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

Figure 3

Comparison of spectra and peptides assigned by FDR and FlexiFDR for concatenated search.

Comparison of spectra and peptides assigned by FDR (pink) and FlexiFDR (blue) for concatenated database search. The number of spectra is shown on top with the number peptides in brackets beneath them. For the standard mixtures, the true positives (green) and false positives (red) identified exclusively are highlighted. FlexiFDR identifies a higher number of true unique spectra and peptides than FDR in almost all cases. The proportion of false positives in exclusively identified set is higher in FDR than FlexiFDR. A star symbol (*) depicts that although there are non-zero true positive spectra identifications in few cases of FDR, they could not bring in any new peptide identification. The peptides they identified were already identified by other spectra (which are shared by both FDR and FlexiFDR).

Figure 3

doi: https://doi.org/10.1371/journal.pone.0050651.g003