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?