. Author manuscript; available in PMC: 2012 May 1.

Published in final edited form as: Nat Methods. 2011 Oct 2;8(11):937–940. doi: 10.1038/nmeth.1714

Table 1. MS2 versus MS3 identifications and quantifications.

A comparison of the number of peptide and protein identifications and quantifications from 20 SCX fractions of the human yeast multi-proteome model using the MS2 and the MS3 methods.

		Total peptides	Unique peptides	Total proteins	% MS2 method^c
Identifications^a	MS2 method	117,849	43,656	8,216
Identifications^a	MS3 method	96,202	38,122	7,578	92%

Quantifications^b	MS2 method	109,967	41,804	8,803
Quantifications^b	MS3 method	75,330	33,849	7,089	88%

All human and yeast identifications.

All human and yeast quantifications. See Supplementary Table 1 for a more detailed breakdown of the data. TMT reporter ions had to be present (signal > 0) in all six channels for yeast peptides and for channels 126, 127 and 128 for human peptides.

The proportion of identified or quantified proteins using the MS3 method compared to the MS2 method