Supplementary Figure 10: TagGraph is compatible, though less effective, with low-resolution tandem mass spectra.
From: TagGraph reveals vast protein modification landscapes from large tandem mass spectrometry datasets
a) Over 300,000 MS/MS spectra from 33 lung-derived LC-MS/MS runs (Peptide Atlas PAe001771; used in the Wilhelm et al. draft of the human proteome) were searched with TagGraph (blue), and compared with the original X!Tandem search results (orange) or SEQUEST (green). The total number of high-confident identifications TagGraph made was 2.4x greater than those originally reported with the X!Tandem approach, but 2.0x less than those found with SEQUEST. Spectra for which TagGraph and the traditional database search algorithm returned high-confidence identifications agreed at rates >99% (square brackets). The low overall rates of confident identifications from all search methods (for example, 9.3% of all acquired spectra were confidently assigned by TagGraph) is much less than was observed for the high-resolution lung dataset reported by Kim et al. (~50%). b) TagGraph added dozens of modifications to this this dataset, in similar proportions to the Kim et al. dataset. The majority of modifications from both datasets were consistent with post-isolation, rather than biological modifications.
