The exhaust of the mechanical pump associated with any mass spectrometer is hazardous and MUST be vented to a fume hood or filleted. Scientific Instrument Services (
http://www.sisweb.com) has a nice kit that includes a mist eliminator and a carbon filter for vacuum pumps see it on their Home Page). Even if the pump has an exhaust line that runs into a fume hood, it should also have a mist eliminator on it.
You must remember to change the carbon filter EVERY 30 DAYS. The paper filter in the mist eliminator should changed every time you change the pump oil. Check the pump oil often to see if it needs to be changed. If the instrument is in continuos use, you should change the pump oil on a minimum every 60 days.
If you are doing slit injections on a GC-MS, the split vent should exhaust to a fume hood or have a carbon filter. The gases coming out of the mechanical pump and the split vent are toxic and should not be breathed under any circumstances.
The pump oil is a hazardous waste and should be properly disposed of.