Supplementary Figure 9: Examples of high-scoring peptide-spectrum matches with deviant monoisotopic mass assignments rescued by TagGraph.
From: TagGraph reveals vast protein modification landscapes from large tandem mass spectrometry datasets
Pairs of MS1 and MS/MS spectra are shown above one another, both assigned to the same peptide with EM-estimated probabilities above our selection threshold (0.99). The top MS/MS spectrum yielded an acceptably low mass deviation (ppm) whereas the bottom spectrum would be excluded from analysis using a rigid mass deviation filter. The MS/MS spectra are obviously similar, and the mass deviations can be explained by computational errors in the initial monoisotopic mass assignment. TagGraph rescues such MS/MS spectrum assignments by considering mass deviation as one of several peptide attributes which contribute to a peptide-spectrum match’s overall confidence (Supplementary Fig. 2).
