Shutting Down GC-MS System

Hello Everyone,


I am new to the forum and full disclosure not an expert at GC-MS systems. However, I am a chemistry professor at a small liberal-arts school which kind of makes me a jack of all trades and puts me in charge of our instrumentation (I have the most experience of the faculty here). Anyways, we recently purchased and installed a refurbished Agilent 6890-5973 GC-MS system using He gas as our carrier. Currently, this instrument will only be used for teaching purposes, meaning it will only be used a couple of times of year in our Instrumental Analysis course and not for very sensitive quantitative work. With money always tight, I was wondering if it would be okay to shut the system down while it is not being used to conserve He gas. I know it is preferred to keep the system on and pumped down and gas flowing, but we are working to save as much as money as possible, and since the instrument will sit idle for several months, it seems somewhat wasteful to keep it running.


So first, is it possible to leave the MS system under vacuum without the carrier gas on? I would guess this means turning the temperature down or off on the filament, which is fine. I also know we would set the GC oven temperature to ambient while it is shutdown. So any advice I could receive from the experts here is GREATLY appreciated! We want to teach our students the importance of GC-MS, but also do so in an economic fashion!


Thanks again for any help!

  • 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.

  • This question has been marked as assumed answered.

  • Hi, it would be possible to switch to a cheaper carrier gas like Nitrogen when the system is not in use. You can do this a few different ways: more recent instruments have a helium conservation module that can be purchased and allows for switching between helium for when the instrument is running or nitrogen when the instrument is idle. Alternatively if you are careful you could get some shutoff valves and tees to set up a manual way to switch carrier gas--just be careful to change the inlet's gas configuration so that you have the right gas selected (otherwise the flows will not be accurate and you could get some odd behaviors.) When you do want to use the instrument I would recommend switching back to helium the night before and allow the system to completely equilibrate back to high purity helium before running experiments. If there will be months of downtime I would vent and power off to save on electricity. 

Was this helpful?