In working with one Skyline user attempting to combine targeted-MS/MS chromatogram data with peptide search results, it became clear that the current Library - Ion match tolerance based only on Th units was confusing for this high resolution data. His data was from a Thermo Orbitrap, where resolution (FWHM in m/z dimension) increases with m/z. That is peaks get wider as m/z increases. He had set his Ion match tolerance to 0.05 Th, and was confused by the fact that the spectrum plot showed a strong peak matching his Y3, but Skyline extracted virtually no chromatogram for it from the same data. Drilling in on the MS/MS plot, we found that the peak was around 0.02 Th away from its expected m/z value. Since the ion was between 200 and 400 m/z, this was 50-100 PPM from the expected m/z, probably not the right peak.

To make it easier for users understand what is going on in cases like this, the Library tab should be changed to:

Ion match tolerance: Units:
[ 0.05 ] [ Th |\/]

Where the options in the Units field would be:
Th
PPM
Resolution

When "Resolution" is chosen, if there is a resolution specified in the MS/MS filtering settings, the tolerance would get set to 2 and disabled, so that the match tolerance matches exactly the chromatogram filter width. This would guarantee that an ion matched in the MS/MS plot should have very similar chromatogram extraction data. Alternatively, PPM could also be used, which at least scales more like resolution on a Thermo Orbitrap.

If no MS/MS filtering settings are present, then choosing "Resolution" would show an error message in Skyline, explaining that MS/MS filtering setting must be set before this option can be used.

Something now in Rita's area. Perhaps someday. We no longer use the term "Th" but instead refer to "m/z" as the units. Otherwise, it would still be nice to be able to refer to PPM values in our m/z Tolerance fields.

I think this is the same as 830, right? I guess 9-10 years is long enough to lose track of a good idea.