Overlap of peptide and protein identifications using different search algorithms. The 4-way Venn diagrams generated by the VENNY program  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.