Table 2.

Summary of Search Results When MS/MS FDR ≤ 0.01

	IPI	PEPPI_KB	PEPPI_without_SNP	PEPPI_with_SNP
Size (M)	47	115.2	1181.1	1769.7
Elapsed Time(h:mm:ss)	0:11:05	0:10:39	1:02:32	1:33:04
MS2 FDR	0.01000	0.00992	0.00996	0.00999
Target MS2 hits	22685	21473	68137	116363
Decoy MS2 hits	114	107	341	584
Peptide FDR	0.01575	0.01527	0.01242	0.01571
Target peptide hits	125	129	159	188
Decoy peptide hits	2	2	2	3
Protein/gene FDR	0.02797	0.02778	0.02439	0.02339
Target protein/gene hits	368/141	142	162	169
Decoy protein/gene hits	5/2	2	2	2
PEPPI FDR		0.01376	0.01283	0.01376
Target PEPPI hits		433	1549	2886
Decoy PEPPI hits		3	10	20