Xlink-Identifier: An Automated Data Analysis Platform for Confident Identifications of Chemically Cross-linked Peptides using Tandem Mass Spectrometry
Identifieur interne : 000636 ( Main/Exploration ); précédent : 000635; suivant : 000637Xlink-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:
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000286
- to stream Pmc, to step Curation: 000286
- to stream Pmc, to step Checkpoint: 000457
- to stream Ncbi, to step Merge: 000185
- to stream Ncbi, to step Curation: 000185
- to stream Ncbi, to step Checkpoint: 000185
- to stream Main, to step Merge: 000638
- to stream Main, to step Curation: 000636
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Xlink-Identifier: An Automated Data Analysis Platform for Confident Identifications of Chemically Cross-linked Peptides using Tandem Mass Spectrometry</title><author><name sortKey="Du, Xiuxia" sort="Du, Xiuxia" uniqKey="Du X" first="Xiuxia" last="Du">Xiuxia Du</name><affiliation wicri:level="2"><nlm:aff id="A1">Department of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, NC 28023, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, NC 28023</wicri:regionArea><placeName><region type="state">Caroline du Nord</region></placeName></affiliation></author><author><name sortKey="Chowdhury, Saiful M" sort="Chowdhury, Saiful M" uniqKey="Chowdhury S" first="Saiful M." last="Chowdhury">Saiful M. Chowdhury</name><affiliation wicri:level="2"><nlm:aff id="A4">National Institute of Environmental Health Sciences – National Institutes of Health, Research Triangle Park, NC 27709, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>National Institute of Environmental Health Sciences – National Institutes of Health, Research Triangle Park, NC 27709</wicri:regionArea><placeName><region type="state">Caroline du Nord</region></placeName></affiliation></author><author><name sortKey="Manes, Nathan P" sort="Manes, Nathan P" uniqKey="Manes N" first="Nathan P." last="Manes">Nathan P. Manes</name><affiliation wicri:level="2"><nlm:aff id="A3">National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Wu, Si" sort="Wu, Si" uniqKey="Wu S" first="Si" last="Wu">Si Wu</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><author><name sortKey="Mayer, M Uljana" sort="Mayer, M Uljana" uniqKey="Mayer M" first="M. Uljana" last="Mayer">M. Uljana Mayer</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><author><name sortKey="Adkins, Joshua N" sort="Adkins, Joshua N" uniqKey="Adkins J" first="Joshua N." last="Adkins">Joshua N. Adkins</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><author><name sortKey="Anderson, Gordon A" sort="Anderson, Gordon A" uniqKey="Anderson G" first="Gordon A." last="Anderson">Gordon A. Anderson</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><author><name sortKey="Smith, Richard D" sort="Smith, Richard D" uniqKey="Smith R" first="Richard D." last="Smith">Richard D. 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></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">21175198</idno><idno type="pmc">3048902</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048902</idno><idno type="RBID">PMC:3048902</idno><idno type="doi">10.1021/pr100848a</idno><date when="2011">2011</date><idno type="wicri:Area/Pmc/Corpus">000286</idno><idno type="wicri:Area/Pmc/Curation">000286</idno><idno type="wicri:Area/Pmc/Checkpoint">000457</idno><idno type="wicri:Area/Ncbi/Merge">000185</idno><idno type="wicri:Area/Ncbi/Curation">000185</idno><idno type="wicri:Area/Ncbi/Checkpoint">000185</idno><idno type="wicri:doubleKey">1535-3893:2011:Du X:xlink:identifier:an</idno><idno type="wicri:Area/Main/Merge">000638</idno><idno type="wicri:Area/Main/Curation">000636</idno><idno type="wicri:Area/Main/Exploration">000636</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Xlink-Identifier: An Automated Data Analysis Platform for Confident Identifications of Chemically Cross-linked Peptides using Tandem Mass Spectrometry</title><author><name sortKey="Du, Xiuxia" sort="Du, Xiuxia" uniqKey="Du X" first="Xiuxia" last="Du">Xiuxia Du</name><affiliation wicri:level="2"><nlm:aff id="A1">Department of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, NC 28023, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, NC 28023</wicri:regionArea><placeName><region type="state">Caroline du Nord</region></placeName></affiliation></author><author><name sortKey="Chowdhury, Saiful M" sort="Chowdhury, Saiful M" uniqKey="Chowdhury S" first="Saiful M." last="Chowdhury">Saiful M. Chowdhury</name><affiliation wicri:level="2"><nlm:aff id="A4">National Institute of Environmental Health Sciences – National Institutes of Health, Research Triangle Park, NC 27709, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>National Institute of Environmental Health Sciences – National Institutes of Health, Research Triangle Park, NC 27709</wicri:regionArea><placeName><region type="state">Caroline du Nord</region></placeName></affiliation></author><author><name sortKey="Manes, Nathan P" sort="Manes, Nathan P" uniqKey="Manes N" first="Nathan P." last="Manes">Nathan P. Manes</name><affiliation wicri:level="2"><nlm:aff id="A3">National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Wu, Si" sort="Wu, Si" uniqKey="Wu S" first="Si" last="Wu">Si Wu</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><author><name sortKey="Mayer, M Uljana" sort="Mayer, M Uljana" uniqKey="Mayer M" first="M. Uljana" last="Mayer">M. Uljana Mayer</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><author><name sortKey="Adkins, Joshua N" sort="Adkins, Joshua N" uniqKey="Adkins J" first="Joshua N." last="Adkins">Joshua N. Adkins</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><author><name sortKey="Anderson, Gordon A" sort="Anderson, Gordon A" uniqKey="Anderson G" first="Gordon A." last="Anderson">Gordon A. Anderson</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><author><name sortKey="Smith, Richard D" sort="Smith, Richard D" uniqKey="Smith R" first="Richard D." last="Smith">Richard D. 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><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)
EXPLOR_STEP=$WICRI_ROOT/Ticri/CIDE/explor/CyberinfraV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000636 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000636 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Ticri/CIDE
|area= CyberinfraV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= PMC:3048902
|texte= Xlink-Identifier: An Automated Data Analysis Platform for Confident Identifications of Chemically Cross-linked Peptides using Tandem Mass Spectrometry
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:21175198" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a CyberinfraV1
| This area was generated with Dilib version V0.6.25. |  |