GC-MS Reference Guide
Contents
1. EasylD QEdit Quant Result Edit Non Target Peaks Parametric Retrieval Align GC Review Peak Purity Results Screener RTLock Setup Help Help Topics Using Help Review Revision History View Revision Readme file About EasylID Menus EasylD Co Next Compound Goto Compound Xpand Chromatographic Window 2 minutes Original Chromatographic Window Graphics Report to the Printer Restart Quick QEdit Set Extract Window Start Set Extract Window Stop Abort Changes and Exit Exit and Save Changes QEdit Menus QEdit CO Next Compound Goto Compound Xpand Chromatographic Window Original Chromatographic Window Graphics Report to the Printer QDEL Compound Next File Load Data File Restart Quick QEdit Abort Changes and Exit Exit and Save Changes Spectrum Draw Next Draw Previous Tabulate Add Subtract Spectrum Draw Next Draw Previous Tabulate Add Subtract Select Library Edit Strategy Edit Library Display Reference Spectra Update Reference Spectrum ChromEval Evaluate Resolution Evaluate Tailing Integrate Integration Parameters Save compound specific integration parameters Remove compound specific integration parameters Integrate ChromEval View Evaluate Resolution Data Analysis Evaluate Tailing Evaluate Degradation Select View EasylD in Data Analysis to access these menus Display View Normal Data Analysis Qualifiers Evalua2. w e gt g Hide Back Forward Print Options Contents Index Search Overview of the MSD Productivity C Using Help Visit our Website gt Acquiring Data Instrument Control Analyzing Data Using Methods gt Using Sequences gt Using Batch Mode gt Tuning Calibrating the MSD Troubleshooting the 5973 MSD Secured Control Report Manager Commands and Functions gt Using and Writing Macros gt Glossary of Terms Help Icons 5 x 20 io Overview of the MSD Productivity ChemStation The MSD Productivity ChemStation controls acquisition of 6890 GC data or GC MSD data performs library searches and quantitation and generates selected reports via methods or sequences It offers a number of productivity tools for data processing such as QEdit DOSCAN DOLIST and EasylD toolbars as well as two levels of security for access to the system The instrument system is represented in the software by a set of views e Top view e Instrument Control view e Enhanced Data Analysis e June view The MSD Productivity ChemStation software can be configured to Support two types of instruments gas chromatographs GC only and gas chromatograph mass spectrometer systems GC MS A GC only instrument will have some menus and menu items that differ from those on an instrument configured as a mass spectrometer These differenc
3. Sampe le Chromatography D inlets columns Oven GC Status Messages aa Total lon mel Ett Volts E Oven Temperature O Column 1 Flow EKE MS Source MS Quad TurbosSpd Acquisition Status Lets you tell at a glance the status of the current instrument or run if any Offline Soe ae Start Button Lets you start a run When a run is not in progress the a Data File evalderma d arrow is green To start a run click the green arrow fill in the Sample Information and click Start Run When a run is in progress the arrow IS gray This button also shows the current data file name sample information if any and the vial number 1if no ALS a Run Time 12 00 Ka d pA ped g CB Srah pe acess MS Total lon Run Time Clock S hows the elapsed time since the beginning of the run if a run is in progress The scheduled run time is shown below the digital clock When a run is not in progress the Run Time clock Shows the elapsed time since the last run Stop Button Lets you stop the system when it is in Pre Run Run or Post Run mode The stop sign is red when a run is in progress and gray when a run is not in progress Logbook Button Displays a menu where you can choose to view open clear Save or print a particular logbook Help Button Displays a menu where you can Select an online help topic for the Instrument Control view Choose Help Topics to go to the online help for the entire sy
4. To acquire data 21 To analyze MS data 22 To use spectral libraries 23 Maintenance Schedule 24 Operating Tips 25 Troubles hoot ing Tips 26 Document History First Edition 9 03 G1 0 IDA MSD ChemStation Rev D 0 100 64784 38858 soci ss Copyright 2003 Manual Part Number Agilent Technologies G1 0190050 Printed inU S A 9 03
5. To set up the GC for use with the MSD 1 Select Instrument Inlet Injection Types Select the appropriate injection source and select the Use MS checkbox Click OK 2 Click the Aux button Verify that you are using auxiliary channel 2 the heater is on and set to the desired temperature and that MSD is selected as the Type Click OK 3 Click the Columns button Verify that the detector is MSD and that Vacuum is selected for Outlet psi Click OK To inject a sample with the autosampler 1 Place the autosampler vial containing the Sample into the autosampler tray 2 Select Runfrom the Method menu inthe Top or Instrument Control view 3 Whenthe Start Run box appears specify the Sample information O Specify a unique data file name for the Sample O Enter the position number of the sample vial in the Vial field 1 100 O optional Fill in the Operator Name Sample Name and Misc Info fields to document the injection O Make sure that the Data Acquisition option is selected Select the Data Analysis option if you want to generate any of the reports specified in the method 4 Click Run Method to initiate the run CAUTION Do not usethe Start button ontheGCtostart a run when using the autosampler To inject a sample manually 1 Select Manual as the injection source on the Inlet and Injection Parameters box 2 Press the Prep Run key onthe GC keypad This cancels the gas saver flow brings the inlet flowto its
