjusted height 18 29 amount 8 5 peak height definition 18 28 response 8 5 valley height 18 30 valley to peak 18 14 width 18 14 raw data files loading 10 8 Raw Points command 10 16 Raw Points with Bunching command 10 16 Read RVP command 13 4 reagent values 6 38 real time plot changing origin of 12 30 parameters setting 6 10 rescaling 12 28 setting scale 6 10 viewing 12 26 viewing multiple 12 28 Real Time Plot command 12 26 Real Time Plot Scale command 6 2 6 10 Real Time Plot window menus and commands 12 26 opening 12 26 Real Time programs 11 46 reference calibration factors 18 75 reference chromatogram hiding or showing 10 21 manipulating 10 21 reducing 10 20 resizing 10 21 Reference Chromatogram command 10 6 reference components calibrating by 8 24
401. s Interface will receive rack information For more details refer to the 900 Series Intelligent Interface Operator s Manual As you enter the rack and vial information you will see the Autosampler Code change These codes have the format abnnmm where a NorP designating negative N or positive P logic b BorD designating binary B or BCD D coded logic nn 1 through 8 designating the number of vial bits in base 4 format mm Othrough 6 designating the number of rack bits in base 4 format You can revert to the original settings in the dialog box at any time by choosing Reset gt To save the configuration e Choose Finish TotalChrom creates a configuration file CFG for the instrument In the Configuration Editor Summary list YES appears in the Configured column Configuration 3 7 Configuring Instruments gt To set Post Sequence Options 1 Select Post Sequence from the Instrument menu in the Configuration Editor Configuration Editor Post Sequence Options appears Post Sequence Options 9 2 Selecta Post Sequence Action and choose OK e Selecting Clear Setup will leave the instrument uninitialized at the end of the sequence No other options in the Post Sequence Options tab will be available This is the only action available for a bracketed sequence e Selecting Use Last Active Method From The Sequence will leave the instrument set up with the last used method No other options in the
402. s all instruments defined in the System Configuration program and includes the following data Name Your name for this particular instrument Location Where the instrument is installed Type The instrument model or type Acq Port The physical data acquisition port to which the interface is connected LINK Port The physical port to which the instrument is connected This applies only to instruments that are connected through a 600 Series LINK interface Configured Displays YES if you have provided all the information TotalChrom needs to configure the instrument Otherwise the status is NO The Configuration Editor IPM Shows whether or not the Instrument Personality Module IPM for this device has been downloaded This applies only to instruments connected through a 600 Series LINK interface The area below the list displays key information about the currently selected instrument On the left is information about the interface 900 Series or LINK including the type model number EPROM version number memory size assigned to the instrument in bytes and serial number On the right for LINK controlled instruments is a summary of the chromatograph s configuration and any attached autosampler Menus Configuration The Configuration Editor includes the following menus File Menu Lets you set up and print the current instrument configuration file refresh the view of the system configuration pre
403. s depend on which type of instrument you have 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 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 Configuration 10 11 12 13 Configuring Instruments 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 Choose OK A check mark in the LINK Configuration dialog box indicates that the instrument has been configured gt Toset LC configuration options 1 In the LINK Configuration dialog box choose the Configure button next to the port selection The LC Configuration dialog box appears T
404. s described in a separate procedure gt To choose a data acquisition port 1 Inthe Navigator choose Configuration from the Build menu The Configuration Editor opens which shows the instruments that are connected and turned on 2 Select the instrument you want to configure Configuration 3 9 Configuring Instruments 3 Choose Configure from the Instrument menu The Acquisition Port dialog box opens Acquisition Port 4 Click the marks to expand the tree and select the data acquisition port to which the interface is physically connected When a port is highlighted you can click Query Port For Type to see which type of interface is connected to it 5 Choose Continue The LINK Configuration dialog box opens LINK Configuration 3 10 Configuring Instruments gt To set LINK configuration options 1 Selecta LINK port for the instrument 2 Select the Instrument Module that is physically connected to this port in the Instrument Module list and a Detector Module and Autosampler Module if applicable The LINK port becomes unselectable and any detector and autosampler selected will occupy the subsequent available LINK ports 3 Select the instrument names to configure additional instruments on remaining LINK ports If you make a mistake choose Back to return to the Acquisition Port dialog box Choosing Restart disconnects any configured instruments and clears all ports on the LINK
405. s window If you open a new file with Auto Size off the new window will appear on top of the existing windows instead of being stacked tiled or cascaded Displaying Chromatograms in Overlay View When you choose the Overlay command on the Window menu two or more open chromatogram files will appear in the same window Overlaying chromatograms enables you to compare their similarities and differences Because overlaid chromatograms use the same set of axes you distinguish them by their colors which you control through the Configuration function in the Navigator Displaying Chromatograms 14 7 Controlling the Appearance of Chromatogram Windows 14 8 In the overlay window one chromatogram will appear in front of the others you can change the chromatogram that appears in front by selecting the window that you want to be the topmost or active chromatogram in the overlay window The topmost active chromatogram determines which axis labels appear If you select Show Baselines Show Retention Times or Show Components from the Options menu when you open one or more result files the retention times that appear will be those for the topmost chromatogram The Overlay command functions as a toggle when you select it a check mark will appear next to it and all open chromatograms will appear in a new window All single plots will remain open and the chromatogram that was selected when you chose Overlay will be topmost in the overlay window
406. sequence paths The path entry will not be used in this case To override the path that is defined in the sequence you selected enter a different path in the Raw and Result file paths text boxes and select the Store data in above paths or subdirectories in preference to sequence paths For example if the path in the sequence is C TC MARY and you enter C TC JOHN in the Setup Instrument dialog then the files will be stored in C TC JOHN 12 9 Setting Up Data Acquisition 12 10 However if the path in the sequence specifies a subdirectory of the default path that you enter here then that subdirectory will be used For example if the path in the sequence is C TCJOHN DATA and you enter C TC JOHN in the Setup Instrument dialog then the files will be stored in CXTCUJOHNWDATA If the sequence you selected does not specify a path enter the path you want in the Raw and Result files path text box The state of the Store data in above paths or subdirectories in preference to sequence paths check box is irrelevant in this case Setup Instrument Listoment ilirice Basenenane agaran Bonmmanraline Setting Up Data Acquisition e Ifyou are constrained to use default paths or a subdirectory then the Store data in above paths or subdirectories in preference to sequence paths check box is always checked and disabled Setup Instrument C AmoldME Sequence Path audittest seq C PenE xes C PenEx
407. ser program To pass the names of files that TotalChrom uses or generates during the run use the variables shown below When Analyze runs a user program it adds the command line by taking the specified information and providing file name substitution for the variables as follows RAW Full path and file name of the raw data file RST Full path and file name of the result data file MET Full path and file name of the method file SEQ Full path and file name of the sequence file IDX Full path and file name of the index file AIA Full path and file name of the AIA metafile file Developing Processing Parameters in the Method 7 17 Running User Programs 7 18 The names of the sequence and method can be obtained from either of the data files so you need not specify all of them If you must include the name of an explicit file rather than one of the tokens listed above and the file name contains a space you must enclose the name in quotation marks If TotalChrom is running in a networked environment and the command line must include the name of an explicit file use the UNC name instead of a mapped share name When you run TotalChrom user programs calplot exe suit exe and summary exe from the command line they run in the quiet mode q by default TotalChrom automatically enters the q to the command line User programs that run in the quiet mode run in the background and do not display a window
408. serts the new step in the table using the same values as the original step that you selected 4 Drag the new step point s anywhere within the allowable boundaries to change the parameters and solvent percentages for each step After you release the mouse TotalChrom updates the table and the gradient curve Developing Instrument Parameters in the Method 6 29 Setting Control Options 6 30 gt To delete steps from the gradient curve 1 With the right mouse button click on the point on the gradient curve that represents the step that you want to delete The Delete Duplicate pop up menu appears 2 Choose Delete TotalChrom deletes the step from the curve removes the corresponding row from the table and shifts all remaining rows up one place 0 0 10 0 20 0 30 0 3 To reverse the last change that you made choose Cancel to close the dialog box The gradient program reverts to the previously saved version You can also delete steps using the solvent table by entering a zero in the Time column However this approach deletes all subsequent steps in the table as well Setting LC Detector Parameters The Detectors tab of the Instrument Control dialog box for LCs varies depending on the type of detector you are using LC 235 Series 200 or 785 Each is described in a separate procedure below Setting LC 235 Detector Parameters The Detectors tab for an LC 235 detector includes a table you can use to create a detector prog
