Varian ion trap 3800 GC 4000 MS Calibration Gas Adjustment tips

Document created by yamame on May 21, 2020Last modified by yamame on Jun 9, 2020
Version 2Show Document
  • View in full screen mode

Manual: Varian GC 3800Varian 4000 MS

We had a Trap Frequency Calibration failure and the service team helped us to fix it.

The service team operated the following procedure:

Air/Water check

Ion Lens Tuning (131)

Calibration Gas Adjustment

RF Ramp Adjustment


Here I will share about Calibration Gas Adjustment for Varian 4000 MS.

I will share tips that I learned from the service team that I found it hard to find in the manual. 


Trap Frequency Calibration failure


Do manual tune: Calibration Gas Adjustment

see manual P. 40 Varian 4000 MS



1) Load service method (if you have, if you don't, skip this but do not save/overwrite your analysis method), and go to manual control tab

2) Turn on the trap by clicking the image of the trap or checking the box. When the trap is on, words in the image of trap will turn green.


3) Make a check in Calibration Gas box.


4) Choose Active method segment Number 3 : Cal Gas
You can change active method segment by up and down arrow.


5) Select Cal Gas Adjustment from Check and Adjustments tab.


6) Check if you see the Cal gas mass in spectra; Cal gas mass are 69, 131, 264, 414, 502, 614 m/z.


7) Click on Start. And See the mass spectrum for base peak Ion. Ion time μs (us) should be around 800 μs (us) ±30 μs (us).


8) When Ion time is off from 800 μs (us), you can make this ion number change by tuning CAL GAS valve (CAL GAS valve is inside the MS front door. Door will be open by just pulling to right. ).


9) Slowly turn the CAL GAS valve and let the number be around 800 μs (us) ±30 μs (us), and also RIC should be <10,000.



10) Adjust the valve until the Adjustment Result number is 800 μs (us) ±30 μs (us) and bar is in the rage of Low to OK.


11) Click Done when Adjustment Result is in the right range.

12) Uncheck the Calibration gas box and check you don’t see any Cal gas ions; Cal gas mass are 69, 131, 264, 414, 502, 614 m/z.
If you see them, do bake out.



Baking out the system: see manual P. 50 Varian 4000 MS




This is a pretty old system and you might not use them anymore, but if you do, I hope these tips help!