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Q-Exactive ppm mass error question

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Q-Exactive ppm mass error question johnny perez  2018-05-02 13:33
 
Hi Brendan,

I ran a targeted PRM assay method for a set of peptides with an inclusion list that was produced using skyline. The method takes a full MS spectrum followed by 32 MS/MS spectra for 16 peptides with two precursors each all listed in the inclusion list. When importing into skyline, it filters the Thermo .raw files beautifully and gives great looking data. I had a question about the ppm error measurements. I've attached a screenshot for your review. Is the ppm mass error measurement the linear combination of mass errors for the skyline determined fragment ions? I cannot imagine it has anything to do with the precursor due to the Q-Exactive fragmenting all ions within the + or - m/z window.

Thank you!

Johnny
 
 
Nick Shulman responded:  2018-05-02 14:03
When Skyline is showing you one chromatogram per precursor like that, the mass error that is displayed is the mass error of the transition with the greatest height across the selected peak.

If you have both ms1 and ms2 transitions, then usually that mass error would be the one associated with the monoisotopic precursor, since that would have the most intensity.