409. ss the Fit Analysis function through the Method Editor It lets you examine calibration curves change fit types and overlay the fits to determine visually which fit is the best for your data This function also allows you to add custom labels and generate high quality plots of the calibration curves Fit Analysis is described in Chapter 17 Performing a Fit Analysis Generating Summary Reports The Summary function in TotalChrom lets you generate a single report that includes a tabular listing of the results for multiple components from a series of runs You can select result files to be summarized from a sequence file by specifying a common base file name or by choosing from a list of result files on your disk Summary also includes a report editor that lets you select the information you want to include in your summary report This program also lets you store the summary report in a comma delimited ASCII file which you can then import directly into a spreadsheet program such as Microsoft Excel The Summary function is described in Chapter 16 Summarizing Component Data Review and Approve The Review and Approve process requires one or more people other than the analyst generating the data to review and sign the work done by that analyst Once data have been reviewed and the reviewer s signature applied that data is then available for one or more levels of approval signatures After final approval has been applied to the rep
410. ssary For more information on levels refer to Working with Calibration Levels on page 8 37 You can perform a calibration by using the calibration of another component TotalChrom calculates the amount for the component based on the calibration curve of the other component This type of calibration is called calibrating by reference The calibration reference component in this case can be any component it does not have to be one previously defined as a reference peak gt To calibrate using a reference component 1 Select the Calibration tab of the Components dialog box 2 Select Calibrate By Reference as the Calibration Type r Calibration Type C Use calibration factor C Avg calibration factor ol 1 C Use curve 3 Select a component to use as a reference from the Cal Reference list Developing Calibration Parameters in the Method 8 35 Adding and Editing Components gt To calibrate using a calibration curve 1 Select the Calibration tab of the Components dialog box 2 Select Use Curve as the Calibration Type r Calibration Type C Use calibration factor C Avg calibration factor C Calibrate by reference 3 Under Response select whether to use Area or Height The last column of the table changes to Area or Height depending on the option you choose 4 Selectthe Curve Fit Type you want to use from the list Depending on the calibration curve type the minimum number of levels required ar
411. st From a Peak List During the peak detection phase of data analysis TotalChrom assigns a sequential number to each detected peak This list is referred to as the peak list The component list in contrast is the list you create in the method that identifies each peak as a specific component The Load From Peak List and Merge From Peak List commands in the Calibration menu let you add components to the method from the current peak list gt To create a component list from a peak list e Choose Load From Peak List from the Calibration menu TotalChrom adds a component to the list for every unidentified peak in the chromatogram Component names take the form peak n where n is the index number of the peak You can use the Load From Peak List command even if a component list already exists TotalChrom retains in the list any existing components that are matched with peaks and deletes any component that is not matched with a peak Previously unidentified peaks will be added to the component list as described above The Merge From Peak List command in contrast retains all existing components whether they are matched to peaks or not It adds a new component for each previously unidentified peak gt To merge a peak list with the component list e Choose Merge From Peak List from the Calibration menu TotalChrom retains all current components whether the components are identified with a peak or not TotalChrom then adds a component na
412. stem groups of function buttons that give you access to TotalChrom applications and a box that shows the status of instruments The names on the Navigator buttons are the names of commands and the text above the buttons shows the menu on which you can find each command J TotalChrom Navigator dad Build Instrument Run Wew Reprocess Display Apps Admin Heb Ready 3 s Instrument ACQ No Data z3 VF Ready EJ CMD None P Pump Off Setup A S Ready re pig ns Like toolbar buttons Navigator buttons represent the functions that you are likely to perform frequently in TotalChrom Most buttons have a corresponding menu command Some infrequently used functions have menu commands only Choose a TotalChrom function by clicking a button or by choosing a command from a menu When you choose a menu command you can subsequently select which instrument the command will apply to When you click a button the command is carried out for the instrument that is selected in the Instrument panel Navigator Buttons and Commands Navigator Buttons and Commands This section describes Navigator buttons and commands in more detail Instrument Panel This panel has two tabs Primary a list of up to eight instruments that you use most often and All a list of all configured instruments on your network to which your computer has access rights When you select an instrument on either tab on this panel other TotalChrom operations that yo
413. t data into an external spreadsheet application gt To copy and paste data 1 E Select the block of data that you want to copy Choose Copy from the Edit menu Identify the paste location by selecting the upper leftmost cell Choose Paste Each cell in a pasted block must pass a validation check for format such as length or numeric range If any single cell fails validation the entire paste operation is canceled and all cells remain unchanged The basic rules of validation for pasting are e Alphanumeric cells such as Sample Name can accept from any cell within length constraints 11 33 Editing the Sequence Spreadsheet 11 34 e Numeric cells such as ISTD Amount can only accept numbers within the allowed range e Cells with enumerated lists such as Type can only accept strings that match one of the allowed entries exactly except for case e Method cells which require a path will accept a string If the string does not include a valid path the default path will be added Changing the Values in Multiple Cells You can save time by changing the contents of multiple spreadsheet cells in one operation by using the Change Values command gt To change the values in multiple cells at one time 1 2 Select the cells that you want to edit Choose the Change Values command from the Change menu or the shortcut menu The Change Values dialog box has a data entry field for each cell you selected In the f
414. tandard Windows printing options gt To print the information from a sequence 1 Choose Print from the File menu to open the Print Options dialog box Print Options x Printer System Printer SSWHITNEYSHPLJA Print hidden columns Audit trail r Channel A Selections v Sample descriptions I Process information Sample notes User data LIMS IDs r Channel B Selections Sample descriptions Process information Sample notes User data LIMS IDs tesa 2 Under Options select the check boxes for the print options you want To print every column in all cycles in the entire sequence for both channels select Full Detail All Channel A and Channel B selections will be disabled To start a new page for each type of information select Form Feed Between Sections To include every column in the printout select Print Hidden Columns When this is not selected the printout includes only the visible columns To print a history of changes made to an audited file select Audit Trail 3 Foreach channel select the check boxes for the options that you want to include in the printout then choose OK 4 Make any changes in the Print dialog box and then choose OK Chapter 12 Acquiring and Viewing Data This chapter explains how to use TotalChrom to acquire and view data from your chromatographs To learn about Go to page Setting Up Data Acquisition Controlling Data
415. te 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 temperature program 6 Youcan 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 6 14 Setting Control Options 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 7 Under Cryo select the type of subambient cooling that you want to use or set Coolant to Off 8 If you are using sub ambient cooling enter the values for the cryogenic cut in temperature and the oven timeout in the respective text boxes 9 Under Oven enter the maximum oven temperature allowed TotalChrom will not allow any temperature in the table to be greater than this value 10 In the Equil Time text box enter the number of minutes that you want the oven to equilibrate at the initial temperature before it becomes READY 11 Under Heated Zone Setpoints if you have non programmable inlets enter the temperature for injectors A and B If you have programmable inlet type POC or PSS configured in
416. te a new calibration level enter the new level name in the Level text box In the Amount text box enter the standard amount of the component 12 13 14 15 Working with Components Under Calibration Type select Average or Replace Average Adds an entry to the calibration replicate list for this component in the current method Replace Deletes all calibration replicates in the current method and replaces them with one replicate for the current data file This option also applies to retention time replicate information Choose Reset RT if you are editing an existing component and want to set the expected retention time to the actual value in the current data file For a new component this will already be true TotalChrom deletes any existing retention time replicate information Choose Next or Prev to implement the changes and move to the next or previous component in the list Choose Return to close the Edit Components dialog box Component names for peaks that are close to each other might not appear on the plot Expand the plot to see all component names Re Identifying Peaks You can re identify the peaks displayed in the Graphic Method Editor in two ways e By using the Re Identify command e By explicitly assigning a component name to a selected peak When you Choose the Re Identify command TotalChrom runs the peak identification stage of data analysis and incorporates any changes you have made
417. te blocks of cells and you can paste data from and copy data into external spreadsheet applications Change Menu Lets you change values in your sequence file such as filling rows with repeating or incrementing values You can also browse for file names change global parameters create sample notes and include program information 11 4 Using the Sequence Editor Build Menu Lets you append add new cycles to the current sequence append cycles based on a template and append another sequence file to the current sequence The Build menu also contains commands that let you create a sequence by loading appending or merging a text file Format Menu Lets you hide and unhide columns adjust column width synchronize column width for channels A and B and select a font for the spreadsheet Actions Menu Lets you switch to Setup reprocess data in the sequence using the Batch Reprocessing program and switch to the Method Editor to change the method parameters referenced in the current sequence View Menu Lets you display or hide the Sequence Editor toolbar and Edit Bar The Status Bar at the bottom of the window displays important information about the sequence and Help messages for each command and toolbar button that you select You cannot hide the Sequence Editor Status Bar The Status Bar also displays the word Modified if you change any part of the current sequence The Sequence Spreadsheet TotalChrom displays sequence in
