Mass Error Plots

Mass Error Plots philip remes  2022-04-30

When I attempt to view the Mass Error plots for PRM QIT data, no data are displayed. I don't know if this is because mass error plots are not supported for this type of data, or the errors are larger than what the tools are anticipating, or something else. It would be useful to have this feature working for the fragment ions. Ask Lilian if you need some data or a skyline document. It would let the user know what mass tolerance is feasible. A larger request would be if you could implement Jarrett's Fine Tune algorithm to calibrate the mass scale.


Nick Shulman responded:  2022-04-30
The thing that determines whether mass errors will be available is the precursor and product mass analyzer that you have specified at:
Settings > Transition Settings > Full Scan
If the mass analyzer is "QIT", then Skyline will not calculate mass errors when extracting chromatograms.

The reason that Skyline does not calculate mass errors when the mass analyzer is QIT is that we thought that a low resolution mass spectrometer like that would not be able to resolve the isotope peaks. If the observed signal comes from multiple isotope peaks, we did not think that it would make sense to talk about the mass accuracy.

You can change the mass analyzer to something else if you would like. Skyline uses the resolution and mass analyzer to decide how wide of an m/z channel to sum across when extracting chromatograms. You can choose different values for the resolution and mass analyzer, and Skyline will end up choosing a different m/z width to sum across, which in many cases could result in better data.
-- Nick
philip remes responded:  2022-04-30
Thanks for the workaround. The thing about PRM with a lower resolution analyzer is that the isolation step may often be done with 0.7 Th width, therefore there is only one isotope for the fragment ions. The mass accuracy of these fragments is of great interest. Even for MS1 I can see it being possibly useful for a DDA experiment. Many QIT analyzers will give you isotopically resolved precursors for up to 2 or 3+, and even if it was only the average mass being measured, this would also be useful to know if one was to search with SEQUEST and average mass instead of monomass.