Xlink-Identifier: An Automated Data Analysis Platform for Confident Identifications of Chemically Cross-linked Peptides using Tandem Mass Spectrometry
Identifieur interne : 000457 ( Pmc/Checkpoint ); précédent : 000456; suivant : 000458Xlink-Identifier: An Automated Data Analysis Platform for Confident Identifications of Chemically Cross-linked Peptides using Tandem Mass Spectrometry
Auteurs : Xiuxia Du [États-Unis] ; Saiful M. Chowdhury [États-Unis] ; Nathan P. Manes [États-Unis] ; Si Wu [États-Unis] ; M. Uljana Mayer [États-Unis] ; Joshua N. Adkins [États-Unis] ; Gordon A. Anderson [États-Unis] ; Richard D. Smith [États-Unis]Source :
- Journal of proteome research [ 1535-3893 ] ; 2011.
Abstract
Chemical cross-linking combined with mass spectrometry provides a powerful method for identifying protein-protein interactions and probing the structure of protein complexes. A number of strategies have been reported that take advantage of the high sensitivity and high resolution of modern mass spectrometers. Approaches typically include synthesis of novel cross-linking compounds, and/or isotopic labelling of the cross-linking reagent and/or protein, and label-free methods. We report Xlink-Identifier, a comprehensive data analysis platform that has been developed to support label-free analyses. It can identify inter-peptide, intra-peptide, and deadend cross-links as well as underivatized peptides. The software streamlines data pre-processing, peptide scoring, and visualization and provides an overall data analysis strategy for studying protein-protein interactions and protein structure using mass spectrometry. The software has been evaluated using a custom synthesized cross-linking reagent that features an enrichment tag. Xlink-Identifier offers the potential to perform large-scale identifications of protein-protein interactions using tandem mass spectrometry.
Url:
DOI: 10.1021/pr100848a
PubMed: 21175198
PubMed Central: 3048902
Affiliations:
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Smith</name><affiliation wicri:level="2"><nlm:aff id="A2">Pacific Northwest National Laboratory, Richland, WA 99352, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Pacific Northwest National Laboratory, Richland, WA 99352</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author></analytic><series><title level="j">Journal of proteome research</title><idno type="ISSN">1535-3893</idno><idno type="eISSN">1535-3907</idno><imprint><date when="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p id="P1">Chemical cross-linking combined with mass spectrometry provides a powerful method for identifying protein-protein interactions and probing the structure of protein complexes. A number of strategies have been reported that take advantage of the high sensitivity and high resolution of modern mass spectrometers. Approaches typically include synthesis of novel cross-linking compounds, and/or isotopic labelling of the cross-linking reagent and/or protein, and label-free methods. We report Xlink-Identifier, a comprehensive data analysis platform that has been developed to support label-free analyses. It can identify inter-peptide, intra-peptide, and deadend cross-links as well as underivatized peptides. The software streamlines data pre-processing, peptide scoring, and visualization and provides an overall data analysis strategy for studying protein-protein interactions and protein structure using mass spectrometry. The software has been evaluated using a custom synthesized cross-linking reagent that features an enrichment tag. Xlink-Identifier offers the potential to perform large-scale identifications of protein-protein interactions using tandem mass spectrometry.</p></div></front></TEI><pmc article-type="research-article" xml:lang="EN"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<pmc-dir>properties manuscript</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-journal-id">101128775</journal-id><journal-id journal-id-type="pubmed-jr-id">30137</journal-id><journal-id journal-id-type="nlm-ta">J Proteome Res</journal-id><journal-title>Journal of proteome research</journal-title><issn pub-type="ppub">1535-3893</issn><issn pub-type="epub">1535-3907</issn></journal-meta><article-meta><article-id pub-id-type="pmid">21175198</article-id><article-id pub-id-type="pmc">3048902</article-id><article-id pub-id-type="doi">10.1021/pr100848a</article-id><article-id pub-id-type="manuscript">NIHMS261257</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Xlink-Identifier: An Automated Data Analysis Platform for Confident Identifications of Chemically Cross-linked Peptides using Tandem Mass Spectrometry</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Du</surname><given-names>Xiuxia</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref ref-type="corresp" rid="CR1">*</xref></contrib><contrib contrib-type="author"><name><surname>Chowdhury</surname><given-names>Saiful M.