Learning from Decoys to Improve the Sensitivity and Specificity of Proteomics Database Search Results
(A) The composition of databases used for searching standard mix datasets is shown. Database consists of standard mix proteins and common contaminants, both of which are considered true proteins (shown in green). It also consists of sequences from an unrelated organism which represent the entrapment sequences or false proteins (shown in red). The sizes of these two parts show that the true proteins were outnumbered by entrapment sequences. (B) For evaluating the FlexiFDR method, the definitions of true and false positives and negatives are relative to the unique sets identified by only one method- either FDR or FlexiFDR.