Chromatography Forum

Our GCMS 7890/5975c system produces a fine looking autotune report with very little background noise, but when we run a sample there is significant ion abundance detected at nearly every m/z that make the chromatogram uninterpretable. Has anyone ever seen anything like this?

So, your baseline noise is large at all times during your chromatographic run? From a mass standpoint, how low are you scanning in the MSD?

Same GC-MS problem, different operator replying...

We scan down to m/z 16 and can see N2 and water peaks, a little above background, background count at all other m/z up to 460 are almost exactly the same. The total ion count varies through the chromatogram, but not in any predictable way.

Same GC-MS problem, different operator replying...

We scan down to m/z 16 and can see N2 and water peaks, a little above background, background count at all other m/z up to 460 are almost exactly the same. The total ion count varies through the chromatogram, but not in any predictable way.

What do you have the threshold set to?

If set to zero or near that you will have that problem.

Our GCMS 7890/5975c system produces a fine looking autotune report with very little background noise, but when we run a sample there is significant ion abundance detected at nearly every m/z that make the chromatogram uninterpretable. Has anyone ever seen anything like this?

Same as above, check your threshold setting. Since you see less abundance in tune than in an analytical run, check to see if the threshold setting in the tune window is the same as you are using in the analysis run. Also see if the EM voltage is the same in both instances, if you increase the EM volts higher in the analysis than in tune you will see more background.

With a clean system I still normally run with a threshold setting of 50-150 counts to keep the baseline clean. Anything below that is not really usable anyhow for identifying peaks.

The threshold is set at 100. The background that we are seeing has abundances in the 1000 - 5000 range

The threshold is set at 100. The background that we are seeing has abundances in the 1000 - 5000 range

Can you lower the EM volts and still get the sensitivity you need for your analytes. In manual tune you should be able to scan the PFTBA and have an abundance of m/z 69 of 1,000,000 counts with out that much background. If you push it to 3,000,000 counts or over then you begin to see background like that.

The only other cause I can think of would be a massive air leak that overwhelming the mass filter. You see such when you have a lot of water pass through the column when running volatiles but it is normally only a couple minutes wide portion of the background.