</given-names></name><xref ref-type="aff" rid="A4">4</xref></contrib><contrib contrib-type="author"><name><surname>Manes</surname><given-names>Nathan P.</given-names></name><xref ref-type="aff" rid="A3">3</xref></contrib><contrib contrib-type="author"><name><surname>Wu</surname><given-names>Si</given-names></name><xref ref-type="aff" rid="A2">2</xref></contrib><contrib contrib-type="author"><name><surname>Mayer</surname><given-names>M. Uljana</given-names></name><xref ref-type="aff" rid="A2">2</xref></contrib><contrib contrib-type="author"><name><surname>Adkins</surname><given-names>Joshua N.</given-names></name><xref ref-type="aff" rid="A2">2</xref></contrib><contrib contrib-type="author"><name><surname>Anderson</surname><given-names>Gordon A.</given-names></name><xref ref-type="aff" rid="A2">2</xref></contrib><contrib contrib-type="author"><name><surname>Smith</surname><given-names>Richard D.</given-names></name><xref ref-type="aff" rid="A2">2</xref><xref ref-type="corresp" rid="CR1">*</xref></contrib></contrib-group><aff id="A1"><label>1</label>Department of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, NC 28023, USA</aff><aff id="A2"><label>2</label>Pacific Northwest National Laboratory, Richland, WA 99352, USA</aff><aff id="A3"><label>3</label>National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA</aff><aff id="A4"><label>4</label>National Institute of Environmental Health Sciences – National Institutes of Health, Research Triangle Park, NC 27709, USA</aff><author-notes><corresp id="CR1"><label>*</label>To whom correspondence should be addressed. Xiuxia Du, 500 Laureate Way, Suite 2350, Kannapolis, NC 28081, Phone: (704) 250-5754, Fax: (704) 250-5759, <email>xiuxia.du@uncc.edu</email></corresp></author-notes><pub-date pub-type="nihms-submitted"><day>11</day><month>1</month><year>2011</year></pub-date><pub-date pub-type="epub"><day>16</day><month>2</month><year>2011</year></pub-date><pub-date pub-type="ppub"><day>4</day><month>3</month><year>2011</year></pub-date><pub-date pub-type="pmc-release"><day>4</day><month>3</month><year>2012</year></pub-date><volume>10</volume><issue>3</issue><fpage>923</fpage><lpage>931</lpage><abstract><p id="P1">Chemical cross-linking combined with mass spectrometry provides a powerful method for identifying protein-protein interactions and probing the structure of protein complexes. A number of strategies have been reported that take advantage of the high sensitivity and high resolution of modern mass spectrometers. Approaches typically include synthesis of novel cross-linking compounds, and/or isotopic labelling of the cross-linking reagent and/or protein, and label-free methods. We report Xlink-Identifier, a comprehensive data analysis platform that has been developed to support label-free analyses. It can identify inter-peptide, intra-peptide, and deadend cross-links as well as underivatized peptides. The software streamlines data pre-processing, peptide scoring, and visualization and provides an overall data analysis strategy for studying protein-protein interactions and protein structure using mass spectrometry. The software has been evaluated using a custom synthesized cross-linking reagent that features an enrichment tag. Xlink-Identifier offers the potential to perform large-scale identifications of protein-protein interactions using tandem mass spectrometry.</p></abstract><kwd-group><kwd>Chemical cross-linking</kwd><kwd>mass spectrometry</kwd><kwd>peptide identification</kwd><kwd>protein-protein interaction</kwd><kwd>protein structure</kwd></kwd-group><contract-num rid="RR1">P41 RR018522-09
||RR</contract-num><contract-sponsor id="RR1">National Center for Research Resources : NCRR</contract-sponsor></article-meta></front></pmc><affiliations><list><country><li>États-Unis</li></country><region><li>Caroline du Nord</li><li>Maryland</li><li>Washington (État)</li></region></list><tree><country name="États-Unis"><region name="Caroline du Nord"><name sortKey="Du, Xiuxia" sort="Du, Xiuxia" uniqKey="Du X" first="Xiuxia" last="Du">Xiuxia Du</name></region><name sortKey="Adkins, Joshua N" sort="Adkins, Joshua N" uniqKey="Adkins J" first="Joshua N." last="Adkins">Joshua N. Adkins</name><name sortKey="Anderson, Gordon A" sort="Anderson, Gordon A" uniqKey="Anderson G" first="Gordon A." last="Anderson">Gordon A. Anderson</name><name sortKey="Chowdhury, Saiful M" sort="Chowdhury, Saiful M" uniqKey="Chowdhury S" first="Saiful M." last="Chowdhury">Saiful M. Chowdhury</name><name sortKey="Manes, Nathan P" sort="Manes, Nathan P" uniqKey="Manes N" first="Nathan P." last="Manes">Nathan P. Manes</name><name sortKey="Mayer, M Uljana" sort="Mayer, M Uljana" uniqKey="Mayer M" first="M. Uljana" last="Mayer">M. Uljana Mayer</name><name sortKey="Smith, Richard D" sort="Smith, Richard D" uniqKey="Smith R" first="Richard D." last="Smith">Richard D. Smith</name><name sortKey="Wu, Si" sort="Wu, Si" uniqKey="Wu S" first="Si" last="Wu">Si Wu</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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