6. Data Analysis Commands CUSTOMTOOL2 Lets you run a user created macro This macro must first be created and then named CUS TOMTOOL2 See the online help for Using and Writing Macros and Data Analysis Commands CUSTOMTOOL3 Lets you run a user created macro This macro must first be created and then named CUS TOMTOOL3 See the online help for Using and Writing Macros and Data Analysis Commands TE KB e lala i m 2 l ite Draw Chromatogram Redraws the original chromatogram of the current data file without labels or integration marks Set Up Quantitation Lets youset upa quantitation database by specifying quantitation database globals and entering compounds into the database Scale Chromatogram Scales the selected chromatogram by the specified scale factors AutoQuant Setup Provides a semi automated way to create a quantitation database Extract lon Chromatogram Extracts and displays extracted ion chromatograms EICs from the total ion chromatogram TIC of the current data file Edit Compounds Lets you review and edit information in the quantitation database compound by compound Update Calibration Lets you add delete or update a calibration level in the current quantitation database Merged Format Causes extracted ion chromatograms to be displayed overlaid on each other Calculate Quant Report Quantitates the current file and generates a quantitation report Overlay Chromatograms Lets you
7. Run View Sequence Log Help View Sequence Quality Log Help Topics Print Sequence Log Using Help Import Sequence Information from CSV file Batch M ode More View Revision Readme File Review Revision History About Select View Top to access these menus The software menus shown on the following pages are for an MSD ChemStation in Enhanced Mode Top Toolbar Load Sequence uy Save Sequence Run Sequence Edit Sequence Print Sequence Simulate Sequence Load Method Save Method Run Method Edit Method Print Method Loads the selected sequence Saves the specified sequence Saves the specified sequence Lets you set up or modify the sample log table Prints the current sequence Simulates the current sequence Loads the selected method Saves the specified method Runs the current method The Start Run dialog box is displayed Lets you modify the method parameters for the current method Prints the current method Instrument Control Menus Method Run Load Save Edit Entire Method Additional Method Information Print PUNE Exit Window Cascade Tile Horizontal Tile Vertical Arrange Icons Arrange Plots and M onitors WN F Instrument Inlet Injection Types GC Edit Parameters GC Plot GC Monitors Acquire RTLock Calibration Data Unlock Method
8. control for the 6890 GC This allows you to use the soft ware instead of the GC keypad to program the instrument However there are times when you may want to use the keypad to quickly perform one of the following tasks Prepare a run manual injection Display column information Stop a run Start a run manual inject ion Dis play the front injection port temperature D o 35 N T T Nn a Display the oven temperature cial a i aE EE Display the GC MSD interface temperature m Flow Det Ramp Thermal Aux 2 DAAE port temperature Ho aan aan Taon a a002 Method Storage and Automation Load Method Run Front Valve Seq Table Injector Control Store Seq Clock Back Sample Table Injector Tay Instrument Control View The Instrument Control view is displayed when you start up the MSD ChemStation This is where you set and monit or See the online help for more details instrument parameters If you are in a different view select on the menus buttons or windows View Instrument Control when you are ready to set up the used in the soft ware system for data acquisition Example 5973 DEFAULT M El Method Instrument View Abort Window Qualify Help Instrument Control gt Sample Mame Idle Data File P evaldermo d aie Run Time
9. easily compared To use Autotune 1 Fromthe Instrument Control view select Perform MS Autotune from the Instrument menu 2 Select one of the following options depending on the instrument performance required by your application then click OK O Autotune Results in maximum sensitivity over the full scan range O LowMass Autotune Tunes for the low mass range O Standard Spectra Tune Results ina standard response over the full scan range This option may reduce Sensitivity O QuickTune Adjusts the peak width mass assignment and abundance without changing ion ratios 3 Review the Tune report 4 To viewthe history of tune results select View Tunes from the Qualify menu To use Manual Tune Manual tuning lets you interactively set the MSD parameters such as lens voltages and tuning masses to values that meet the needs of your particular analysis You can often obtain greater sensitivity than you can with aut ot une Manual tuning allows you to ramp individual parameters and to specify the range and step size for the ramp The results of the ramp are displayed visually with the optimum value for the parameter clearly marked on the plot You can acquire two types of data in manual tune profile scans plots the abundance and peak shape of the tune masses and spectrum scans scans plot response across the entire mass range S ee the online help for more details about manual tuning a To acquire data
