Chromatography Forum

Hi
I'm having some problems with my GC/MS. The system is a 7890 GC with a 5975C MS. The system was just set up last week and everything seemed to be fine. However when I run a sample the peaks look fine but when I do a library search my results are poor. When the TIC is looked at there are peaks that shouldn't be there. For example a simple ester like ethyl acetate has small ion peaks that run from 102 to 448.4. This type of thing has been present in all the samples I've run.

The column was conditioned before use and the injection temperature is 200 C with oven ramping going from 90-250 C so I would think the septum would not be the cause. Any ideas or tips would be appreciated.

don't know what test you are running and what the IS response is, in my experience, if EM voltage is too high, it genarates some background ions. If you click on the baseline of the chromatogram and see ions other than 44 and 40, the EM voltage is probably too high.

Are you taking an "average" spectrum or single point? Are you subtracting the background before searching?

I've tried lowering the EM voltage and that seems to have helped. The other peaks are still showing up but are reduced. So I guess it will just be a trial and error type procedure.

We are running an "average" spectrum and I have subtracted the backgrounds before searching.

you can also raise the threshold to reduce unwanted ions.

What tune do you do? in the 5975 to compare well with the library you must do de stune. If you do de atune the % of the ions aren't similar the library. If you nedd more sensitivity (for trace analysis) you can do the HiSense tune

I'm using an stune. I have also lowered the EM voltage which seems to have helped. Thanks for all the help everyone.

Flavordrew,

How many ions are present in your autotune? If you have a lot, you either have too low a threshold (as per JI2002) or you have a contaminated system. I have never taken my EM down after running an autotune, always kept it or raised it so I would have to disagree with the need for taking it down.

If you are not looking for low levels, then you can just ignore the advice and turn the EM down. However, you run the risk of ignoring a potential problem (especially while still under warranty.) If you are looking for low levels then the question becomes what are the ions and do they spectral match with anything if you click on "clean" baseline? Also, if you click on the apex and click on the background and subtract the two, do you get a library match?

Best regards.

I have found that our new 5975 has much more sensitivity at a given EM Voltage than the 5973, so I'm not suprised that lowering the voltage helped.