Supplementary Figure 4: Conflicting high-confidence peptide-spectrum matches strongly favor TagGraph interpretations over SEQUEST.
From: TagGraph reveals vast protein modification landscapes from large tandem mass spectrometry datasets
a) Of 46,191 MS/MS spectra for which both TagGraph and SEQUEST returned a high-confidence result, 98.36% agreed (left box; identical peptide-spectrum matches (PSMs)), consistent with an estimated 1% FDR for both algorithms. Of the MS/MS spectra which were exclusively identified by TagGraph (right box), 60% bore at least one modification that was not considered in the SEQUEST search parameters. All PSMs were derived from the A375 dataset (Dataset 1). Modification categories were assigned based on Uniprot annotations, and are not mutually exclusive for a given PSM. b) Of the 1.64% of high-confidence PSMs for which SEQUEST and TagGraph disagreed, PSM attributes including missed cleavage sites (top) and algorithm-assigned score (bottom) were more consistent with high-confidence identifications for TagGraph (right) than for SEQUEST (left).
