Aux EPC or PCM for Collision Gas 7890/7200

There will always be measurable oxygen - or at least I've never seen a QTOF with none.  On a 7200A, one week is barely pumped down. We recommended two weeks between installation and checkout.  Getting all of the molecules off that are adhered to the walls of the flight tube takes time.  For every molecule flying around there are ~500 adhered to all of the surfaces.

The collision cell is part of the magic. Gas on and gas off totally changes the way it functions and totally changes the way the QTOF system calibrates. You cannot necessarily troubleshoot this like a single quad system.

The entrance lens is not part of the Removable Ion Source, it is inside on the analyzer. To clean it means venting, removing the source radiator, removing the entrance lens, cleaning it, and going backwards to reassemble. 

Wow, I wish I had posted earlier in the process because you have been a tremendous help - I probably could have saved a week if I knew all this beforehand. 

That all makes a lot of sense. I just finished the one hour bakeout and here's how the EI calibrant spectrum looks:

Pretty happy with that signal for now anyway. The transferline is just capped off from when I split the system to try and track down if/where it was leaking so I still need to reinstall the column and 7890 but do you recommend letting it pump down for a few more days before we test/tune/calibrate everything?

Yes, wait longer, especially since you just cleaned the source.   You might get a no-column-flow tune out of it maybe Monday?  The spectral tilt, the relative abundances of 69/131/219/502 won't be ...right... with no column flow, but if they are there and the resolution is even sort of good, I'm impressed it got this far.