Protein prospector/search compare and Xcalibur/qual browser

Upon completion of a search, a Search Compare page appears. Selecting Report Type: Crosslinked Peptides yields the “Search Compare Search Results” page listing the crosslinked peptide results from the Batch-Tag search. This page contains sequences of candidate crosslinked peptides, identifies the crosslinked residues, shows a score and score difference for each crosslinked pair, and other useful parameters. It also provides a link to an MS/MS spectrum for the crosslinked peptides that includes a list of observed and theoretical fragment masses, and a matched intensity score [24]. Protein Prospector scores and score differences are based on the number and types of fragment ions identified, as well as their sequence and charge [24]. Crosslinked candidates from the Search Compare page were screened using the criteria described in sections “Features of an MS/MS spectrum that support an isopeptide crosslink” and “Features of an MS/MS spectrum that raise doubts about a candidate crosslinked peptide pair” from Results.

We also evaluated the crosslinked peptides reported on the “Search Compare Search Results” page with the aid of MS-TAG, a program in Protein Prospector to test for linear peptides that fit the data better than the crosslinked candidate. For MS-Tag search details refer to the section below entitled “MS-Tag search for alternative interpretations”.

We used Xcalibur/Qual Browser (Thermo Scientific, Waltham MA) to manually evaluate each crosslinked candidate. Manual evaluation included identifying ions consistent with the crosslinked peptide sequence, and identifying ions that could fit other sequences that were not identified by Protein Prospector. The S1 Text file describes details of our manual evaluation protocol.