418. te injections is the same The two options are Vial Number and Sample Number If you select Vial Number all sample information for cycles with the same vial number is changed to match the first cycle with that number If you select Sample Number it changes all sample information for cycles with the same sample numbers to match the first cycle with that sample number Because the Sample Fill In function involves comparing each sequence row against every other row the time required for it to be completed increases geometrically with the number of rows gt To set sample information for replicate injections 1 Choose the Sample Fill In command from the Change menu or the shortcut menu Cancel Use vial number to fill in sample info 2 Select Vial Number or Sample Number 3 Choose OK Changing Paths The Path command allows you to change the path associated with all or specific method and or data files The default entries in the Change Path dialog box reflect what you select in the spreadsheet before you choose the command You can edit these defaults as necessary gt To change paths 1 If you want to change the path s in specific rows or columns select them then choose the Path command The Change Path dialog box appears 6 Editing the Sequence Spreadsheet Starting row f Apply to other channel Ending row fi Path to change J C Change path for T Instrument method Raw data file
419. ter a value in the Calibration Factor text box and if necessary select a calibration option Under RRT Calculation select the way you want TotalChrom to calculate relative retention time The second option is not available until you add a component to the method If you select this option also select the specific component from the list below Your selection here is reflected in the Components dialog box where you can also control this setting as you identify individual components Conversely if you change the RRT reference there that change will be reflected in the state of the options in this dialog box If you have Connect complete the LIMS Results tab according to the Connect documentation Make any other changes to the values in the Global Information dialog box and then do any of the following e To save your work and close the dialog box choose OK e To save your work without closing the dialog box choose Apply e To discard your changes since the last time you chose Apply and close the dialog box choose Cancel Understanding Component Parameters Understanding Component Parameters The Component List window displays the components in the method The component parameters in the middle section of the window show how you want the components to be quantitated LIU Mm E R eqiaed Omn Poht PohtFIt No FitCoemokit Response levell 1 0000 42012000 33427 20 116 851 inl 3n You provide th
420. ter explains how to use the Configuration program to set up your instruments and set user options such as which screen colors to use and what information to include in the screen display Throughout this chapter and in other parts of the manual the name AutoSystem refers to both the AutoSystem GC and the AutoSystem XL GC Also 900 Series refers to the NCI 901 902 the 900 Series and the 900A Series Intelligent Interfaces To learn about Go to page The Configuration Editor Configuring Instruments Configuring a 900 Series Interface Configuring a 600 Series LINK Interface and Attached Instruments Configuring User Options Printing Configuration Information 3 1 The Configuration Editor The Configuration Editor 3 2 The Configuration Editor lets you edit configuration data for those instruments and interfaces to which your application manager has given you access gt To open the Configuration Editor e In the Navigator choose Configuration from the Build menu The Configuration Editor appears gp Configuration Editor oll File Instrument Interface User View Help SQ a B Slee ie a ry GC Series 200 LC Pumy j Interface instrument Configuration AutoSystem XL GC with Autosampler BUILT IN NONE NONE FID NPD NP NONE SPLIT NONE NONE VALVE NONE NONE INTJNT Press H2 PPC Flow H2 Press PSI NONE NONE NONE Summary List The Configuration Editor Summary list show
421. ters Building a Method When TotalChrom collects and processes data and creates a result file the method parameters used to create the results are stored with the result file Because a sequence can specify different methods for instrument processing and calibration the method parameters stored in a result file can represent sections from different methods You can use the Import command in the File menu to import the method parameters stored in a result file You may also import parameters from instrument process and sample files created in older versions of TotalChrom prior to Version 4 0 When a method that is embedded in an imported result file has auditing enabled then auditing is also enabled for the method into which you import the file gt To import method parameters from other files 1 Choose Import from the File menu 2 Inthe TotalChrom File Open dialog box select the file type that you are looking for RST for result INS for instrument PRC for processing or SMP for calibration files 3 Locate and select the file whose parameters you want to use and choose Open TotalChrom replaces the values in the method with those from the imported file 5 9 5 10 Chapter 6 Developing Instrument Parameters in the Method This chapter explains how to use the Method Editor to set instrument parameters in the method For general information about using the Method Editor refer to Chapter 5 Building a Method
422. th channels select the Set Other Channel To The Same Width check box Choose OK 11 31 Editing the Sequence Spreadsheet Synchronizing Column Widths The Synchronize Column Widths command lets you set all column widths in the inactive channel window to the same width as their corresponding columns in the active channel You might want to synchronize column widths after you change them in one channel of your spreadsheet gt To synchronize the width of spreadsheet columns in both channels 1 Select the spreadsheet that contains the desired column widths 2 Choose the Synchronize Column Widths command on the Format menu Changing the Font The Font command on the Format menu allows you to change the font type style and size of the text in the sequence spreadsheet You may use any fonts installed on your computer 1 Choose Font from the Format menu 2 Select the font style and font size that you want to use 3 Choose OK Editing Individual Cells You can change the contents of spreadsheet cells individually or in groups Each cell in the spreadsheet is one of the following types e Cells that you type into directly e Cells that contain a list e Cells that require a file name Editing Cells Directly Certain columns contain cells that you can edit directly by selecting and typing required information gt To edit cell contents directly 1 Select the cell that you want to change 2 In the cell or in the Edit Bar t
423. that specify how you want to handle the control acquisition storage analysis quantitation calibration and reporting of data Instrument The instrument section of the method contains parameters for all tasks associated with real time data collection and display Processing The processing section of the method contains parameters for all tasks associated with post run analysis of the data Calibration The calibration section of the method contains a list of components with associated identification and calibration information Each component in the method can have unique calibration tables reference peaks internal standard peaks calibration curve fits number of calibration levels and search windows The Method Editor is described in Chapters 5 6 7 and 8 Setting up a Sequence In TotalChrom you create a sequence file to designate the method you want to use for each injection A sequence also specifies where TotalChrom stores data and indicates whether or not an injection is to be used as a calibration standard A sequence can also be used for dual channel acquisition and it allows you to set up totally independent sample IDs storage integration calibration and reporting for each channel You must have a sequence file in order to perform dual tower and random access injections with a LINK controlled instrument to change methods and to perform other functions in TotalChrom The Setup function in the Navigator lets
424. the active method For LC instruments you do not have the option to modify the active method only subsequent runs that use the same method For GC instruments if you change the mode during a current run e g from Flow to Velocity it will not change the GC until the next run The commands and options available in the Method Editor depend on the type of instrument you are using and whether the method is active or not When you modify the active method the term Modify Active is displayed in the title bar of the Method Editor When you modify a method that is not active you can modify any parameter except the instrument name When you modify the active method the instrument parameters that you can modify are limited to those that can be downloaded during a run When you finish editing the method TotalChrom downloads it to the interface so that the modified version will be present during the run in which the method is used Working with Instruments Interactively 13 13 Modifying a Downloaded Method 13 14 gt To modify a downloaded method 1 If the instrument is not bound choose Bind from the Instrument menu then select the instrument that you want to bind Select the instrument in the Instrument panel then click the Modify button in the Navigator and choose Downloaded Method Eon OR Choose Modify Downloaded Method from the Instrument menu then select the instrument If the setup contains more than one method se
425. the label that you want to move and use the mouse to drag it to another position in the chromatogram If the label displays time into the run that value will change relative to the position of the label Deleting a Label gt To delete a label 1 Click the right mouse button in the label that you want to delete 2 Choose Delete from the Labels pop up menu Editing Label Text When you create a label TotalChrom inserts a time into run value by default You can create custom labels by editing the text You can also restore the time into run value in a label whose text you have edited previously Displaying Chromatograms 14 17 Adding and Editing Chromatogram Labels 14 18 gt To edit the text in a label 1 2 Click the right mouse button in the label whose text you want to edit Choose Edit Text from the Labels pop up menu The label will become a text box Type the text that you want the label to contain Press Enter to accept changes You can restore the time into run value at any time by deleting your replacement text gt To restore the time into run value 1 2 Right click in the label whose time into run value you want to restore Choose Edit Text from the Labels pop up menu The label will become a text box Press the Delete key to remove the existing text Press Enter to accept the change The time into run value will be restored reflecting the current position of the label Setting the Text Col
