Fig. 6.

Application of SWATH MS targeted analysis to identify peptide modifications. The six most intense fragment ion traces for the ¹⁴N-labeled (light) and ¹⁵N-labeled (heavy) forms of the peptide MIEIMLPVFDAPQNLVEQAK, extracted from the swath 750–775, are shown for the yeast diauxic shift sample y8 (late time point). None of the classical SRM criteria (fragments co-elution, light-heavy peptide co-elution, relative intensities of the fragment ions) can discriminate the three candidate peak groups found here. By extracting additional, nonshared fragment ion traces, the identification of the peptide can be confirmed, and the site of the oxidized methionine modification can be unambiguously assigned onto the peptide sequence (supplemental Fig. S10).