Table 2.

Comparison of identifications in clustered and non-clustered datasets. The table contains a breakdown of the identifications of spectra, peptides and proteins as displayed in Table 1. For each similarity threshold the table shows how many identifications were common both when searching the clustered and non-clustered datasets, how many appeared only in the search of the non-clustered data, and how many identifications were unique to the clustered data.

Similarity threshold	Spectra identifications			Peptide identifications			Protein identifications
	Botha	Non-C.b	Clust.c	Both	Non-C.	Clust.	Both	Non-C.	Clust.
0.30	64472	19194	49083	16957	4133	1395	5447	744	325
0.35	67464	16896	44410	18129	2961	1374	5672	519	319
0.40	70580	14420	39047	18854	2236	1288	5795	396	301
0.45	71294	14054	32355	19314	1776	1278	5867	324	311
0.50	73635	11956	28133	19733	1357	1245	5938	253	291
0.55	75582	10324	23130	19980	1110	1162	5987	204	295
0.60	76849	9190	18272	20186	904	977	6020	171	255
0.65	78642	7604	14433	20360	730	864	6047	144	219
0.70	80381	6030	12014	20522	568	827	6075	116	225
0.75	81721	4773	9360	20638	452	774	6102	89	208
0.80	82679	3845	7181	20698	392	688	6103	88	186
0.85	83584	3002	5457	20774	316	640	6118	73	168
0.90	84423	2203	3927	20799	291	568	6119	72	149
0.95	84887	1760	2767	20789	301	487	6118	73	127
1.00	85170	1505	2099	20787	303	452	6121	70	121

^aIdentifications common to both searches;

^bIdentifications unique to the non-clustered search;

^cIdentifications unique to the clustered search.)