426. the operator s name and Name by the sample name An option is provided to prevent the user from changing these file names i e those columns will be set read only in SeqEdit for that user Another option active by default is the appending of a file number suffix to the file name Default Base Names x Num lt User DOY gt lt Mon gt lt Year gt lt Chan gt Data channel lt Rack gt Rack Number Name gt Sample name lt DOM gt Day ofthe month at start of run KSDOM Day of month at time of set up SDOY gt Day of year at time of set up SMon Month at time of set up L underscore m Separator Instrument name Sample number User logon Raw Data File Clear Cancel Day of the year at start of run Month at start of run Year at start of run Clicking on a displayed token in the Tokens list box adds it to the Raw Data File string The Tokens list box displays a list of allowed tokens lt Calib gt lt Chan gt Inst Rack Name Num User DOM lt DOY gt lt Mon gt lt Year gt lt SDOM gt lt SDOY gt lt SMon gt 2 6 Calibration level null if the run is not a calibration Channel A or B Instrument name Rack number Sample name Sample number User logon name Day of the month at start of run Day of year at start of run Month at start of run Year at start of run Day of month at setup does not cha
427. the reagent transfer 11 In the Reaction Time column enter the reaction time for the mixture This time specifies how long the Autosampler waits after the transfer before it injects the sample or proceeds to the next vial The timing begins after the addition and mixing operations complete 12 Repeat steps 8 through 11 for each reagent in the series 13 Choose OK Setting up a Dilution Use the Dilution dialog box to program dilution operations The options in this dialog box change slightly depending on whether you choose air or liquid as the mixing mode The Dilution operation allows you to dilute a consecutive range of target vials in the tray and make additions of liquid from another range of vials to the same group of target vials Dilution Example Use the Entry Table in the dialog box to program each separate step of the operation For example suppose you configure your tray so that the first 20 positions contain sample vials the next 20 contain internal standard and the last 20 positions contain the target vials Set the vial numbers for the target vials vials 41 through 60 in this example in the Sequence Editor You then want to program the Autosampler to e Add 100 uL of diluent from the tank to each of the 20 target vials e Add 50 uL of liquid from each of the 20 sample source vials into the corresponding target vials e Add 25 uL of internal standard from each of the 20 internal standard vials into the cor
428. the reciprocal of the square of the amount log X Plots response as a function of the base 10 log of the amount 1 log X Plots response as a function of the reciprocal of the base 10 log of the amount If you are using internal standard calibrations X represents the amount ratio If you use one of these scaling alternatives some values will not be valid For example you cannot use 0 0 with I X or I X X and you cannot use an amount less than 1 0 with a logarithmic option Weighting Factor By default the software weights each data point equally when it calculates the calibration curve equation However you can use different weighting options to affect how the curve is fit to the data The Weighting options are None Applies no weighting 1 X Uses the reciprocal of a point s amount value VY Uses the reciprocal of a point s response value 1 X X Uses the reciprocal of the square of a point s amount value 1 Y Y Uses the reciprocal of the square of a point s response value Purity Value for Components Enter a Purity number that represents the percent purity of the standard material for the component The amount at each calibration level is multiplied by the purity value before being used to calculate the calibration curve The range of permitted values will be 0 0001 to 100 0000 The default value will be 100 0000 Developing Calibration Parameters in the Method 8 17 Understanding Component Parameter
429. the whole chromatogram select Set Plot Limits To Data Limits e To specify a particular time period for the replot deselect Set Plot Limits To Data Limits and then enter the Start Time and End Time to designate which portion of the plot you want to print 9 In the Plot Title text box enter the name you want to appear on the replot s This option is not available for a replot that is embedded in a report 10 In the X Axis Label text box enter the label you want to use for the time axis of the replot s Developing Processing Parameters in the Method 7 13 Editing Replot Parameters 11 12 13 15 In the Y Axis Label text box enter the label you want to use for the response axis of the replot s Select Draw Baselines if you want to print baselines for each peak Select Timed Events if you want each timed event to appear on the printed replot s Under Scaling Type select the scaling option you want to use for the replot s Vertical Scaling Scales the plot so that the largest peak prints at full scale Autozero Offset Scales the plot so that the Y axis minimum data point value is at 5 percent of full scale TotalChrom determines the Y axis maximum based on the value you enter in the Full Scale text box Absolute Scaling Lets you enter precise full scale and offset values In this case the Y axis minimum is equal to the Offset value and the range of the Y axis is equal to the Full Scale value
430. tion about 17 11 fitting and weighting 17 9 from regressive calculations 18 58 overview 17 5 18 47 plotting 17 2 data copying 17 17 printing and plotting 17 16 17 18 defaults setting 8 23 external standard 8 5 external vs internal standard 18 49 18 53 internal standard 8 5 8 14 levels adding 8 26 8 37 changing 8 38 definition 8 26 deleting 8 38 guidelines 8 26 8 37 internal standard 18 52 overview 8 37 18 46 parameters changing for a range of components 8 44 curve fit type 8 16 17 9 definition 5 2 8 2 editing global 8 7 entering 8 2 regression weighting 17 10 reject outliers 8 5 replace versus average 18 55 scaling 8 17 setting 8 33 types 8 2 weighting 8 17 replicates definition 8 46 deleting excluding 8 47 8 49 report example 18 61 standard options 8 5 types 8 15 8 33 10 41 updating 8 46 10 48 within a sequence 11 9 calibration curve fit 8 36 calibration curve parameters 8 25 8 36 calibration of components overview 18 46 Calibration Plotting Calplot application See Fit Analysis Cancel Run command 12 21 carrier parameters 6 15 CB See common baseline timed event cell values duplicating 11 43 17 15 CFG See configuration file Change Calibration Info command 8 43 Change Component Info command 8 43 Change Password command 4 2 Change Scaling command 17 8 Index Change Values command 11 34 chapter summary 1 8 child peaks definition 18 28 chromatograms See also plot adding labels to 14 4 14 16
431. tion to Processing Parameters 7 2 The processing section of the method contains parameters that control the following steps in data analysis e How peaks are detected and integrated e How reports and replots are printed e Which user programs are run at which point in the data analysis process Use the Process menu in the Method Editor to set and edit processing parameters in a method If you are using a single channel instrument you need to develop only one set of processing parameters If you are acquiring data using a dual channel instrument you can either use the same processing parameters for both channels or you can create two separate methods each method with different processing parameters one for analyzing Channel A and one for Channel B gt To enter processing parameters in the method 1 In the Method Editor choose a command in the Process menu to open the Process dialog box The dialog box opens to the tab corresponding to the command you selected The following figure assumes you chose Baseline Timed Events Integration Baseline Timed Events Optional Reports Replat User Programs Time min p 00 Add Event Set Bunching Factor BF Delete Replace mor us Clear List m Defined Events Time Event Value Code Level Correct actual times of all baseline events based on actual RT of nearest reference peak Cancel Apply Time into run at which this event is to occur 0
432. to Duplicate a Cell Value Building a Sequence The Fill Down command provides a quick way to fill a column from a designated cell downward with the same value You may perform this operation for any column in the spreadsheet but you must begin by selecting an individual cell The spreadsheet contains several columns that are likely to contain a constant value over a range of injections Study Sample Volume the Method file columns Method Inst Method Proc Method and Calib Method and the columns that contain conversion factors For the Number Vial and Data File columns consider using the Smart Fill command instead of Fill Down because when you use the latter incorrect values that might invalidate the sequence can be introduced The Fill Down command has a special action in the Notes column of the spreadsheet if you select a cell in a Program row the Program information is copied to all other Program rows in the spreadsheet If you select a cell that is in any non program row the Sample Note is copied to all other non Program rows in the spreadsheet gt To insert a repeating value in an entire column 1 Selecta cell whose value you want to copy to all cells below it in the current column 2 Select Fill Down from the Change menu or the shortcut menu 11 43 Editing the Sequence Spreadsheet 11 44 Using Sample Fill In for Replicate Injections The Sample Fill In command ensures that sample information for replica
433. togram Using Keystrokes esee 20 55 Selecting Objects ina Plot eee etel E Rete rip fe PEE RR eet ien 20 56 Plot Window Properties Dialog eese enne nennen 20 59 Plot Window Plot Title Properties Dialog eene 20 65 Plot Window Baseline Events Dialog eene 20 68 Plot Window User Label Properties Dialog eene 20 71 Plot Window Instrument Event Properties Dialog eeeeeee 20 74 Viewing Peak Component Information esee nnne 20 77 Plot Window Viewing Peak Components Properties Dialog 20 78 Peak Component Properties Dialog Calibration Tab eee 20 83 Report Window Overviews oie eiie tiep hei tat ee c ipee ed Res trench 20 87 Interactions Between Windows eese nennen eren nrene enne 20 87 Report Window Show Hide Dialog eese eere 20 88 Report Properties Dialog epit d Dn UR Oc Re EE 20 89 Report Properties Dialog General Tab sese 20 89 Report Properties Dialog Text Properties Tab esee 20 90 Viewing Reports and Results from a Single TotalChrom Report TCR File 20 90 Viewing Reports and Results from a Single Result File eee 20 92 Report Window Group Detail Tab 00 eee eeecseeeceseeecsseceeesecneesecsaeeeesaeeeeeseenees 20 10
434. tor 5 Repeat Steps 2 through 4 to add other events Add an OFF condition for every relay event you turn ON because TotalChrom does not reset relays at the end of the run 6 Choose Return to close the timed events display gt To delete an instrument timed event 1 Choose Instrument Events from the Process menu to open the instrument timed events display 2 Choose Delete Events to open the Delete Events dialog box Delete Relay Events x Select the event s to be deleted 3 Select the events you want to delete and choose OK TotalChrom removes the events from the list and the plot Editing Methods and Results Graphically 10 35 Working with Components Working with Components 10 36 This section describes the different procedures for components tasks for the Graphic Method Editor and Reprocess Results Since you modify the actual method with the Graphic Method Editor there are more component specific commands in that application Using the Calibration Commands in the Graphic Method Editor The commands in the Calibration menu in the Graphic Method Editor allow you to establish or revise the component information in the calibration section of the method This part of the method defines which peaks TotalChrom identifies and as what component You can add delete or change components create or modify groups change search windows and modify other calibration characteristics Creating a Component Li
