Table 3. Number of PSMs, Peptides, and Proteins Identified Using the HPP Guidelines (PSM FDR < 1%, protein FDR < 1%) in the Samples Selected from PRIDE for the Analysis of the Missing Proteins^a.

	PXD001468	PXD002367	PXD001242	PXD000754	PXD000605	PXD000004	PRD000269	PXD002145	Total
Spectra	836145	114970	452880	519326	1299378	357899	370218	1198042	5148858
Total PSMs	328554	48609	110624	80213	19086	136506	21969	6676	752237
FP PSMs	161	34	136	201	5	154	11	116	818
Total Peptides	68377	9848	14413	10122	1228	16679	2001	199	93012
Total Peptides (proteotypic)	24510	3990	5393	4226	788	5737	746	56	33756
Total Peptides (nonproteotypic)	43867	5858	9020	5896	440	10942	1255	143	59256
FP Peptides	70	12	20	46	2	41	3	8	202
Total Proteins	7206	1437	2681	2127	363	2340	351	54	8712
Total Conclusive Prot	4539	909	1501	1140	146	1069	193	29	5626
FP Proteins	33	8	15	11	2	33	1	8	111
Total Assigned Spectra	191095	24736	66707	51392	18091	133602	14936	2495	503054
Missing PSMs	798	473	117	0	0	0	0	0	1388
Missing Peptides	83	258	25	0	0	0	0	0	357
Missing Proteins	10	47	5	0	0	0	0	0	60
Missing Assigned Spectra	479	367	68	0	0	0	0	0	914
Total Proteins HPP (≥1 peptide)	4276	888	1450	1115	146	1053	188	28	5284
Total Proteins HPP (≥2 peptides)	3326	750	1260	1000	120	924	169	22	3950
Missing Proteins HPP (≥1 peptide)	10	45	5	0	0	0	0	0	58
Missing Proteins HPP (≥2 peptides)	5	27	1	0	0	0	0	0	32

^aFP = false positives.