10. select multiple chromatograms to be displayed Superimposed on each other Autolntegrate Tries to find the best integration parameters for the current chromatogram and then integrates the chromatogram Generate Quant Report Generates a quantitation report for a file that has already been quant it ated Print Quant Report Prints the Integrate Integrates the current quantitation report chromatogram using parameters set for the current integrator S eeBAREK O Custom Reports Starts the Custom i Subtract Spectrum Subtracts one ro Reports software If the method does not Spectrum from another and displays the have a quantitation database or no data difference file is loaded you can use default values Print Custom Report Prints the custom report template specified by the method using the current data file Select Library Lets you select the libraries that will be used for PBM searches of the currently selected spectrum Online Help Displays the MSD ChemS tation online help Library Search Report Integrates the current TIC searches the current library and generates a report eS PE To vent Shut down the MSD 1 If your system is equipped with a gauge controller switch off the triode gauge cont roller 2 Before venting a Cl MSD press the Gas Off button turns off the reagent gas flow and closes the isolation valve WARNING On a CI MSD the Gas Off light must be on when the MSD is venting 3 Fr
11. setpoint value and closes the purge valve for splitless injection only 3 Select Run from the Method menu from the Top or Instrument Control view 4 When the Start Run box appears specify the Sample information as described below O O S pecify a unique data file name for the sample optional Fill in the Operator Name Sample Name and Misc Info fields to document the injection Make sure that the Data Acquisition option is selected optional Select the Data Analysis option if you want to generate any Data Analysis reports specified in the method 5 Click Run Method to initiate the run If the temperatures are stable the Prepare To Inject box appears Otherwise the message Waiting for GC ready is displayed 6 When the GC temperatures have stabilized the Pre Run light onthe GC is steady inject the sample and press Start onthe GC CAUTION Do not inject before the GC is ready This will cause Inconsistent results ota To analyze MS data To load a data file 1 In Data Analysis select Load from the File menu 2 Select a data file double click on a file name or type a name and click OK The chromatogram for the data file is loaded and displayed in window 2 A data file must be loaded to perform any of the following tasks To integrate a chromatogram 1 If the integrator you wish to use is not currently selected open the Chromatogram menu and click Select Integrator Choose an integrat
12. to reach thermal equilibrium 7 Large variations in the temperature of the lab au AeA UNP High background in mass spectra 1 Air leak 2 Foreline or vacuum manifold pressure too high 3 Other contamination lons at m z 18 28 32 and 44 1 Detector vented recently residual air and wat er 2 Air leak Isotopes missing or isotope ratios incorrect Incorrect tuning Dirty ion source High background Electron multiplier volt age too high Repeller voltage too high High scan speed Scan mode Low dwell time SIM mode Peaks too wide or too narrow Repeller and ion focus leads have been reversed wont ou BPW N Foreline or vacuum manifold pressure too high 1 Excessive column flow Air leak Diffusion pump fluid level too low Diffusion pump fluid is contaminated Foreline pump oil level too low Foreline pump oil is contaminated Constricted foreline hose this would cause the vacuum manifold pressure to be too high but the foreline pressure to be too low a OH OF FP W NI Refer to the Troubleshooting the MSD section of the online help for more detailed information oy 2 Agilent Technologies What s in this Book What s New in Revision D 0100 2 Using Online Help 3 5973 MSD witha 6890 GC 4 GC Keypad 5 Instrument Control View 6 S oft ware Menus Enhanced Mode 8 Data Analysis Toolbar Buttons 16 To vent Shut down the MSD 18 To pump down start up the MSD 19 To tune your MSD 20
13. Agilent G1701DA MSD ChemStation 5973 MSD ChemStation Quick Reference fide Agilent Technologies What s New in Revision D 0 100 A new toolbar has been added to the Top view and an expanded set of toolbars have been added to Data Analysis Moving the cursor of the mouse over a toolbar will display tool tips quick descriptions for each of the buttons The sequence user interface or sample log table has been transformed into a Spreadsheet user interface During sequencing the ABORT button in the Status panel has been changed to Pause When this is selected the sequence will pause immediately When the sequence is started it will restart the sequence from where it was paused Long files names are supported Data file and method paths can be up to 100 characters long The names of individual data files and methods can be up to 50 characters long User Interfaces for selecting or saving files and directories have been enhanced with browse buttons Support for 5973A and 6890A instruments using GPIB has been restored It is now possible to disable Method Resolution for most changes in the 6890 configuration The Manual Tune and Diagnostics Vacuum Control views have be merged into a single view Tune and Vacuum Control A Tune Wizard has been provided to simplify the modification of criteria tune limits target ratios used by the tuning algorithms Loading data files in Data Analysis will now preview the chr
