Bumping this to the top. Any help is much appreciated! Thank you.
Unfortunately, no you can't keep it under vacuum but you can turn off the helium and vent the system. I would recommend keeping the nuts on the side door of the MS closed though to prevent debris entering the MS chamber.
You can vent either by using the software on the PC (under View - Tune and Vacuum control, then Vacuum - Vent) it should take an hour then you can turn it off.
Or there is an option to Vent from the front panel so if you go to Maintenance on the front panel and then it will ask if you wish to vent the MS, then press Yes. Should take again about an hour.
You can then turn the MS and GC off and turn the helium off too.
When starting back up, turn on the helium, hold the MS chamber door to the chamber (without touching the electronic) and turn the MS on (roughing pump will be loud then go quiet). Wait until this happens then you can let go of the chamber door. wait 10 seconds then turn the GC on.
Once at temperature check for leaks and leave overnight to clear any air int eh system. by the following day it should be ready for analysis.