Figure 3

Overlap of peptide and protein identifications using different search algorithms. The 4-way Venn diagrams generated by the VENNY program [33] illustrate the intersections of (A) all peptides, (B) RefSeq proteins, and (C) putative splice variants identified by Mascot, OMSSA, X! Tandem, and InsPecT. In addition to 42% (1651/3891) of identified peptides overlapping, all four algorithms agreed on 51% (568/1114) of RefSeq protein identifications but only 15% (11/72) of the putative splice variants. All search results had an estimated FDR < 2% for peptide identification.