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 FDR	PSMs			Peptide identifications			Protein identifications
		Target	Decoy	Decoy/Target	Target	Decoy	Decoy/Target	Target	Decoy	Decoy/Target
0.05	954,661	47,725	0.05	117,293	36,419	0.310	16,459	14,354	0.872
0.01	795,502	7,947	0.01	82,628	6,394	0.077	11,089	4,974	0.449
0.001	614,486	614	0.001	65,779	519	0.008	8,477	506	0.060