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. 

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...

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...