B. xiSEARCH+xiFDR(Xi), pLink 2 and Kojak(+PeptideProphet) comparison at 5% residue-pair FDR. The same trypsin dataset of the 26S proteasome was searched with all three software packages. xiSEARCH was run twice - once giving same likelihood for matching Lysine, Serine, Threonine and Tyrosine (xiSEARCH), as is the case for Kojak and pLink 2, and once giving priority to Lysine (Xi*). 