I think we may want to do this also for the "Method match tolerance m/z:" on the Instrument tab as well, changing it to:
Method match tolerance:
[__________________________] [ m/z |\/]
| ppm |
This would be to match the settings in a DDA search tool (like Comet) so that when MS/MS acquisition mode is set to DDA, we end up considering exactly the same spectra as the search engine and in the same way for the fragment ions in the spectra. In the comet.params file I am looking at, I see the following:
peptide_mass_tolerance = 20.00
peptide_mass_units = 2 # 0=amu, 1=mmu, 2=ppm
Which seems to indicate that the spectrum matching is only considering precursors within 20 ppm of the expected monoisotopic mass. In other words, it expects high accuracy precursor m/z assignment from the mass spectometer.