14. Disable Method Resolution Select MS Tune File MS SIM Scan Parameters Change MSD Temperatures MS Monitors Edit MS Tune Parameters Perform MS Autotune EMF Utilities Qualify Checkout Tune Tune Evaluation View Tunes Sensitivity Check Software Validation Installation Checklist Familiarization Checklist View Abort Top Abort Instrument Control Data Analysis offline Tune and Vacuum Control Help Help Topics Using Help Review Revision History View Revision Readme File About Select View Instrument Control to access these menus Tune and Vacuum Control Menus File Reset to Defaults Load Tune Values Save Tune Values Trace on View Trace Instrument Trace Print Printer Orientation Generate Report View Tunes Set View Tunes Report Options Restore Previous Tune s Exit Calibrate Mass axis Mass 2 widths Mass 3 widths Peakwidth Linearity Adjust Abundances Ramp Repeller Ramp lon Focus Ramp Entrance Lens Ramp Entrance Lens Offset Maximize Sensitivity Tune Tune MSD QuickTune Autotune Atune U Low Mass Autotune Lomass U Standard Spectra Tune Stune U DFTPP Tune DFTPP U BFB Tune BFB U Tune Wizard Air and Water Check Tune Evaluation Parameters M anual Tune Edit Tune and Display Parameters Edit MS Temperatures Edit Ramp Parameters Edit Dynamically Ramped Parameters Se
15. Non Target Peaks Use Method Aligned GC trace Trace Mode Quant Custom Reports Print Report Update Database Select Template Database Select View Data Analysis offline to access these menus The View menu in Data Analysis lets you access other Data Analysis modes Shown on the following pages Chromatogram Chromatogram Scaling Draw Chromatogram No Labels Draw Chromatogram With Labels Select Chromatogram Labels Extract lon Chromatograms Display lon Chromatograms in Merged Format Select Integrator MS Signal Integration Parameters GC Signal Integration Parameters Autolntegrate Integrate Integration Results Percent Report Tools DOLIST DOSCAN Process Scan List Export 3 D Data Locate A Compound Locate All Compounds Set Overlay Parameters Overlay Chromatograms Signal to Noise check Change Data State Options Configure Report Headers Generate Screen Results for Current File Generate Screen Report for Current File Generate Print Screen Report for Current File Generate Print Screen Report for Multiple Files Specify Method Screen Database Change Screen Database Parameters List Screen Database Exclude Zero Qualifiers Copy Window Reset Windows Spectrum Add Subtract Tabulate Select Library Edit Strategy Edit Library Library Search Report Change Spectral Display Find Mass Spectrum View
16. d in the list e Click the Text button to view the header information stored in the library for the current reference spectrum Click the Print button to print a copy of the displayed Spectra Click the Done button to clear the library search results from the screen Maintenance Schedule Maintenance tasks are described in the hardware Safety warnings manuals supplied with your system How often you need to perform system maintenance may vary for your system Keep a maintenance record WARNING Do not perform maintenance with the MSD on or Every day connected to its power source unless specifically instructed to by documentation supplied with the MSD Check and if necessary replace the septum y PP Check the tightness of the injection port liners Check the tightness of the column nuts WARNING The GC MSD interface can be on and at a dangerously Every week high temperature even though the MSD is off After it is Check the foreline pump fluid level ome off H ear Heber are ieat ape Change the injection port liners and O rings AE E ee A EE Every month WARNING Clean the split splitless inlet vent line tra p Be careful when working behind the GC During Check for leaks inlet column connections cool down cycles the GC will emit hot exhaust that could cause burns Every three months Replace gas cylinders when below 500 psig WARNING Every six months The oil trap provided for your foreline pump stops only foreline pum
17. es will be pointed out in the online help for menus It is also possible to acquire and review mixed mode GC detector and GC MS data xj Indicates a book containing more help topics To open a book select it then double click Indicates an open book of help topics To close an open book select it then double click Indicates a help topic To jump to a help topic select it then double click 5973 MSD witha 6890 GC o woo ALS tray Column oven 5973 MSD Wa ae ia Status display E lt 6890 GC On off switch ALS tower lt D 0 gt f i a6 00 i oo U 7 0 iii 00 000 000 0 0 00 0 00 0 00 000 00 0 OO ae OUU 0 0 0 00 Local control panel Status board Keypad GC Keypad The MSD ChemS tation software provides instrument
