Problems with oxygen, in GC/MS

I had this similar issue with our GCMS after replacing a helium purifier. The best way to reduce the oxygen and nitrogen showing in your tunes is to run approximately 20-40 blanks depending on your cycle time. I have about a 30 minute cycle time and finally got my tunes back to normal after 25 blanks. I would also check for leaks and make sure the screws fastening your column in the oven aren't lose. Give it time to purge the column, and if this doesn't work I recommend a steam clean. 

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?

Running blanks with a leak may damage the column.  The original poster's problem seems like a leak, not just high nitrogen after replacing a trap.

Agilent Gas Clean carrier gas traps are manufactured and shipped with nitrogen.  The easy/simple way to purge out the nitrogen is to cool off the GC oven, set the inlet pressure to 2 psi - or as low as it will maintain, then set the inlet mode to SPLIT, Gas Saver OFF, Split flow 500 ml/min.  This wastes helium but will clear most of the nitrogen in the trap in ten to fifteen minutes or so.  After that time has elapsed, reload your normal standby or run method and continue.

There is another more technical way to purge it and maybe that needs to be my next blog entry...

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?

Good morning, thank you very much for your indications, we are going to check for leaks, so as not to make injections before lowering N and O. The equipment has been stabilizing for two weeks, and the parameters remain stagnant at the indicated values.

(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.