• Medientyp: E-Artikel
  • Titel: ECL: an exhaustive search tool for the identification of cross-linked peptides using whole database
  • Beteiligte: Yu, Fengchao; Li, Ning; Yu, Weichuan
  • Erschienen: Springer Science and Business Media LLC, 2016
  • Erschienen in: BMC Bioinformatics
  • Sprache: Englisch
  • DOI: 10.1186/s12859-016-1073-y
  • ISSN: 1471-2105
  • Schlagwörter: Applied Mathematics ; Computer Science Applications ; Molecular Biology ; Biochemistry ; Structural Biology
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  • Beschreibung: <jats:title>Abstract</jats:title><jats:sec> <jats:title>Background</jats:title> <jats:p>Chemical 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.</jats:p> </jats:sec><jats:sec> <jats:title>Results</jats:title> <jats:p>We have developed a cross-linked peptides identification tool named ECL. It can exhaustively search a whole database in a reasonable period of time without any heuristic pre-selection procedure. Tests showed that searching a database containing 5200 proteins took 7 h.</jats:p> <jats:p>ECL identified more non-redundant cross-linked peptides than xQuest, pLink, and ProteinProspector. Experiments showed that about 30 <jats:italic>%</jats:italic> of these additional identified peptides were not pre-selected by Kojak. We used protein crystal structures from the protein data bank to check the intra-protein cross-linked peptides. Most of the distances between cross-linking sites were smaller than 30 Å.</jats:p> </jats:sec><jats:sec> <jats:title>Conclusions</jats:title> <jats:p>To the best of our knowledge, ECL is the first tool that can exhaustively search all candidates in cross-linked peptides identification. The experiments showed that ECL could identify more peptides than xQuest, pLink, and ProteinProspector. A further analysis indicated that some of the additional identified results were thanks to the exhaustive search.</jats:p> </jats:sec>
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