18. layed in window 1 To subtract two spectra 1 Select a spectrum double click the right mouse button in the chromatogram Select the spectrum to be subtracted double click the right mouse button in the chromatogram Select Subtract from the Spectrum menu The spectrum selected in Step 2 is subtracted from the spectrum selected in Step land the resulting Spectrum is displayed in window 1 To subtract background spectra 1 22 Select a spectrum or average a range of spectra to Subtract from the data file Select Subtract Background BSB from the File menu The system performs the following tasks e The selected spectrum is subtracted from every scan inthe current data file e The subtracted data is stored ina BSB Subdirect ory inthe same directory as the data file e The subtracted data file becomes the current data file and is displayed in window 2 To use spectral libraries To integrate and search peaks Use the following procedure to integrate a total ion chromatogram and automatically generate a library search report for each peak detected 1 In Data Analysis load a data file The TIC Is displayed 2 Select Spectrum Library Search Report 3 When the Library Search Report Options dialog box appears select the options you want for the library search report Select either Summary or Detailed to determine the report format e Select one or more destinations Screen Printer and Fi
19. le Select an Integration Parameter File leave the field blank to autoint egrat e using the ChemS tation integrator e Select which spectrum from each peak to use Apex Apex Start of Peak Apex Background at time or Peak Average 4 Click OK to initiate the search The chromatogram is integrated and a spectrum from each peak is searched The results of the integration appear on the screen The library search report is sent to the destinations selected in Step 4 5 Select Chromatogram Integration Results to view the tabulated integration results To search a single spectrum 1 2 23 In Data Analysis load a data file The TIC is displayed Select a spectrum The selected spectrum appears in a window below the chromatogram Initiate the library search by double clicking the right mouse button in the window containing the spectrum When the search is complete the search results appear on the screen The spectrum for the unknown the reference spectrum you select from the list of hits and if available the chemical structure of the reference compound Is displayed To view other spectral data e Click on another compound in the hit list to display a different reference spectrum e Select the Difference checkbox to display the difference bet ween the unknown and the reference Spectra To view other information e Click the Statistics button to display information about the quality of each hit foun
20. lect View Tune and Vacuum Control from Instrument Control to access these menus Vacuum Vacuum Status Pump Down Vent Purge Calibrant Valve Power on Temperatures Initialize MS Interface Status MS Status MS I O Test MS Temperature Controller Status View Instrument M acro Log View Tune Log Clear Instrument Macro Log Clear Tune Log MS Error Codes Execute MS ON MS OFF Profile scan Repeat profile Detailed profile Ramp Lenses Spectrum scan Find mass Determine Mass Axis Correction Factors Optimize Quadrupole Frequency View Top Instrument Control Data Analysis offline Logbook Sequence Log Error Codes Abort Help Abort Help Topics Troubleshooting Using Help About File Load Data File Next Data File List Header Edit File Info Take Snapshot Subtract Background BSB Select Signals Select Printer Printer Setup Print Abort Export Data to CSV File Export Data to AIA format Import AIA Raw Data Files 1 2 3 Exit Calibrate Set Up Quantitation AutoQuant Setup Edit Compounds Update List Clear Data Analysis Menus Method Run Method Run CustomAnalysis Load Method Save Method Edit Method Edit CustomAnalysis Generate AutoSIM Method 1 2 3 Batch Mode Quantitate Calculate Generate Report Use Classic Reports Report Options Report
21. om the Tune and Vacuum Control view select Vent from the Vacuum menu in the Soft ware Follow the instructions presented 4 Set the GC MSD interface heater and the GC oven temperatures to ambient 25 C WARNING If you are using hydrogen as a carrier gas the carrier gas flow must be off before turning off the MSD power If the foreline pump is off hydrogen will accumulate in the MSD and an explosion may occur Read the Hydrogen Carrier Gas Safety Guide 5955 5398 before operating the MSD with hydrogen carrier gas CAUTION BesuretheGC oven and GC MSD interface are cool before turning off carrier gas flow 5 When prompted turn off the MSD power Swit ch 6 Unplug the MSD power cord 7 Remove the analyzer cover 8 Turnthe vent valve knob counterclockwise only 3 4 turns or until you hear the hissing sound of air flowing into the analyzer chamber CAUTION Do not turn the knob too far or the O ring may fall out of its groove Be sure to retight en the knob before pumping down WARNING Allow the analyzer to cool to near room temperature before touching it CAUTION Always wear clean gloves while handling any parts that go inside the analyzer chamber WARNING When the MSD is vented do not put the ChemS tation into the Top view Doing so will turn on the interface heater To pump down start up the MSD 1 Make sure your system meets all of the following conditions before you pump down O The vent
