Chromatography Forum

I am brand new in GC/MS area. Please forgive me asking simple questions.
We just installed 6890N GC /5975 MS from Agilent techniques.
1. When the installer was here, she got autotune result N2/H2O~30%. After the installer left, I did autotune, and got N2/H2O~200%, could that be a problem? H2O (0.91%), N2 (1.76%), O2 (0.81%), CO2 (0.32%).
2. I have some contamination peaks (with mass 207, 281, 355 etc) with small intensities (about 10^3~10^4 abundance height). Is this really bad? Is this related to N2/H2O ratio?

Thanks a lot!

Most likiley you have less H2O in the system now then when you last autotuned. Or it is possible that you have a small leak causing N2 abundance to be greater than H2O (most likely at the GC/MS transfer line) the ferrule at the transfer line can develope small leaks when it is heated, so you just have to tighten that nut a little more once everything has gotten hot and cooled back down. Be sure to give >4 hours before drawing conclusions about autotunes(I give 24 hours)

The other masses: 207, 281, and 355 are common siloxane masses and are likely due to the column. Possibly the trasnfer line is cooking off the stationary phase of the column and that is what you are seeing. Give it time and check again.

This is not bad. These are common things you will see, I haven't used the 5975 yet, but it's supposed to be really sensitive, so I'm not surprized that you see your column mobile phase in your autotunes. Give the mass spec plenty of time to heat up and stabalize, try autotune again. Even with the abundances you have sited, you should have no problem with using the mass spec.

Good job keeping an eye on changes from autotune to autotune, that will come in handy when troubleshooting, but don't always conclude that changes are bad, the mass spec has to tune for a reason, and usually it is a change for the better. If you are looking for a good resource for agilent GC/MS systems go to ECSMDL.com and look up Mark Ferry. He can tell you about as much as anyone can about those mass specs.