ECL: an exhaustive search tool for the identification of cross-linked peptides using whole database

摘要

BackgroundChemical cross-linking combined with mass spectrometry (CX-MS) is a high-throughput approach to studying protein-protein interactions. The number of peptide-peptide combinations grows quadratically with respect to the number of proteins, resulting in a high computational complexity. Widely used methods including xQuest (Rinner et al., Nat Methods 5(4):315–8, 2008; Walzthoeni et al., Nat Methods 9(9):901–3, 2012), pLink (Yang et al., Nat Methods 9(9):904–6, 2012), ProteinProspector (Chu et al., Mol Cell Proteomics 9:25–31, 2010; Trnka et al., 13(2):420–34, 2014) and Kojak (Hoopmann et al., J Proteome Res 14(5):2190–198, 2015) avoid searching all peptide-peptide combinations by pre-selecting peptides with heuristic approaches. However, pre-selection procedures may cause missing findings. The most intuitive approach is searching all possible candidates. A tool that can exhaustively search a whole database without any heuristic pre-selection procedure is therefore desirable.