22. omatogram The method has been expanded to permit printers other than the default printer to be used for reports generated during Run Method Headers in Data Analysis reports are now configurable for the reports generated by Run Method An improved BOOTP service has replaced the previous BOOTP program The new BOOTP service will not interfere with shutting down or logging off the comput er The SICL drivers have been updated to version L 02 01 Version M 0101is on the software CD and is for GPIB support Online Help Use the online help to learn about these new features as well as to learn about instrument control data acquisition data analysis methods sequencing tuning and howto usesystem commands and variables Troubleshooting the MSD is included to help you diagnose problems Using Online Help To access the online help select Help Topics from the Help menu in any window or click the Help button on any dialog box Item Description Hide Show Lets you turn on or off the display of the list of help topics Back Goes back to the previous help topic Print Lets you print the current book or help topic Contents Displays the list of help topics shown above Index Lets you use keywords to search the help index for a particular topic Search Lets you type a word or phrase and then displays a list of all the topics in the online help that contain those words E MSD ChemStation Help Enhanced mode
23. ompound Xpand Chromatographic Window Original Chromatographic Window Graphics Report to the Printer QDEL Compound Next File Load Data File Restart Quick Screener ReRun Screen Abort Changes and Exit Exit and Save Changes RTLock Menus RTLock View Current Method Setpoints Review Peak Purity Menus Spectrum Add Subtract Tabulate Help Help Topics Peak Purity Using Help Select View Review Peak Purity in Data Analysis to access these menus Spectrum Draw Next Draw Previous Tabulate Add Subtract Select Library Edit Strategy Edit Library Display Reference Spectra View Data Analysis Calculate New Curve from Selected Peaks Restore Nominal Chromatogram Report RTLock Calibration Print Relock Method Use AutoRelock Unlock Method ChromEval Display Evaluate Resolution Normal Evaluate Tailing Qualifiers Evaluate Degradation Select View Results Screener in Data Analysis to access these m Help Help Select View RTLock Setup in Data Analysis to access these menus View Data Analysis enus Data Analysis Toolbar Buttons Zot ah Ff e e e Load Data File Loads the selected data D file and displays the total ion chromatogram TIC for that file Load Method Loads the selected method M file Save Method Saves any changes made to the current method Take Snapshot Displays the data that has been acquired up to
24. ool uh WN Pe Peaks with flat tops 1 Solvent delay time too short 2 Display scale is wrong 3 Injection too large 4 Electron multiplier voltage too high Peaks with split tops 1 Bad injection technique 2 Injection too large Rising baseline 1 Column bleed 2 Other contamination Retention time RT drift Column has been shortened shorter RT Old column shorter RT Active sites in sample path longer RT Reduced column flow longer RT Injection port leak longer RT Initial oven temperature changed up shorter RT down longer RT au PWN Poor sensitivity Incorrect tuning Tune file does not match type of analysis Incorrect temperatures Incorrect Sample concentration Leaking injection port Incorrect split ratio Purge off time in splitless mode too short Excessive pressure in the MSD 9 Dirty lon source 10 Air leak Il Detector is not working correctly 12 Poor filament operation B Incorrect mass filter polarity 0O N ou RP WN J6 Poor repeatability 1 Dirty syringe needle Leaking injection port 3 Mismatched injection port liner and injection size 4 Loose column connections 5 Variations in pressure column flow and temperature 6 Dirty ion source Loose connections in the analyzer 8 Ground loop J Inconsistent peakwidths Incorrect tuning No PFTBA in calibration vial Calibration valve failure Dirty ion source Worn out electron multiplier MSD has not had enough time
25. or and click OK 2 Select Integrate from the Chromatogram menu 3 optional Select List Results from the Chromatogram menu A report of tabulated results is displayed on the screen When you are finished viewing the results click Done To select a spectrum e Double click the right mouse button on the time point of interest inthe chromatogram The spectrum appears in window 1 To zoom in 1 Position the pointer at one corner of the area you wish to expand in a chromatogram or spectrum 2 Press and hold the left mouse button while dragging the mouse to select the area you wish to expand 3 Release the mouse button The selected area expands to fill the existing window To zoom out 1 Position the pointer anywhere in the zoomed window 2 Double click the left mouse button To average spectra 1 Position the pointer in the chromatogram at the Starting time for the range you want to average Press the right mouse button while dragging the mouse to the end of the range you want to average Release the mouse button The spectra in the selected range are averaged and the averaged Spectrum is displayed in window 1 To add two spectra 1 Select a spectrum double click the right mouse button in the chromatogram Select a second spectrum double click the right mouse button in the chromatogram Select Add from the Spectrum menu The t wo Spectra are added together and the resulting Spectrum is disp
