Summary of identified spectra, peptides, proteins and estimated FDR levels.

a)According to our peptide classification scheme [38], [46], class 1a peptides unambiguously identify a single unique protein sequence encoded by a unique transcript. Class 1b peptides also unambiguously identify a unique protein sequence encoded by several transcripts of the same gene model with identical coding region and differences in the 5′ and/or 3′ untranslated regions. Class 2a peptides identify a subset and class 2b peptides all protein sequences encoded by a gene model. Class 3a peptides unambiguously identify one protein sequence, but this sequence could be encoded by several gene models from distinct loci (e.g. histones). Finally, class 3b peptides can be derived from different protein sequences encoded by several gene models from distinct loci and have the least information content.
b)For protein groups identified by class 2a or 2b peptides (a gene model identification) all possible protein accessions are listed in Table S1.
c)The minimal number of additional protein identifications by 3b peptides is shown.
d)Based on the total hits in target and decoy databases (DB), the FDR was estimated at the spectra, peptide and protein level.