435. tor 4 7 Navigator Tasks and Other Application Tasks To perform this task Use this button or For more information command See View a real time plot ku Chapter 12 Note Although this is a separate application it Fina Time Pict cannot run unless the Navigator is running View Real Time Plot Produce customizable TC Publisher Help File high quality summary and single injection reports Build Develop Reports View instrument details Chapter 12 Note Although this is a separate application it Details cannot run unless the Navigator is running View Details Control a run and affect Chapter 12 instrument status Run button or menu Work with instruments Chapter 13 interactively Hands On Instrument Hands On Modify a downloaded Chapter 13 method or the active sequence Modif Instrument Modify Change password Admin menu Change Chapter 4 Password 48 Navigator Tasks and Other Application Tasks Opening Applications from the Navigator To open an application Use this button or For more that lets you command information see Using The Navigator Configure instruments on your system Build a chromatographic method Build a report format file Edit the method graphically Reprocess data graphically Build or edit a sequence file Display and compare chromatograms Display Chromatograms Build Configuration Method Build Method Chapter 3 Chapters 5 6 7
436. trument is reconfiguring such as updating an IPM No Method The instrument is turned on and connected to the computer but is not set up Post Run Post run activity is in progress or a LINK controlled autosampler is cleaning up after the previous injection Pre Run A LINK controlled autosampler is preparing the next injection Ready The interface is ready to collect data and is waiting for the run to start Seq Done An automated LINK controlled analysis is complete The instrument must be initialized again for any future analyses Seq Paused The user has paused the current sequence by choosing Pause Modify Downloaded Method or Modify Active Sequence Setting Up The instrument is being initialized with acquisition information System Re config Navigator is carrying out a system reconfiguration User Pgm A user program from a sequence is running synchronized with instrument operation Host Not Found Navigator could not communicate with the acquisition server for this instrument Unknown Inst The instrument is unknown to the Acquire Client server No License No license is available for the instrument Not Yet Online The instrument is being initialized Port Comm Error The Acquire Client server is unable to communicate with the port Cancelled The last run on the instrument was cancelled Starting The instrument is waiting to start a run Ser Dil The instrument is
437. ts of the components during auto or manual calibration TotalChrom bases the adjustment on the difference between the total component amounts from the component list excluding internal standards and the actual sample amount in the sequence file TotalChrom only makes this correction if you change the sample amount in the sequence from the default value For more information refer to Chapter 11 Convert Unknown Samples To Concentration Units Uses sample amount as a divisor for sample cycle types Unidentified Peak Quantitation Specifies how TotalChrom calculates unidentified peak amounts in the analysis The options are Always Use Calibration Factor Calculates component amounts based on the constant calibration factor you enter in the dialog box Use Nearest Component Calculates each unidentified peak using the same options as the nearest component The amounts are calculated as if the unidentified peak is the same as the component Use Nearest Reference Calculates each unidentified peak using the same options as the nearest reference peak TotalChrom calculates the amounts as if the unidentified peak is the same as the reference peak For more information on the quantitation of unidentified peaks refer to Chapter 18 Discussion of Data Analysis RRT Calculation Specifies the way that TotalChrom calculates relative retention time The calculated value is available for reporting purposes it has no effect
438. ttings 13 3 restarting 12 22 timed events 6 36 Index versions C 4 viewing detailed status of 12 32 950 Series interface using IVM with C 13 A Abbreviations 20 156 absolute plot scale 7 16 absolute window 10 40 ACF See average calibration factor acquisition status messages 12 40 Acronyms 20 156 Active Sequence command 13 13 13 16 active sequence modifying 13 16 Add Label command 14 4 14 16 adjusted height ratio 18 29 amount ratios converting to raw amounts 18 76 definition 8 5 8 14 amount values definition 17 5 prohibited 17 9 solving for 17 11 analog output magnitude 6 19 analyses optimizing 10 2 analysis reports see report format Summary TurboRGEN Append command 11 37 17 14 Append New Cycles command 11 48 Append New Template command 11 49 Append Sequence File command 11 49 Append Text File command 11 57 applications opening from Navigator 4 9 area slice 18 26 area threshold 10 26 18 9 18 15 area threshold timed event 18 16 ASCII text files See text files AT See area threshold timed event Attach command 12 24 audit trail 2 8 2 10 Auto Size command 14 7 auto calibration reports 18 61 18 67 autosampler configuring 3 6 parameters for gas chromatographs 6 12 for liquid chromatographs 6 21 status messages 12 43 autoscaling 3 20 Autozero A B command 12 30 auto zero plot offset 7 15 average calibration factor 8 24 8 35 18 56 18 59 backlogged data A 8 base data file names renumbering 11 42 Base Fil
439. u can designate the largest peak in the window or the peak closest to the expected retention time as the component The search window has two parts Absolute window Defined by an amount of time in seconds Relative window Defined by a percentage of the component s expected retention time Because the relative search window is a percentage of the expected retention time the window increases as retention time increases This increase helps compensate for the greater uncertainty that occurs in peaks eluting later in the run The calculation for the total size of the search window W in seconds centered at the expected retention time of the component RT oxp in minutes is RT x relative window x 60 W 2 absolute window 2 160 For example consider a peak with an expected retention time of 15 minutes an absolute search window of 10 seconds and a relative search window of 596 The window size on each side of the expected retention time is then 55 seconds 10 seconds plus 596 of 15 minutes or 45 seconds The total width of the window is then 110 seconds Reference Components Retention times for components can vary greatly from run to run If you create an excessively wide search window to find these peaks you can cause windows to overlap Overlapping windows complicate the peak identification process because it then becomes difficult for you to predict the component assignments TotalChrom will make Fo
440. u might not want to When you use a sequence to acquire data you can specify the directory in which to store the data in the Setup dialog box in the Navigator This lets you specify a different destination for the data each time you run the sequence without having to modify the sequence In the Base File Name text box enter the base file name that you want to use when building the file names If you leave the text box blank TotalChrom will use the current base file name Base file names may contain 80 characters 11 41 Editing the Sequence Spreadsheet 11 42 6 Ifyou want to change the beginning file number and therefore successive file numbers enter your changed value in the Starting Number text box 7 Choose OK Using Renumber Files to Renumber Base Data File Names The Renumber Files command allows you to renumber either a range or all base data file names in a sequence of one or multiple file types raw result and or modified for all or only specific base names Renumber files is similar to using Smart Fill to rename data files The differences are e Renumber Files affects only the numeric portion of the file name e Renumber Files can operate on multiple file types raw result modified e Renumber Files can apply to only a specific base name rather than to all base names in the selected range The default entries in the Renumber Files dialog box reflect what you select in the spreadsheet before you choose
441. u select the status bar at the bottom of the window displays the word MODIFIED if you change any part of the open method Building a Method 5 5 Using the Method Editor 5 6 General Procedure for Creating a Method This section contains the general procedure for creating a new method You can also create a new method by editing an existing method file and renaming it with the Save As command Another option for building a method is to import parameters from a result file or from methods created with older versions of TotalChrom prior to Version 4 0 For information refer to Importing Method Parameters on page 5 9 When you create a new method TotalChrom opens a series of dialog boxes in succession These dialog boxes contain instrument processing and calibration parameters respectively You can stop this automated display of dialog boxes by choosing Cancel in any of the dialog boxes gt To create a new method 1 Do one of the following e In the Navigator choose Method from the Build menu or click the Method button select Create New Method in the Startup dialog box and choose OK Your application manager may have disabled the display of the Startup dialog box Method e Ifthe Method Editor is already open choose New from the File menu 2 Complete each dialog box that is displayed choosing OK to go to the next one Refer to Chapters 6 7 and 8 for procedures 3 When you are finished developing the met
442. u subsequently perform from the Navigator will pertain to that instrument Status Box and Command The Status box displays the status of the instrument that is currently selected in the Instrument Panel You can choose the Status command in the Status box or from the View menu to open the Instrument Status Window which contains additional instrument status information Series 200 LC Pump No Method ACQ No Data VF Not Ready CMD None 4 4 Navigator Buttons and Commands Build Buttons and Menu The Sequence Report Format Method and Graphic Edit buttons have corresponding commands on the Build menu Use these buttons to open the Sequence Editor TC Publisher Method Editor and Graphic Method Editor Repart F ormat Method Graphic Edit Other commands on the Build menu open the Report Format Editor and the instrument Configuration Editor Sequence Instrument Buttons and Menu The Setup Hands On and Modify buttons have corresponding commands on the Instrument menu Use these buttons to set up instruments for data collection to change instrument settings and to modify an active method or sequence Hands On and Modify do not become active until you set up and bind an instrument Hands On Modify The icon that appears on the Hands On button changes depending on the type of instrument that is active Other commands on the Instrument menu allow you to bind and unbind instruments to perform a wave
