|Title||»||Add PPM and resolution options to Transition Settings - Library - Ion match tolerance|
|Assigned To||»||Brendan MacLean|
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:
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.