Table 1.

Identification counts for all included samples

Sample and Replicates	Instrument and Site	Identified Spectra	Distinct Peptides	Multipeptide Proteins
Study5 NCI20	LTQ@73	1085	358	8
(5 replicates)	LTQ2@95	888	300	7
	LTQc@65	1446	455	8
	Orbi@86	968	374	11
	OrbiP@65	1660	424	10
	OrbiW@56	1708	444	11
Study5 Yeast	LTQ@73	19341	6261	880
(6 replicates)	LTQ2@95	14054	4574	730
	LTQc@65	21209	7118	993
	Orbi@86	33301	8977	1280
	OrbiP@65	19118	4652	627
	OrbiW@56	23245	5708	813
Study6 Yeast	LTQ@73	8832	4263	681
(3 replicates)	LTQ2@95	7471	3537	568
	LTQx@65	7763	3859	610
	Orbi@86	8448	4354	795
	OrbiO@65	15177	7110	1024
	OrbiP@65	13465	6111	838
	OrbiW@56	11675	5727	823
Study6 UPS 1	LTQ@73	991	378	51
(3 replicates)	LTQ2@95	1257	494	50
	LTQx@65	1367	562	56
	Orbi@86	877	366	51
	OrbiO@65	1619	692	58
	OrbiP@65	2143	798	59
	OrbiW@56	1296	617	59
Study8 Yeast	LTQ@73	22740	8322	1039
High concentration	LTQ2@95	13909	5470	819
(3 replicates)	LTQx@65	14010	6642	951
	Orbi@86	18943	7362	939
	OrbiO@65	17037	6891	918
	OrbiW@56	25082	9816	1111
Study8 Yeast	LTQ@73	13801	5586	751
Low concentration	LTQ2@95	6274	2859	478
(3 replicates)	LTQx@65	6899	3467	583
	Orbi@86	17304	7407	957
	OrbiO@65	12018	5133	789
	OrbiW@56	19782	8132	1048