443. u want this instrument to have a name other than its default name Configuration 3 5 Configuring Instruments 3 If you have an autosampler follow the procedure To configure an autosampler Otherwise go to the final procedure To save the configuration gt To configure an autosampler Some autosamplers are equipped to communicate the rack and or vial numbers of each injection TotalChrom can store this information in the raw data file with the chromatographic data from the injection and include it in the header of each report that is printed after data analysis TotalChrom can interpret the coded rack and or vial numbers from a long list of autosamplers However if the autosampler you are using does not appear in the A D Configuration dialog box you can choose Other Type and manually enter the information needed to interpret rack and vial codes To read the rack and or vial numbers you must have the correct cable for the make and model of autosampler connected to your 900 Series Interface 1 From the Autosamplers list in the A D Configuration dialog box select the type of autosampler that is connected to the 900 Series interface A D Configuration x Instrument at port gordonsr1 COM 2 Name Instrument 3 Autosamplers Rack Vial Mask Info for Other Types Logic Sign Logic Type Other E T C Positive C Binay Negative BCD Number of vial bits 1108 PE AS300 z PE AS2000 Number of ra
444. uantitation tab of the Append New Cycles dialog box and select Channel A or Channel B For a single injection sequence an asterisk next to a column indicates that the value will be entered for both Channels Append New Cycles x Identification Files Quantitation Calibration C Channel B Sample amount 1 000000 Multiplier 1 000000 STD amount 1 000000 Divisor 1 000000 Sample volume 1 000 Addend o 000000 Dilution factor 1 000000 Norm factor fico 000 Values entered for these columns will be used for both channels regardless of the channel selected Close Add Select to enter sample amounts and conversion factors for Channel A 2 Inthe Sample Amount text box enter the actual amount of sample injected excluding the amount of any internal standards used Based on settings in the method this value can be used for correcting calibration standards and for converting unknown samples to concentration units e When sample amount is used for correcting calibration standards you must use the same units as those used for component amounts in the calibration section of the method TotalChrom calculates the correction factor as actual sample amount expected sample amount 11 24 Building a Sequence Vial by Vial where the actual sample amount is the Amount entry in the sequence and expected sample amount is the sum of the component amounts in the calibration section of the method
445. uence command 11 10 15 4 Sequence Editor commands and menus 11 4 overview 11 4 Sequence Information window 12 17 serial dilution program including in sequence 11 48 Set Background Color command 14 4 Set Chromatogram Pen command 14 4 Set End Time command 14 4 14 20 Set Font command 14 17 14 18 14 19 Index Set High Voltage command 14 4 14 24 Set Low Voltage command 14 4 14 24 Set Start Time command 14 4 14 20 Set Text Color command 14 17 14 18 Set Up command 11 50 Setup function 12 2 Setup Problems window 12 25 Shift Time command 14 4 14 22 Shift Voltage command 14 4 14 25 Show Axes command 14 11 14 14 Show Baselines command 14 8 14 11 14 14 Show Components command 14 8 14 11 14 15 Show Coordinates command 14 3 14 11 14 14 Show Reference Chromatogram command 10 22 Show Retention Times command 14 8 14 11 14 15 Show Title Bars command 14 11 14 14 Show Windows command 10 47 10 50 Show Hide Dialog 20 38 Sign Toolbar 20 43 signature table 20 14 single injection sequence sample identification 11 18 skims exponential 18 42 tangential 18 42 SM See smooth peak ends timed event Smart Fill command 11 38 11 42 smooth peak ends timed event 18 23 solvent gradient program creating 6 24 solvents adjusting composition after setup 13 8 labeling 6 24 specifications 900 Series interface C 17 SQL LIMS sending results to 8 19 Stack command 14 7 Stacked display 20 51 Start Monitor command 12 30 12 31 start new peak tim
446. uent from the diluent tank 8 Inthe Volume column enter the volume of the liquid you want the Autosampler to transfer from the source vial or tank to the target vial The dilution tank is always the first line in the table The value you set for the tank is transferred from the tank to every dilution active vial in the sequence 9 Inthe Mix Cycles column enter the number of times you want the Autosampler to mix the mixture in the target vials For best results set this value to 2 10 In the Equil Time column enter the amount of time you want the mixture in the target vial to equilibrate between vial to vial transfers of liquid or before injection in the case of the last step 11 Repeat Steps 7 through 10 for each dilution operation 12 Choose OK Developing Instrument Parameters in the Method 6 43 Creating Derivatization and Dilution Programs Series 200 Autosamplers Only 6 44 Chapter 7 Developing Processing Parameters in the Method This chapter explains how to use the Method Editor to set processing parameters in a method For general information about using the Method Editor refer to Chapter 5 Building a Method To learn about Go to page Introduction to Processing Parameters Entering Peak Detection and Integration Parameters Entering Baseline Timed Events Selecting Optional Reports Editing Replot Parameters Running User Programs 7 1 Introduction to Processing Parameters Introduc
447. umber and it will be increased by an increment of one each time you choose Add 8 In the Study text box enter the name of the study to which this sample belongs 9 In the Vial text box enter the vial number from which you want a LINK controlled autosampler to take the injection If you do not have a LINK controlled autosampler this number is informational only The default value is the next available number and it will be increased by an increment of one each time you choose Add 10 If necessary change the number in the Rack text box 11 Repeat steps 5 through 10 for the other channel Building a Sequence 11 21 Building a Sequence Vial by Vial Specifying File Information You complete the Files tab in the Append New Cycles dialog box to define processing and data parameters gt To enter file information 1 On the Files tab of the Append New Cycles dialog box select Channel A or Channel B Identification Files Quantitation Calibration C Channel amp C Channel B m Processing Eracessing method D PenExe TcCS Wer6 0 0 Examples Gasolin Calibration method D PenExe TcCS Wer6 0 0 Examples Gasolin fel Report format file D PenExe TcCS Wer6 0 0 Examples Gasolin r Data Data files baat Result file pA t i CSOSOSCOCCCCCCWS Baseline file O Modified data file E E 2 Report device Deut E Plot device Dea E Close Add Select
448. umber pattern HHH Starting number fi Iv Synchronize with vial numbers Assign sample numbers to calibrations tees First row to be changed 1 to 2 If you change your mind about the rows to which a change should apply change the value for the Starting Row and or Ending Row If necessary change the entry in the Sample Number Pattern text box The sample number pattern is an alphanumeric entry that defines the basic form of the sample number Use characters to indicate the position and length of a numeric string within the sample number Numeric digits can be located anywhere in the sample number The following are valid patterns ABC HABC2 THHHHE ABCIHHHHEXYZ Use only one set of pound signs A pattern such as ABC DEF will give sample numbers of the form ABCO1DEF because only the first set of characters is replaced by a number If you want the numbering to change enter the new value in the Starting Number text box If you want the sample numbers to correspond to the vial numbers in this sequence click the Synchronize With Vial Numbers check box 11 39 Editing the Sequence Spreadsheet 11 40 8 When the same vial number appears several times the same Sample Number will be used in each case This applies to a occurrences of a given vial number not just in adjacent rows If you want to assign sample numbers to calibration rows select the Assign Sample Numbers To Calibrations check b
449. umn that uniquely identifies the sample within the SOL LIMS system Task ID LIMS Uniquely identifies a SOL LIMS test to be run on the sample User 1 through User 10 Ten columns available for any user defined purpose Type Column Entries Each cell in the Type column must contain an entry that either determines how TotalChrom analyzes data or specifies that TotalChrom run a special procedure Among the Type column entries are Bracketed Calibration cycle types They involve using standards both before and after a group of samples to derive the calibration information used to quantify the samples A single sequence can contain several brackets sets of calibration standards with intervening samples TotalChrom prevents you from entering conflicting calibration types For example if you select Cal Grand Avg all other calibration types are removed from the list of selections You select an entry for the Type column from the following options Cal Average Sample Cal Average Cal Replace Cal Bracket Overlapped Cal Bracket NonOverlapped Sample Indicates an unknown sample to be analyzed Your application manager might define additional names that function in the same way as Sample Using the Sequence Editor Cal Average Represents a calibration run TotalChrom will add the results to the replicate information for the specified calibration level in the calibration section of the method The resulting
450. up dialog box and begin acquiring data using the current sequence without having to return to the Navigator gt To switch to Set Up from the Sequence Editor e Choose Setup from the Actions menu If you have changed the current sequence file the Save As dialog box appears You can save the changes to the current file or create a new sequence file The Setup dialog box opens displaying the currently selected instrument and the appropriate sequence file Refer to Chapter 12 Acquiring and Viewing Data for information Switching to Batch Reprocessing The Batch command in the Actions menu allows you to reprocess the data files that are referenced in the sequence gt To switch from the Sequence Editor to Batch Reprocessing e Choose Batch from the Actions menu If you have changed the current sequence file the Save As dialog box appears You can save the changes to the current file or create a new sequence file The From Sequence dialog box opens For information on how to use the options in Batch Reprocessing refer to Chapter 15 Reprocessing Files in Batch Editing Method Files for the Current Sequence Although you can identify the methods whose instrument processing and calibration parameters you want to use for a given sequence you cannot change those parameters from the Sequence Editor You must return to the Method Editor 11 50 Building a Sequence Changing Environments From Within the Sequence Editor
