Ghost peaks and sudden baseline shifts

5975C MSD and 7890 GC. I am fairly new to GC-MS and am having issues with my baseline. I have recently begun seeing ghost peaks and sudden baseline shifts after replacing a column. I did inlet maintenance and added an in-line gas purifier as well as conditioned the column to help resolve, but the bottom spectra which was run after this maintenance is actually showing the ghost peaks again as well as the sudden baseline shifts I saw before. 

Could this be a detector issue? I have a CI detector but know nothing about how to clean or troubleshoot it. 

  • Hi 

    Updated tags to increase visibility.

  • Does the 28 and 40 ion abundance increase as it runs? 

  • Not really. I've listed the ghost peaks and the 18 and 40 abundance below. Please scroll over to the right to see all the numbers.

    I did run an air/water check this morning and my N2 values are quite high. O2 and water seem okay. Not sure where high N2 would come from.

    Forgive my ignorance, but what's the significance of m/z 40? I get that 18 is water.

    Thanks for the help.


    R.T. 18.440R.T. 20.431R.T. 23.574R.T. 25.681R.T. 33.717R.T. 36.266
    R.T. 38.685R.T. 42.9544R.T. 43.729
  • I am wondering if your gas is contaminated with Nitrogen (28) and argon (40).  You have no 44 peak of CO2 which would indicate a leak. Is this an old column? 

  • We're using UHP helium (something like 99.99995% pure?).

    Yes, it is an old column. The other column I was using broke in the middle, so I had no choice but to install this backup column. Ordering a new column is on my list of things that need to be ordered.

    I did give both column nuts a tweak and ran a blank run. Ghost peaks are better now, but I am still getting a few at the end. N2 numbers are also down. I'll continue to tweak and see if I can get the N2 numbers even lower.

  • Is it necessary for you to scan for ions under mass 35?  That is probably a reason your baseline is so crappy. We scan from 35-500. 

  • No, I didn't realize that. The lightest component I would be interested in is around 44 MW. Do I do that via the Tune and Vaccum menu?

  • No it's in the method. Go to edit entire method and go through the screens. I forget exactly where it is in the MS area of the method, just look around or look in the manual if you have one or the help in the software.

  • You can change your scan range under MS Parameters.  Go to Method and Run Control view, I think it is Instrument menu, Edit MS Parameters.

    Some gas filters cartridges are filled with N2 during manufacturing for shipping, so it takes some time after installation to purge it all out.  The low O2 shows that it's not a leak.  (Air leak would have N2/O2 ratio approx. 4.)  Agilent's Gas Clean filters are like this.  When I install one on a new system, I'll set the split flow to 250-300 mL/min overnight to purge the N2 from the filter.  Argon (40) sometimes shows up as an impurity in helium, and a gas filter won't remove it.

  • Interesting about the N2 in the filters. The N2 content does seem to be coming down slowly, but last check still showed over 10%. O2 and H2O numbers are low. I did find a large leak on a helium regulator further downstream of the regulator supplying the GC-MS so isolated that regulator, but it didn't seem to help bring my N2 numbers down much. Question, if I had an O2 scrubber in-line, couldn't that remove most of the O2 and skew the N2 to O2 numbers so they weren't 4:1?


    I really appreciate all the help and suggestions regarding my issue. I am still learning about MSDs and feel like I have a long way to go. Meanwhile, the baseline is much improved and most of the ghost peaks seem to have vanished.

Was this helpful?