26. p oil If you are analyzing toxic chemicals or Replace the foreline pump fluid using toxic solvents remove the oil trap and usea hose Check and if necessary refill the calibration vial to route the foreline pump exhaust out of your laboratory Every year Check and if necessary replace the diffusion WARNING pump fluid Use chemical resistant gloves and safety glasses when Recondition or replace internal and external replacing pump fluid Avoid all contact with the fluid traps and chemical filters on the GC As needed WARNING Tune the MSD The insulation around the inlets detectors valve box CI the i and insulation cups is make of refractory ceramic fibers Ca MENE ION SOULE RCF Avoid inhalation of RCF particles Ventilate your Replace the carrier gas trap work area wear long sleeves gloves safety glasses and Replace worn out parts filaments EM etc a dis posable respirator Dispose of insulation in a Replace the column sealed plastic bag Wash your hands with mild soap and Lubricate seals cold water after handling RCFs Operating Tips C Back up your data and methods regularly to E avoid loss of data if the files are accidentally overwritten or deleted or if a hardware problem develops with your disk drive L Make sure the tune file you are using is appropriate for your samples L Save Tune reports in a notebook for future reference L Perform system maintenance as indicated by the maintenance sched
27. s Analyze a mixture with known Scan or components in unknown S IM amounts quantitate Identify the presence of a few S IM known compounds at low levels within a mixture When choosing masses for SIM use the exact mass printed in the Tabulation report not the nominal mass annotated on the spectrum display This provides more accurate data When doing SIM analysis use low resolution mode unless you are trying to determine the ratios of masses one amu apart Low resolution provides maximum sensitivity and repeat abilit y Choose the narrowest scan range that still produces good library search results This allows more spectra across the peak and better quantitation Troubles hooting Tips MSD is on but status flashing Server not found Check LAN connection This is normal when the MSD is initially turned on It means the ChemStation has not yet established contact withthe MSD If the flashing continues after the pumpdown is initiated 1 Temporary power failure interrupted communications 2 Bad connection between the MSD and the ChemStation and or the hub No peaks 1 Incorrect sample concentration 2 No analytes present 3 Syringe missing or not installed correctly ALS only 4 Empty sample vial 5 Injection in split mode instead of splitless mode Tailing peaks Active sites in sample path Injection too large Injection port too cool Column flow too low GC MS D interface or ion source too c
28. stem Injector Button Lets you set parameters for the injector when you have configured your system with an ALS Inlets Button Lets you set parameters for the GC inlet injection port that is configured on your system Columns Button Lets you configure columns and set up ramped flow and pressure programs Oven Button Displays a menu that lets you edit GC oven parameters or GC monitor parameters When the GC is ready the Small Square in the upper right corner is green When the GC Is not ready the square is red Aux Button Lets you set the temperature of the GC MSD interface usually Thermal Aux 2 MS Button Displays a menu that lets you edit MS acquisition parameters select another tune file or edit MS monitors Monitor Each monitor displays one instrument parameter See the online help for a description of the instrument monitors Top Menus Method Sequence View Secured Control Run Run Top Enable Security Instrument Control Load Load Data Analysis offline Start Secured Control Save Save l Select Methods for Secured Control Edit Entire Method Edit Sample Log Table Set Change Startup Method lt gt Print Set Change Standby Method lt gt Load and Run Sequence 1 Print Sequence Assign Sample Names to Method 2 Use Sample centric Secured Control 3 1 4 2 Report M anager password 3 Edit Accounts Set New Default Paths 4 Exit Simulate Sequence Position and
29. te Degradation Select Library Edit Strategy Edit Library Display Reference Spectra Select View QEdit Quant Result in Data Analysis to access these menus File Load List Header Take Snapshot Subtract Background BSB Print Current View Save Parameters Parametric Retrieval Menus Spectrum Draw Next Draw Previous Tabulate Add Normalized Subtract Library Retrieve Set Parameters Select Library Select Library Edit Strategy Edit Library Continue Results Library Search Report Read J CAMP File Write J CAMP File Abort Exit Subset Library Add Current Entry Structures Options View Help Select Structure Database Select Normalization lon Standard Menu Help Topics Set Structure Parameters Extend Database Headers Command Line Library Entry Only About Stack TIC and Library Entry M anual Integration Unknown and Library Entry Unknown Library Entry and Difference Copy Window Reset Windows Select View Parametric Retrieval in Data Analysis to access these menus Align GC Menus Alignment View Show Current Method Alignment Points Data Analysis Perform Alignment Restore Alignment Chromatograms Abort Exit Save Select View Align GC in Data Analysis to access these menus PkPurity Next Peak Previous Peak Select Peak Print Selected Window Return to DA Quick Screener Menus Screener CO Next Compound Goto C
