MassHunter Qual trying to make a Mirror Plot - specific question

I am using MassHunter Qual to try to make a mirror plot from the MSMS spectrum of a synthesized molecule next to a suspected molecule from a mixed sample.

The steps as far as I can tell are:

  • use “find by targeted MS/MS"
  • Highlight the desired spectrum
  • Click on “Identify Compounds” then “Search Library”
  • Import a specific PCDL file and search
  • Once compound matched, Click on “Difference Results”

The problem that I'm having is that I cannot find the compound in the targeted MSMS. I suspect it is because the signal height is only ~2x10^3 for that fragment. Does anyone know how to lower the threshold to allow Qual to identify that fragment?


  • Hi ,

    The Find by Targeted MS/MS works in the following way. Taken from Version 10.0 help file.

    This algorithm works by making a list of all of the targeted m/z values in the data file. Then, for each of these, it extracts a chromatogram of the MS/MS product ion data with that precursor ion m/z. The chromatogram is integrated, and each of the peaks found is potentially a compound. You can limit which peaks can be compounds using the fields on the Processing tab and the Peak Filters tab. Only peaks which are not filtered become compounds.

    It will also rely on the chosen integrator find a peak. By default the Peak Filter tab is set to filter by relative area, 5% of largest peak. I would start with just turning that off and go from there.

    You could also manually extract the compound you are having difficulty with and then see if you can find the right combination of integrator and peak filters for the algorithm to find a peak.

    Let us know what you find or if you need further assistance.

  • ,

    I just wanted to follow-up to see what you found regarding your targeted MSMS data processing. If you still need help, just let us know and we would be happy to continue working with you.

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