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?


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