Random 1-2 point(s) peaks

These are air burps. They are typically one or maybe two data points wide and frequently close to the same size. Vent. Remove the analyzer door O ring. Wipe it off thoroughly with a lint-free cloth and set aside or replace it with a new one. There's rarely a reason to use solvent on an O ring.   Use clean solvent dipped swabs and wipe out the O ring channel.  Use a solvent dipped lint free cloth and wipe off the analyzer side plate where it seals with the O ring. 

Reinstall the O ring like this.  Hold the O ring in front of you left and right evenly. Push those left/right parts into the groove. Then find the center of the top and bottom and push those into the groove. Then use your fingers to carefully press the rest of it into the groove. If you try to work it from one place around it will stretch a bit and bunch up. This way avoids that.

While it's vented also replace the O ring on the vent valve. Carefully remove the vent valve by unscrewing it all the way - don't drop it.  The O ring is the same as an inlet liner O ring. Don't scratch the surfaces with anything sharp. Remove, dispose, and put a new one on.  Wipe the PFTBA valve sealing surface with a solvent dipped lint free cloth before reinstalling.

Pump it down.  Let it equilibrate at least 2 to 4 hours.  Test it and let us know if that solved it.  This is the main location of air burps but there are some others.

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Some will say to use high vacuum grease on the O ring.  Please don't!  But if you feel you must, remove the O ring, put on the smallest possible amount, wipe it all around the O ring, then using a lint-free cloth -- wipe it  ALL   off.  More than enough will stay in the microchannels and pores.    Vacuum grease can be the cause of air burps, too!   The possible benefits of using it are not worth the possible problems.

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Thanks for the tips.

I did all that with some degree of success.
I'll share the experience in order to add to this thread.

- Removing the O-ring would have been easier if I had seen the cut made for that purpose in the lower right corner of the channel. I tried my best not to damage it with the tool I used (the one included in the package for removing the O-rings for a gas clean filter change),
- I cleaned the O-ring with a lint-free cloth dipped in isopropanol (i-PropOH),
- I first tried to clean the channel with a swab dipped in i-PropOH (the ones provided by Agilent when cleaning the source of the MSD). The swab was too wide and did not enter the channel. So I cut small squares of the lint-free cloth, dipped in i-PropOH, and used long round tweezers to clean the channel and the door of the analyzer,
- As the door of the analyzer does not fully open, it is not easy to work on its left side to clean the channel and the door. It is even harder to reinstall the O-ring while trying not to touch anything of the analyzer. I wish it was designed as a drawer instead,
- I don't use high vacuum grease. An Agilent engineer told me once that passing my finger on the O-ring was enough. So I cut the tip of my glove to pass a finger on the O-ring without touching the analyzer with the skin of the hand (it happened once and the HED was not happy),
- I capped the transfer line, pumped down the MSD and waited for H2O/O2/N2 levels to be acceptable,
- I simulated a run without column (and without heating the oven) and verified that no air 'burps' happened,
- Vented MSD again until hot zones <100ºC and pump speed <40%, uncapped transfer line, quickly inserted the column and pumped down before losing all vacuum,
- After making sure the system was w/o H2O/O2/N2, I ran the same method as before w/o injection and was pleased to see a system 'burp'-free (see image for a before and after O-ring cleaning).

Thank you for the help.

Excellent!  The analyzer is designed to be able to be fully disconnected and lifted off at the hinge point - but I would essentially never recommend any typical user to do that, though.

There are some interesting papers on ultra-high vacuum --- better than a GCMS could achieve --- O rings, seals, grease, outgassing, etc,  There's one from Agilent's Vacuum Products Division that taught me a lot, too.

Excellent!  The analyzer is designed to be able to be fully disconnected and lifted off at the hinge point - but I would essentially never recommend any typical user to do that, though.

There are some interesting papers on ultra-high vacuum --- better than a GCMS could achieve --- O rings, seals, grease, outgassing, etc,  There's one from Agilent's Vacuum Products Division that taught me a lot, too.