ECL: an exhaustive search tool for the identification of cross-linked peptides using whole database
Identifieur interne : 000033 ( Main/Exploration ); précédent : 000032; suivant : 000034ECL: an exhaustive search tool for the identification of cross-linked peptides using whole database
Auteurs : Fengchao Yu [République populaire de Chine] ; Ning Li [République populaire de Chine] ; Weichuan Yu [République populaire de Chine]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2016.
Abstract
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.
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.
ECL identified more non-redundant cross-linked peptides than xQuest, pLink, and ProteinProspector. Experiments showed that about 30
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.
The online version of this article (doi:10.1186/s12859-016-1073-y) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12859-016-1073-y
PubMed: 27206479
PubMed Central: 4874008
Affiliations:
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populaire de Chine</country><wicri:regionArea>Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong</wicri:regionArea><wicri:noRegion>Hong Kong</wicri:noRegion></affiliation></author><author><name sortKey="Yu, Weichuan" sort="Yu, Weichuan" uniqKey="Yu W" first="Weichuan" last="Yu">Weichuan Yu</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Hong Kong</wicri:regionArea><wicri:noRegion>Hong Kong</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff3">Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong</wicri:regionArea><wicri:noRegion>Hong Kong</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">27206479</idno><idno type="pmc">4874008</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4874008</idno><idno type="RBID">PMC:4874008</idno><idno type="doi">10.1186/s12859-016-1073-y</idno><date when="2016">2016</date><idno type="wicri:Area/Pmc/Corpus">000160</idno><idno type="wicri:Area/Pmc/Curation">000160</idno><idno type="wicri:Area/Pmc/Checkpoint">000031</idno><idno type="wicri:Area/Ncbi/Merge">000734</idno><idno type="wicri:Area/Ncbi/Curation">000734</idno><idno type="wicri:Area/Ncbi/Checkpoint">000734</idno><idno type="wicri:Area/Main/Merge">000033</idno><idno type="wicri:Area/Main/Curation">000033</idno><idno type="wicri:Area/Main/Exploration">000033</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">ECL: an exhaustive search tool for the identification of cross-linked peptides using whole database</title><author><name sortKey="Yu, Fengchao" sort="Yu, Fengchao" uniqKey="Yu F" first="Fengchao" last="Yu">Fengchao Yu</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Hong Kong</wicri:regionArea><wicri:noRegion>Hong Kong</wicri:noRegion></affiliation></author><author><name sortKey="Li, Ning" sort="Li, Ning" uniqKey="Li N" first="Ning" last="Li">Ning Li</name><affiliation wicri:level="1"><nlm:aff id="Aff2">Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong</wicri:regionArea><wicri:noRegion>Hong Kong</wicri:noRegion></affiliation></author><author><name sortKey="Yu, Weichuan" sort="Yu, Weichuan" uniqKey="Yu W" first="Weichuan" last="Yu">Weichuan Yu</name><affiliation wicri:level="1"><nlm:aff id="Aff1">Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Hong Kong</wicri:regionArea><wicri:noRegion>Hong Kong</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="Aff3">Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong</wicri:regionArea><wicri:noRegion>Hong Kong</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2016">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><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.</p></sec><sec><title>Results</title><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.</p><p>ECL identified more non-redundant cross-linked peptides than xQuest, pLink, and ProteinProspector. Experiments showed that about 30 <italic>%</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.</p></sec><sec><title>Conclusions</title><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.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12859-016-1073-y) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Young, Mm" uniqKey="Young M">MM Young</name></author><author><name sortKey="Tang, N" uniqKey="Tang N">N Tang</name></author><author><name sortKey="Hempel, Jc" uniqKey="Hempel J">JC Hempel</name></author><author><name sortKey="Oshiro, Cm" uniqKey="Oshiro C">CM Oshiro</name></author><author><name sortKey="Taylor, Ew" uniqKey="Taylor E">EW Taylor</name></author><author><name sortKey="Kuntz, Id" uniqKey="Kuntz I">ID Kuntz</name></author><author><name sortKey="Gibson, Bw" uniqKey="Gibson B">BW Gibson</name></author><author><name sortKey="Dollinger, G" uniqKey="Dollinger 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Zhang</name></author><author><name sortKey="Li, S" uniqKey="Li S">S Li</name></author><author><name sortKey="Chi, H" uniqKey="Chi H">H Chi</name></author><author><name sortKey="Li, Yx" uniqKey="Li Y">YX Li</name></author><author><name sortKey="Chen, Hf" uniqKey="Chen H">HF Chen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chu, F" uniqKey="Chu F">F Chu</name></author><author><name sortKey="Baker, Pr" uniqKey="Baker P">PR Baker</name></author><author><name sortKey="Burlingame, Al" uniqKey="Burlingame A">AL Burlingame</name></author><author><name sortKey="Chalkley, Rj" uniqKey="Chalkley R">RJ Chalkley</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Trnka, Mj" uniqKey="Trnka M">MJ Trnka</name></author><author><name sortKey="Baker, Pr" uniqKey="Baker P">PR Baker</name></author><author><name sortKey="Robinson, Pj" uniqKey="Robinson P">PJ Robinson</name></author><author><name sortKey="Burlingame, A" uniqKey="Burlingame 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Tibshirani</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Bohn, S" uniqKey="Bohn S">S Bohn</name></author><author><name sortKey="Beck, F" uniqKey="Beck F">F Beck</name></author><author><name sortKey="Sakata, E" uniqKey="Sakata E">E Sakata</name></author><author><name sortKey="Walzthoeni, T" uniqKey="Walzthoeni T">T Walzthoeni</name></author><author><name sortKey="Beck, M" uniqKey="Beck M">M Beck</name></author><author><name sortKey="Aebersold, R" uniqKey="Aebersold R">R Aebersold</name></author><author><name sortKey="Frster, F" uniqKey="Frster F">F Frster</name></author><author><name sortKey="Baumeister, W" uniqKey="Baumeister W">W Baumeister</name></author><author><name sortKey="Nickell, S" uniqKey="Nickell S">S Nickell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nesvizhskii, Ai" uniqKey="Nesvizhskii A">AI Nesvizhskii</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kertesz Farkas, A" uniqKey="Kertesz Farkas A">A Kertesz-Farkas</name></author><author><name sortKey="Keich, U" uniqKey="Keich U">U Keich</name></author><author><name sortKey="Noble, Ws" uniqKey="Noble W">WS Noble</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Yu, Fengchao" sort="Yu, Fengchao" uniqKey="Yu F" first="Fengchao" last="Yu">Fengchao Yu</name></noRegion><name sortKey="Li, Ning" sort="Li, Ning" uniqKey="Li N" first="Ning" last="Li">Ning Li</name><name sortKey="Yu, Weichuan" sort="Yu, Weichuan" uniqKey="Yu W" first="Weichuan" last="Yu">Weichuan Yu</name><name sortKey="Yu, Weichuan" sort="Yu, Weichuan" uniqKey="Yu W" first="Weichuan" last="Yu">Weichuan 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