30. the online help for information on troubles hooting air leaks and other vacuum problems 7 When prompted turn on the GC MSD interface heater and GC oven Click OK when you have done so The software will turn on the ion source and mass filter quad heaters The temperature set points are stored inthe Current aut otune u file CAUTION WARNING Do not turn on any GC heated zones until carrier eer gas flowis on Heating a column with no carrier gas Make sure your MSD meets ALL the conditions listed flow will damage the column above Failure to do so can result in personal injury 8 After the message Ok to run appears wait 2 Select Tune and Vacuum Control from the two hours for the MSD to reach thermal 3 Select Pump Down from the Vacuum menu CAUTION 4 When prompted switch on the MSD Data acquired before the MSD has reached thermal equilibrium might not be reproducible ee To tune your MSD You should tune the MSD periodically to maintain its optimum performance Tuning is the process of adjusting MSD parameters so the instrument meets certain performance criteria How often you should tune is determined by the number and type of samples you are running as well as the overall condition of your system Note Always tunethe MSD withthe same GC oven temperature and column flow and the same analyzer temperature that will be used for data acquisition Keep the Tune reports in a notebook so that Successive reports can be
31. the time the Snapshot is activated GC MS data only Print Lets you print the selected window the TIC and spectrum or the current method Copy Window Lets you copy the select ed window to the clipboard Reset Windows Rearranges the graphics windows to their default positions Execute Command Executes the command that is typed into the command line Abort Stops a command or macro Toggle Command Line Turns the display of the command line on or off Edit Colors Lets you adjust the colors of various display items in Data Analysis Toggle Graphics Lets you minimize or maximize the displayed graphics gt e A iil e Close Screen Reports Closes the currently displayed screen reports EasylD Lets you update expect ed retention times and ion ratios for MS data in an existing quantitation database on a compound by compound basis QEdit Quant Result Lets you review and edit quantitation results once a data file has been quantitated Generate Signal to Noise Report Lets you perform a signal to noise check and then display or print the report Review Peak Purity Helps you detect overlapping peaks mult iple component peaks in your chromatogram Retention Time Locking Accesses the RTLock Setup view which is used for retention time locking tasks CUSTOMTOOLI Lets you run a user created macro This macro must first be created and then named CUS TOMTOOL1 See the online help for Using and Writing Macros and
32. ule in the GC and MSD hardware documentation Keep a O record of all maintenance performed L When venting the MSD take advantage of the cool GC to do maintenance such as replacing inlet liners septa etc L After pumpdown wait at least 2 hours for the MSD to reach thermal equilibrium before tuning or acquiring data L Optimum sensitivity generally occurs at column flow rates of 12 ml minute or less L When injecting volumes greater than one E microliter use the pulsed splitless mode and increase the initial oven temperature 10 20 C L Forsplitless injections pulsed splitless mode gives more quantitative sample transfer onto m the column A pulse pressure of twice the initial inlet pressure is typical L Selecting Constant Flow mode will provide the most efficient separation in most cases It also results in constant sensitivity m throughout the temperature program x DR For a new column check that the column nuts are still tight after the first few oven temperature cycles Use the Config Status keys onthe GC keypad to set the 3 display items most important to you time remaining oven temp etc These are then always visible regardless of which ChemS t ation view is on top Rinse and refill autosampler wash vials Do not add more solvent to a partially full vial Use the following table as a guide to using the SIM or Scan acquisition modes Task Mode Analyze a mixture with unknown Scan component
33. valve is closed the knob is turned all the way clockwise O Allother vacuum seals and fittings are in place and fastened correctly The front side plate screw should not be tight ened unless hazardous carrier or reagent gases are being used O The MSD is connected to a grounded power S ource O TheGC MSD interface extends into the GC oven O A conditioned capillary column is installed in the GC inlet and in the GC MS D interface O TheGCis on but the heated zones for the GC MSD interface the injection port and the oven are off O Carrier gas of at least 99 999 purity Is plumbed to the GC with the recommended traps O If hydrogen is used as carrier gas Carrier gas flow is off and the front sideplate thumbscrew is loosely fast ened O The foreline pump exhaust is properly vent ed 5 Press lightly on the side board to ensure a correct seal The rough pump will make a gurgling noise This noise should stop within a minute If the noise continues there is a large air leak in your system probably at the side plate seal the interface column nut or the vent valve 6 Once communication with the PC is established click OK Within 10 to 15 minutes the diffusion pump should be hot or the turbo pump speed up to 80 The turbo pump should eventually reach 95 CAUTION If these conditions are not met the foreline pump willbe shut off You must then power cycletheMSD If the MSD does not pump down correctly see
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