451. use in calculations You can also use this tab to tag components for SOL LIMS reporting if you have Connect 2 Youcan use the Next and Previous buttons to scroll through the list of components that are already in the method 3 To delete the currently selected component from the component list choose Delete Component Developing Calibration Parameters in the Method 8 29 Adding and Editing Components 8 30 4 Make any changes to the values in the Components dialog box and then do any of the following e To save your work and close the dialog box choose OK e To save your work without closing the dialog box choose Apply e Toclose the dialog box and discard your changes since the last time you chose Apply choose Cancel The following sections describe how to complete each tab of the Components dialog box Adding a Component If you are adding a large number of components whose parameters are the same you might want to customize the component defaults before starting this procedure For more information refer to Setting Component Defaults on page 8 20 gt To prepare to add a new component e Do one of the following e Choose New Component from the Components menu to open the Components dialog box in add mode e Choose the New Component command button on the Identification tab of the Components dialog box Entering Component Identification Information When adding components the first step is to complete t
452. usted Amount AD Addend HAH Area Height Ratio HAP Area Percent HAR Area Amount Ratio CP Capacity Factor from Suit HDF Dilution Factor zl Custom expression cen Select the Value to be included in the custom expression Subtraction Negation Multplication Division Esponentiation Group An Expression exp Raise e To A Power xl The list box on the left shows the types of the data that are available for calculations 2 Enter the desired expression in the Custom Expression text box You can enter the expression either by choosing items from the Available Column Values and Available Operations lists or by typing the values and operations directly into the Custom Expression text box To use constants as values type the desired constants directly into the Custom Expression text box Most terms in the Available Column Values list are defined in the Glossary which is available in this manual and in Help 3 Choose OK when the expression is complete The Custom Expression Editor dialog box closes and the Custom Expression dialog box appears Building a Report Format 9 11 Creating a Custom Expression 9 12 Current column none Column number B Column width o Beos Digits Bo ove Column label Delete Second label v Calculate total for this column Cancel Add this column to the report format 4 Enter the column number where
453. ut the instrument timed events for other supported instruments refer to the documentation that came with the instrument In the Graphic Method Editor you can insert instrument timed events directly on the chromatogram at a specified time For more information refer to Chapter 10 Editing a Method and Results Graphically gt To add or edit timed events 1 Select the Instrument Timed Events tab of the Instrument Control dialog box Instrument Control x Autosampler Oven Pump Config Pump Program Detectors Instrument Timed Events Time min 010 Add Event TE1 Delete Hepace Value On r Defined Events Event Value Time Cancel Epp Time into run at which this event is to occur 0 10 to 999 00 2 Inthe Time text box enter the time at which you want this event to occur during the run 3 From the Event list select the event that you want to add Setting Control Options If the event requires a value or setting the Value text box or list becomes enabled 4 Depending on the event use the Value text box or list to specify a value for the event 5 Choose Add to add this event to the Defined Events list 6 Repeat Steps 2 through 5 to add other events TotalChrom lists the events in the order of the time at which they occur gt To change the time or value of a timed event 1 Under Defined Events select the event that you want to change 2 Doone ofthe following
454. ve Fit Type The Curve Fit Type options are Point To Point Averages all replicate amount and response data at each calibration level to derive a point Each pair of points is connected by a straight line segment You can use this fit type with one or more calibration levels 1st Order Polynomial Calculates a first order polynomial linear fit using the coefficients of the curve the intercept and slope A component must have at least two calibration levels to use this type of fit 2nd Order Polynomial Calculates a second order polynomial quadratic fit using the curve coefficients A component must have at least three calibration levels to use this type of fit 3rd Order Polynomial Calculates a third order polynomial cubic fit using the curve coefficients A component must have at least four calibration levels to use this type of fit Understanding Component Parameters For more information about how TotalChrom solves the various calibration curve types refer to Calibration of Initial Component Amounts in Chapter 18 Discussion of Data Analysis Scaling Factor Instead of using response versus amount or response ratios versus amount ratios for internal standard for the calibration curve you can use alternative functions of the amounts The Scaling options are None Does not add a scaling factor 1 X Plots response as a function of the reciprocal of the amount 1 X X Plots response as a function of
455. ve peak detection timed event 18 18 New Calculation Plot command 14 28 14 31 New Component command 8 28 8 30 New Data File command 10 8 New Fit command 17 9 New Report Format command 10 52 New View command 11 30 Next command 12 32 Next Component command 17 4 noise threshold 10 26 18 8 18 15 noise threshold timed event 18 16 Noise Area Threshold command 10 26 Notes command 6 2 6 4 6 5 NT See noise threshold timed event numbers reading rack and vial 13 4 O offsets preventing 8 36 Open Format command 16 11 Opt 1 tab 20 109 Optional Reports command 7 9 Options dialog 20 27 Initial Scaling 20 28 Peaks Components 20 30 origin changing for real time plot 12 30 treatment options 8 19 outlier test 18 65 oven temperature setting 6 14 13 5 Overflow error message 12 24 overlapped peaks 18 14 overlapped search windows 18 45 Overlay command 14 7 14 8 Overlay display 20 52 over sampling compensating for 18 6 P P See peak detection timed event parent peaks definition 18 28 passwords 4 2 Paste command 17 14 Path command 11 44 Path Select dialog box 2 4 paths configuring preset 3 21 Pause command 15 12 15 13 Pause Sequence command 12 22 peak areas adjusting 18 27 determining overview 18 26 clusters 18 14 18 24 components adding 8 31 10 39 editing 10 39 setting as default type 8 22 detection allowing and inhibiting 18 20 18 21 definition 18 3 disabling and enabling 18 16 optimizing 18 16 overview 18 11 para
456. ve that file with either Save or Save As Auditing is automatically enabled for a result file if any of the methods used to create it have auditing enabled Therefore the Audit Trail dialog box is also displayed when you save a result file in the Graphic Method Editor or in Reprocess Results that contains an audited method You enable auditing by selecting Start Audit Trail on the Description tab Once an audit trail is started the Description dialog box will not appear automatically if you choose Save As However you can display it at any time by choosing Description from the File menu Description The Description tab in the Documentation dialog box opens when you save a new file and if auditing is not enabled when you choose Save As to save an existing file with a new name It also opens when you choose Description from the File menu The Description tab also has the options for starting audit trail and electronic signature Your application manager may have set up these options so that they are always selected and unavailable Entering Descriptive Information About a File gt To enter information on the Description tab 1 Enter any descriptive information about the file that you want to store with it Documentation type in descriptive data here 2 If you want to start tracking changes to the file select the Start Audit Trail check box This will cause the Audit Trail dialog box to appear every time th
457. ven temperature or solvent gradient program depending on whether you are using an GC or a LC The figures that follow show the instrument parameters for an AutoSystem GC and a LC 410 pump Data Acquisition and Instrument Control Instrument Name AUTOSYS_ _1 A Injection AUTO Inlet CAP Experiment Time 58 67 min Injection Volume 2 0 pL Inlet B CAP Delay Time 0 00 min Sampling Rate 12 50000 pts s Detector FID Run Time 58 57 min Channel DUAL Detector B ECD Temperature Program Initial Temperature 80 deg for 2 00 min Ramp 1 3 0 deg min to 220 deg hold for 10 00 min Data Acquisition and Instrument Control Instrument Name LC410 1 4 Injection 155 200 Detector LC135 235 Experiment Time 25 00 min Injection Volume 10 uL Wavelength 255 nm Delay Time 0 00 min Sampling Rate 4 88280 pts s Wavelength B 280 nm Run Time 25 00 min Channel L Spectral Mode AUTO Solvent amp MeOH Step StepTime Flow Solvent SolventB Solvent C SolventD Curve SolventB 10 0 1 50 5 0 0 0 0 0 95 0 0 0 Solvent C 1 150 1 50 95 0 0 0 0 0 5 0 1 0 Solvent D H20 2 10 0 150 95 0 0 0 0 0 5 0 0 0 Data Processing and Reporting Shows the number of pages over which you want the replot to appear scaling and offset values the bunching factor noise threshold Building a Method 5 3 Using the Method Editor and area threshold how many timed events and user programs are included in the method
458. vent gradient program which you set on the Pump Program tab Developing Instrument Parameters in the Method 6 33 Setting Control Options 6 34 Setting Series 200 UV VIS Detector Parameters Support for control and data acquisition for the LC Series 200 UV VIS detector includes wavelength programming and digital data acquisition from the detector Series 200 UV VIS configuration is analogous to that of the 785A except that no A D is included in the module options There are no instrument timed events for the Series 200 UV VIS gt To set Series 200 UV VIS detector parameters 1 Select the Detectors tab of the Instrument Control dialog box 2 If necessary you can change a wavelength value in the wavelength table during the run The wavelength program is downloaded to the detector which executes the changes in exactly the same manner as the LC235C detector Time entries have a range of 0 to 999min with a precision 0 01 min Wavelength nm entries have a range of 190 to 700nm for the deuterium lamp and 360 to 700nm for tungsten For each lamp type the precision is inm If the wavelength is greater than 375nm and the deuterium lamp is configured then a warning about possible second order interference will be issued This will be the same warning message as used for the 785A A zero entry for the wavelength indicates an autozero command 3 If necessary select Lamp OFF at end of run by clicking the check box Setting Contro
459. view a print job and exit the Configuration Editor to return to the Navigator Instrument Menu Lets you configure all instruments connected to your computer for which you have permission disconnect instruments and reset channel run counters Interface Menu Lets you configure a physical LINK User Menu Lets you define the font style and size for plot labels set colors define plot preferences such as whether or not to display the reference chromatogram in the Graphic Method Editor define quick paths to locations for storing data and set a Project Directory Options set here apply only to the local TotalChrom workstation 3 3 Configuring Instruments Configuring Instruments 3 4 You can configure instruments for which you have access as set up by your application manager The instruments must be turned on and physically connected to a valid data acquisition port This section includes the following topics e Configuring a 900 Series Interface e Configuring a 600 Series LINK Interface and Attached Instruments e Resetting a LINK Configuration e Disconnecting Instruments e Using Run counters Configuring a 900 Series Interface The 900 Series Interface is an analog to digital converter it converts the analog signal voltage from a chromatographic detector into digital values that TotalChrom can then store analyze and plot You define how TotalChrom acquires data from detectors connected to a 900 Series int
