Table I. Identification from HeLa and yeast lysate triplicate analysis using a standard 90 min gradient.

	MS scans	Isotope pattern	MS/MS scans	Identification rate [%]	Peptide sequences identified	Proteins identified
HeLa_1	7002	759,774	79,704	47.09	35,547	4870
HeLa_2	7181	769,355	79,876	47.22	35,572	4864
HeLa_3	7272	796,086	81,389	46.57	35,621	4828
Total				46.96	48,172	5210
yeast_1	4873	528,682	63,682	31.08	17,066	3361
yeast_2	4732	541,194	66,441	30.88	16,921	3325
yeast_3	4691	556,675	66,978	31.98	17,494	3369
Total				31.32	24,131	3627