General question about peptide quantitation

General question about peptide quantitation caho  2020-04-29

Hi there,

May I please ask, with regards to peptide quantitation, is the sum of the peak areas of all fragment ions taken (so the total peak area of the precursor, precursor [m+1], precursor [m+2] fragment ions), or is generally the fragment ion with the greatest peak area used? May I also please ask how is the peak rank determined for each peptide/fragment ion?

Thank you so much for your help!

Nick Shulman responded:  2020-04-29
Skyline never uses the maximum peak area across the transitions for anything. Skyline sums the peak areas.

The peak rank of a transition result is found by comparing the transition peak area with the peak areas of the other transitions within the same precursor, and in the same result file.
-- Nick
caho responded:  2020-04-29
Thanks for the quick response, Nick. New to this and so really appreciate the help!

To further clarify, that is to say one should quantify a peptide present by summing the peak areas of all isotopic precursors?