Varian ion trap 3800 GC 4000 MS Air/Water check 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 about Air/water check 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: Air/Water

see manual P. 43 Varian 4000 MS



1) Load service method (if you have, if you don't, skip this but do not save/overwrite your analysis method)

2) Go to manual control tab

3) 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.

4) Choose Active method segment Number 1: Air Water. You can change the active method segment by up and down arrow.




5) Select air/water from Check and Adjustments tab.

6) Click start


7) Check the mass spectrum.

7 A) RIC <1000 is good. If > 1000, do bake out.


7 B) 28.2 m/z and 32.1 m/z should be low and equal height. If 28.2 m/z and 32.1 m/z are high and not in equal height, do bake out.


7 C) 40 m/z should not be high. If high, change low mass range to 41 m/z in your analysis method.
Change He tank might help reduce this number.




8) When finished, click Done.

9) In the Air/Water check window.
Mass 28 peak should be around 0.90 m/z (± 0.45 m/z).
Mass 19/18 Raito should be around 23%m/z (± 5%).
If it’s out of the range, 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!