Fig. 5.

Targeted removal of conflicting spectra. A, Database search strategy to identify and discard false identifications derived from modified peptides. Standard search and searches with modification were performed without protein and PSM FDR threshold. Spectra that gave rise to conflicting sequence information were removed (cleaned search). The results were compared with the uncorrected standard search and a search where the variable modifications D+M+C were considered in a single pass (combined). The number of identified spectra (B) and non-redundant peptide sequences (C) is plotted as a function of the PSM FDR.