We should put a "High resolution" check box below the "Ion match tolerance" field on the Transition Settings - Library tab.

Ion match tolerance:
[ ] ppm
[x] High resolution

When it is checked the field units label would change to PPM, and the acceptable mass error would get calculated as PPM. This would make it possible to have this tolerance match the tolerance used in chromatogram extraction in the Transition Settings - Full-Scan tab.

Raising the priority. I would really like to see this in our next release and relatively soon in Skyline-daily.

Another option would be to use a dropdown list for the units.

Ion match tolerance: Units:
[_________________________] [ m/z |\/]
                                                       | ppm |
                                                       -----------------

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.

Fixed by adding the match tolerance unit setting (mz/ppm), PR https://github.com/ProteoWizard/pwiz/pull/2156