Problems with oxygen, in GC/MS

Air is 78.08% nitrogen and 20.95% oxygen - about a 4:1 ratio. Your 7% to 1.9% is right there at 3.68:1 and is probably a small leak.  It only takes 50ppm of oxygen going through a GC column to damage it, so eliminating the leak is important.

Take a look at the 5977 Troubleshooting and Maintenance manual ( available here:5977B Series MSD Troubleshooting and Maintenance Manual (agilent.com)  )  Page 58 tells where leaks may occur.

Start with the easy things. Cool off the inlet and oven and replace the inlet septum and inlet liner and O ring.  Open up the oven, remove the column from the inlet, cut 25 to 50 cm off the front, install a new ferrule, and install it back into the inlet at the proper height for your inlet - 6 to 8 mm above the ferrule for the S/Sl inlet and 14 to 15.5 mm above the ferrule for the MMI.  Do not overtighten the nut or the septum.

If there is still a small leak, vent the GCMS, remove the column from the transferline, and cut and install a new ferrule, then reinstall the column into the transferline so that the end of the column is flush with the tip of the transferline tipseal.  Do not overtighten the transferline nut.  Tighten it only enough so that the column cannot be moved and then a tiny bit further.  Too many folks dramatically overtighten this fitting.  Pump the system back down to ultimate vacuum, waiting at least two hours for stability, and then test again.

If there still a small leak it may be in your gas supply or even in the gas itself.  What is the condition of the trap(s) in the line?  Do you have an indicating oxygen trap?  Do you have a leak checker like the Agilent G6693A available?   What was the last thing that was done before the leak was noticed?

Good morning, thank you very much for your instructions and the manual. Just before detecting the leak, I did just what you tell me, I cut column in injector and inlet to the MS, and I also had to change the oxygen and water trap. The equipment has been at rest for two weeks now, we have not punctured anything, nor have we conditioned the column. A doubt that has arisen to me, now is the following, for MMI injector, is better 14 - 15.5 mm than 11 -12 mm? We have 11 mm, as indicated in the manual, in the column installation section. We are going to change the MS inlet ferrule and tighten it with less intensity, as you indicate. We do not have a leak locator, is there any other way to locate them?

(5) Column Installation - Split/Splitless and Multimode inlets =and= SQ and TQ MS transferlines - Files - GC/MS - Agilent Community   

See slides 8 & 9.

Make sure that you are using graphite/vespel ferrules on both the MMI and the MS connections.  On the inlet it should be the short ferrule.  On the MS with the brass nut it should be with the long ferrule, cone shape into the nut, and with the Self-Tightening column nut the short ferrule, cone shape into the nut.  These are shown on slide 13.

You can use canned air duster without bitterant, which may be a bit more difficult to find. The bitterant is an added chemical to stop huffing the gas to get high.

In Manual Tune
Set all three ions to the primary ion of the air duster chemical. (e.g. 65,65,65)
Repeat Profile with the filament on and the PFTBA off
Set the scale to manual and increase it so that the background is small
Be patient! From the inlet end it can take a minute or two to see any air duster ions

Start at the MS, working your way backwards through the system
MS analyzer door
PFTBA valve
Vent valve
Transferline nut in the GC oven
Purged Ultimate Union in oven if installed
Inlet column nut

Most leaks can be fixed by venting and reinstalling the column into the MS with a new ferrule and wiping off the analyzer door O ring with a lint-free cloth before pumping down.

You can use canned air duster without bitterant, which may be a bit more difficult to find. The bitterant is an added chemical to stop huffing the gas to get high.

In Manual Tune
Set all three ions to the primary ion of the air duster chemical. (e.g. 65,65,65)
Repeat Profile with the filament on and the PFTBA off
Set the scale to manual and increase it so that the background is small
Be patient! From the inlet end it can take a minute or two to see any air duster ions

Start at the MS, working your way backwards through the system
MS analyzer door
PFTBA valve
Vent valve
Transferline nut in the GC oven
Purged Ultimate Union in oven if installed
Inlet column nut

Most leaks can be fixed by venting and reinstalling the column into the MS with a new ferrule and wiping off the analyzer door O ring with a lint-free cloth before pumping down.

Finally we were able to solve the leakage, we changed the MS inlet ferrule, reinstalled the column and set the N values to 3% and O to 0.6%. I keep all your advice.
Thank you very much!!!

Always use the 85% Polyimide/15% Graphite ferrules on the inlet and transferline on GCMS systems.