SOP for Gas Chromatography – Mass Spectrometry Instrument

Standard Operating Procedure for Gas Chromatography–mass Spectrometry (GC-MS) Instrument

SOP for Gas Chromatography – Mass Spectrometry Instrument




To give the Standard Operating procedure for GC-MS Instrument.


Gas chromatography – Mass Spectrometer


  1. Make sure that carrier gas (Helium gas) cylinder is open and flowing at 7.0 bar.
  2. Turn on the main power switch of the GC, MS, PC and printer.
  3. Double Click ‘GCMS’ Real time analysis’ icon from the main screen.
  4. Click ‘Instrument from the main menu and select ‘vacuum control”.
  5. Click “Auto startup’ in the ‘vacuum Control window and wait until the function is completed.
  6. Open the Method file’ required for the analysis and click download initial parameters from ‘Acquisition’ in the main Manu.
  7. Wait for 2 to 3 hours, and it display in green signal as ‘GC Ready & MS Ready.
  8. Check the “Low Vac’ and ‘High Vac’, the low vac should be 5-20 Pascal and the High Vac should be 5-20 X 10-4  Pascal.
  9. Open Peak View monitor screen from assistant bar.
  10. Check H20/N2 with Detector gain 0.70 kVA. Then go to ‘Leak Test’ m/z 69> 28 with Detector gain 0.70 kVA.
  11. Click Start Auto Tuning’ from the Assistant bar, once tuning finished save the Tuning file from ‘save as with today date then click ‘Auto tuning Report.
  12. Click ‘sample login from Assistant Bar, and then enter the sample name, data file. analysis details etc and current Tuning File’ then click OK.
  13. Click ‘Stand by’ from the Assistant bar and wait till GC & MS Ready display on the screen.
  14. Inject 1 µl sample and press Start button from GC control panel.
Note – May be different procedure your instrument.

Analysis of Data

  1. After completion of analysis. Click GCMS post run analysis’ in Desktop.
  2. Go to File’ in the main menu and open the Data required for the report preparation and do the integration.
  3. Click peak table in the side menu and click Select all and register in the Edit menu,
  4. Tab to the next window and click Similarity search.
  5. Click Save from the main menu and close peak table.
Note – May be different procedure your instrument.

Report format Generation:

  1. Open data file.
  2. Click ‘Report format’ in the Assistant bar.
  3. Click and drag items required in the ‘Items’ in main menu.
  4. Save the report format file.
Note – May be different procedure your instrument.


  1. Click “Instrument’ from main menu and select “Vacuum control” icon.
  2. Click ‘Auto shutdown’ in the window, wait till Auto shutdown ‘completed appear on the screen.
  3. Close ‘GCMS Real Time Analysis’ window and shutdown the PC.
  4. Turn off the MS, GC, PC and printer
  5. Close the ‘Cylinder’ tightly.
Note – May be different procedure your instrument.

Maintenance Procedure:

  1. Temperature should be maintained between 18°C and 28°C  respectively.
  2. Humidity should be maintained between 40 % and 70 % .
  3. Purity of helium used for analysis should be 99.995% or greater.
  4. Supply pressure of helium is between 7 and 8 kgcm
  5. Change the vacuum pump oil for every 3000 hours.
  6. Replace the injection septa for minimum of 100 injections
  7. Keep the split/spitless liners clean and free from deposition.
  8. Cleaning is recommended when the deposition is high and reduced response, peak tailing/mounting/fronting is observed.
  9. Monitor the leak parameters for air and water every day.
  10. Monitor the leak test with PFTBA whenever the GC column is changed and water a and air leak parameters fail.


Lab Manager/Analyst


Shimadzu instruction manual


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