Table 1. Summary of Identification Metrics Using CHarge Ordered Parallel Ion aNalysis (CHOPIN) and Universal Method on Tryptic (T), Elastase (E), and Post Digest Mix (PDM) Samples^a.

	peptide score threshold @1%FDR	PSMs	MSMS scans	effective peptide FDR @score threshold	protein score threshold @1%FDR	effective protein FDR @score threshold	protein groups @1% FDR	proteins (unique and razor)
CHOPIN (T)	21.1	307318	582030	0.924	57	1.052	8745	13019
Universal (T)	20.2	226291	539916	0.943	57	1.001	8692	12770
CHOPIN (E)	19.8	170960	660060	0.701	85	1.069	4951	5521
Universal/FT (E)	16.4	171529	349164	0.617	60	0.99	5143	6866
CHOPIN (PDM)	14	284347	714354	0.891	31	0.977	7958	11974
Universal (PDM)	14.9	192500	671699	0.84	32	1.003	7517	11371
CHOPIN (PDM), unlinked fractions	14	433723	1160032	0.999	37	0.977	9824	13000
All data	10.8	2010579	4677255	0.996	64	0.987	13728	14890
						trypsin	10052	13320
						elastase	7038	8257
						PDM	9834	12452

^aFractions have been combined and data searched in PEAKS.