460. want to view the real time plot and click the Real Time Plot button mm Real Time Plot OR Choose Real Time Plot from the View menu The Real Time Plot window opens Real Time Plot 950 olx Ez Instrument View Options Run Details Window Help lej xl Channel A Time min The Real Time Plot window includes the following menus and commands 12 26 Viewing Real Time Plots Instrument Menu Displays a list of instruments currently configured on your system Choosing Select opens the Select Instrument dialog box Select Instrument x Primary All E Ray s Cube E Sherry s Cube teca Select an instrument Choosing an instrument name from the Instrument menu or Select Instrument dialog box opens another window which has the instrument name in the title bar If the instrument is set up for dual channel data acquisition the window will appear divided in two for Channels A and B If the instrument is currently acquiring data TotalChrom will plot that data if it is not acquiring data just the plot axes will appear If the instrument is not set up the plot window shows the status of the instrument Options Menu Lets you change the plot scale for the active window by entering new values for the X axis and Y axis You can also zoom in on the plot to view the data in more detail If you are using a dual channel instrument you can scale the plot for each channel independently
461. x controls which colors appear in the chromatogram display on calibration plots and in the screens that display summaries of configuration and method information gt To define the colors that appear on screen and on printed plots 1 Choose Colors in the Configuration Editor to open the Colors dialog box C 2 Multiplot colors 3 Calibration plot colors C 4 Summary screen colors Color Selection Component names Retention times Timed events C 2 Multiplot colors C 3 Calibration plot colors e 4 Summary screen colors e Chromatogram Colors Defines the colors of the chromatogram display in the Graphic Method Editor Reprocess Results and Real Time Plot windows the background and annotation colors in the Chromatograms window and the output colors if you are using a color printer e Multiplot Colors Defines the colors that appear in one or more chromatograms in the Chromatograms window which allows you to compare multiple plots It also defines the color of the reference chro matogram in the Graphic Method Editor and Reprocess Results windows 3 18 Configuration Configuring User Options e Calibration Plot Colors Defines the colors used in calibration curves which appear in the calibration section of the method and in the Fit Analysis window e Summary Screen Colors Defines which colors appear in the Method Editor screen Select the specific display el
462. y For information on Sequence Editor commands refer to Chapter 11 4 Choose Save from the File menu to save your changes These will be applied to the runs that have not yet been executed 5 Close the Sequence Editor window to return to the Navigator The Resume Sequence dialog box appears Resume Sequence HP6890 1 Sequence HP68 1_1106a v Blatt next run when read Starting row 2 Ending row jo 6 Select Start Next Run When Ready if you want to start the run as soon as the instrument is ready Working with Instruments Interactively 13 17 Modifying a Sequence During a Run 13 18 Normally you will want to select this option only if you are using an instrument configured with a LINK controlled autosampler Change the Starting Row and Ending Row numbers if they are not correct The default starting row will be the first row that has not yet been run The default ending row will be the ending row originally specified in the Setup dialog box If you have added rows to the sequence you must update the ending row number to include those rows in the run Choose OK The messages that appear in the Status box of the Navigator reflect the changing instrument status as the new sequence information is downloaded and implemented for subsequent runs 785 Detector Wavelength Calibration 785 Detector Wavelength Calibration You must periodically perform a wavelength calibration procedure before you set up a 785 detector f
463. y by baselines If you mark peaks that do not have baselines TotalChrom adds the new peaks to the peak list TotalChrom reprocesses the data through peak detection and integration and redraws the plot To start or end a baseline at the exact cursor location hold the Shift key while pressing or releasing the mouse button Otherwise the start or end point will be the raw data value on the Y axis that corresponds to the cursor time position gt To delete a baseline e Choose Baseline Events and delete the UF and UF timed events with the Delete Events command OR e Right click between the UF and UF events and choose Delete Baseline from the pop up menu If you have more than one baseline TotalChrom will delete the baseline closest to the cursor Setting Instrument Timed Events Graphic Method Editor Only The Instrument Events command in the Process menu of the Graphic Method Editor lets you set a variety of instrument timed events depending on the instrument you are accessing These events however do not affect the current data file because they occur only during data acquisition For 900 Series Interfaces you can turn relays on and off and instruct the interface to read rack and vial information from an attached autosampler For LINK controlled instruments the events you can use depend on the type of instrument and its configuration Editing Methods and Results Graphically 10 33 Setting Processing Parameters 10
464. you use a single method for any operation that does not require a sequence The Sequence Editor is described in Chapter 11 Building a Sequence Introduction and Overview 1 4 TotalChrom Functions Reprocessing Data Because TotalChrom stores your raw data on disk you can re integrate and reprocess the data in two different ways e Byreviewing the chromatogram on screen and re integrating it graphically using the Reprocess Results function e By reprocessing a series of data files using a new method or methods using the Batch Reprocessing application The Reprocess Results function lets you change such parameters as integration thresholds or enter new integration timed events After each change TotalChrom replots the chromatogram on the screen and draws the new baselines When you are satisfied with the integration you can generate a new report and plot based on the changes and store a new result file if you wish It is also possible to draw manual baselines and generate a report with the adjusted results The Reprocess Results function is described in Chapter 10 Editing Methods and Results Graphically The Batch Reprocessing application lets you select a series of stored raw chromatograms and re integrate and reprocess them in a batch mode using new processing methods if you wish Batch can also read the data file names and method files to be used for reprocessing from a sequence Alternatively you can specify indiv
465. you want the expression to appear 5 Enter the other parameters for this column 6 Choose Insert A dd The label you assigned to the custom expression appears at the top of the column When TotalChrom generates a report based on this format file the result of that expression will appear in the column When you click on this column in the window the Custom Expression Editor dialog box appears followed by the Custom Expression dialog box Creating Additional Custom Expressions Data from an existing custom expression column is always used as a basis or template for creating additional custom expressions This enables you to derive new custom expressions from existing custom expressions quickly without having to re enter data When there is only one custom expression in the report its data are always used as a template for creating another custom expression But when there is more than one custom expression you must select the specific custom expression whose data you want to use You can either e Clickon the desired custom expression OR e Select Custom Expression from the Report menu to open the Duplicate Columns dialog box Choose the custom expression column whose data you want to use and select OK Whichever method you choose the Custom Expression Editor dialog box appears It is already filled in with expression data Use the procedure described in Creating a Custom Expression to build the custom expression Editing
466. you want to identify as a new component or choose the Next button until that peak is outlined If the peak has already been identified as a component the component information appears in the Edit Components dialog box Otherwise the Name text box is blank and the other parameters have default values In the Name text box enter the new name you want to assign to this peak The name you assign appears on the plot after you complete the remaining entries for the component and choose Next or Prev To cancel a pending entry of a new component click on another peak in the plot Do one of the following e To specify that this component act as a reference peak for other components select the Ref check box e To specify that an existing reference component act as a reference for this component select the component from the Reference list This option is only available if you deselect the Ref check box Do one of the following e To specify that this component act as an internal standard for other components select the ISTD check box Editing Methods and Results Graphically 10 39 Working with Components 10 40 10 11 e To specify that an existing internal standard component act as an internal standard reference for this component select the name from the ISTD list This option is only available if you deselect the ISTD check box To change the size of the search window enter a value in the Absolute Window and Relative
467. ype the value that you want the cell to contain Your edits are mirrored in both the cell and the Edit Bar although the Edit Bar can show more of your text unless you have increased the column width for the current cell 11 32 Editing the Sequence Spreadsheet Editing Cells with a Drop Down List Certain columns contain cells that you can edit by selecting from a list gt To edit a cell that contains a drop down list 1 Select the cell that you want to change the list appears 2 Scroll to the option that you want and select it Editing Cells That Require a File Name Certain columns contain cells that you can edit by selecting a file name from a file selection dialog box You can also select the cell that you want to change and type the file name directly in the cell or in the Edit Bar gt To select a file name from the file selection dialog box 1 Display the TotalChrom File Select dialog box by using one of these methods e Double click the cell e Select the cell by clicking the right mouse button Then choose Browse from the shortcut menu e Select the cell by clicking the left mouse button Then choose Browse from the Change menu 2 Locate and select the file name that you want to use for the selected cell Editing Cells by Copying and Pasting Building a Sequence You can copy data from any cell or group of contiguous cells and paste that data elsewhere in the spreadsheet You can also paste tha

TotalChrom Workstation User's Guide - Volume I

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