Table I Results of a target-decoy database search of the complete C. elegans data set

The number of target and decoy peptide-spectrum matches, peptide identifications, and protein identifications for three different PSM FDRs are shown. For peptides mapping to several protein sequences only the alphabetically first protein identification was considered. For any PSM FDR, the ratio of decoy to target hits is higher for peptides and again higher for proteins. Unlike for the PSMs, this ratio is not to be mistaken for the FDR for peptide or protein identifications.

PSM FDRPSMsPeptide identificationsProtein identifications
TargetDecoyDecoy/TargetTargetDecoyDecoy/TargetTargetDecoyDecoy/Target
0.05954,66147,7250.05117,29336,4190.31016,45914,3540.872
0.01795,5027,9470.0182,6286,3940.07711,0894,9740.449
0.001614,4866140.00165,7795190.0088,4775060.060