ms baseline drops and shifts

Hi All,

I am trying to do a simple Average MS Extraction on data collected using a SQ MSD (G6135C, I believe), with a background subtraction and Gaussian smoothing using OL2.7 build

When I perform the extraction, my method has Gaussian smoothing set to 2.0, Use External time range for background mode is selected and a time is given. 

When I initially extract the spectrum, the baseline is flat and is at 0.00%. However, the data are not smoothed. I reprocess the injection to smooth the spectrum. Now the baseline is raised anywhere from 0.05% and up. I am including an example where smoothing the data causes the baseline to shift to ~0.70%. I know that the 'reprocess' is performing some sort of background subtraction to cause this raised baseline, but the only difference between the spectra displayed below is the Gaussian smoothing. Once the baseline is raised, I can not figure out any setting which I can change (including removing gaussian smoothing, removing background subtraction, changing the background subtraction...) in order to get the baseline back down to 0. 

I believe I am making a mistake in my processing method, I don't know where/how. Any help would be greatly appreciated!




Initial Extraction zoomed in, flat baseline at 0.00%:

Reprocessed to smooth (Gaussian factor: 2.0), baseline raised to 0.66%:

Zoomed out after smoothing to show baseline dips causing the baseline to be at 0.66%:


  • Hello,

    I would suggest opening an informatic support ticket. We will likely need to take a look at the data to understand the issue. Are you smoothing in the spectrum extraction part of the processing method? I am seeing the spectrum change as I reprocess with that selection on and off and do not have to make any other changes. Is this manual extraction or part of the processing method auto extraction for compounds. 


  • Hey Marty,

    It is a manual integration of the TIC, not an identified compound. I tested extracting using the 'Spectral smoothing' in the processing method. The spectra are always extracted un-smoothed. When I reprocess, it does smooth the data, but it raises the baseline from 0.00 to about 0.2. This seems to be an MS background subtraction issue. I tried all the combinations in the 'Arbitrary spectra', 'Peak spectra' and 'External background time range' portion of the processing method. I kept 'Spectral smoothing' on. Since clicking Reprocess raised the baseline in all the spectra, I was trying to have the method smooth the spectra when it initially extracted it, but from testing I think that it is not be possible. I think you must click Reprocess to smooth spectra. So now I am back to trying to fix the background issue giving me a raised baseline from reprocessing. 

    I did try with an identified compound. When I extract the EIC, the Spectrum is automatically extracted with the smoothing applied because I selected the box to re-process after extraction, but the baseline is also elevated. I can't get a baseline at 0.00 with a smoothed spectrum.

    You think I should open a ticket?

    Thanks for you help, Marty!

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