Varian ion trap 3800 GC 4000 MS Ion Lens Tuning (131) tips

Document created by yamame on May 21, 2020Last modified by yamame on Jun 9, 2020
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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 aboutIon Lens Tuning (131) 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:  Ion Lens Tuning (131)

see manual P. 49 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 4 : 131
You can change active method segment by up and down arrow.


5) Check if you see 131 m/z.


6) Uncheck the calibration gas box.


7) Check if the 131 m/z spectra go down.
If it does not go down, it means you had a Cal gas contamination in the MS. Do bake out.


8) Turn off the trap by unchecking the box or click the image.


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!