Source of GCMS Contamination peaks-consistent retention times, m/z's?

I am having trouble chasing down the source of contamination on our 6890N/5975 GC-MS system. The TIC and spectra below were generated using a DB-5 column, "no-injection" manual injection after changing the inlet septum, liner, trimming the GC column end, disassembling the inlet assembly with methanol and hexane, and replacing the split vent filter. Similar data were generated prior to these maintenance operations.  The magnitude of the TIC peaks varies from injection from low 10^5 to low 10^6. The retention time and dominant m/z's is consistent. As you can see from below, the dominant m/z's are the same for the different cinematographic peaks.

Any ideas?

  • If contamination looks like peaks - it's being retained by the column.  Generic contamination is background/baseline rise.  This stuff is coming from before the column and not likely in the column at all or else it would bake away.

    I entered ions into the NIST 20 library search program and the nearest match without spending too much time looking is something like:   Name: Chlorodifluoromethyl trifluoromethyl disulfide, Formula: C2ClF5S2 ...but probably a bit heavier. It would require a background subtraction to narrow it down further. It sure looks like it has a halogen on there somewhere.

    One test to try, set the oven to your final oven temperature and leave it there for at least half an hour. Lower the temperature to your starting temperature and immediately start the blank no-inject run.  Then set it to the final oven temperature for at least half an hour again. Then lower the temperature to your starting temperature and leave it there for - a long time, like 30 minutes or longer. Then start the blank no-inject run. Are the peaks dramatically bigger? If so, the contamination is being cold-trapped on the head of the column and coming in with the gas.

    When you cleaned the inlet and replaced the filter, did you clean the side-arm and the copper split vent line that goes from the inlet to the trap?

    Is this one column direct from the inlet to the MSD or is there a backflush setup inline?

    How long ago did you replace the gas traps?

  • Thank you for this detailed input. Agreed about not being column-derived. After talking with tech support, I replaced the copper split vent entirely and rinsed the split port of the inlet with solvent (methanol, ethyl acetate, hexane). Yes, the column does feed directly from the inlet to the MSD.

    I will try your experiment next week, but anecdotally, I think that I have done this and the peaks do indeed get much bigger (to the point of appearing to show breakthrough). I just found out we are not using a trap (!) so that is an area to address. We are using UHP He. I will update with chromatograms from the experiment you described next week.

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