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Learning from Decoys to Improve the Sensitivity and Specificity of Proteomics Database Search Results

Figure 4

Comparison of unique identifications (spectra and peptides) from concatenated search.

Top and Bottom panels depict spectra and corresponding peptide comparison from a concatenated search. The blue colored bars represent the unique true hits added by FlexiFDR alone while green colored bars represent unique true hits from FDR alone. Similarly, the pink bars denote false hits from FlexiFDR alone while red bars denote false hits from FDR alone. The spectral hits from FDR can be mapped to unique peptides right in the lower panel. The false spectral hits in case of FDR alone bring more false peptide identifications than FlexiFDR (compare bars from A to B vertically). FlexiFDR brings more unique true hits than FDR and brings lesser number of unique false hits. This enhances the true positives and decreases false positives in the datasets shown.

Figure 4

doi: https://doi.org/10.1371/journal.pone.0050651.g004