Links to Exploration step
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><nlm:aff id="A1">Department of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, NC 28023, USA</nlm:aff>
</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><nlm:aff id="A4">National Institute of Environmental Health Sciences – National Institutes of Health, Research Triangle Park, NC 27709, USA</nlm:aff>
</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><nlm:aff id="A3">National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Wu, Si" sort="Wu, Si" uniqKey="Wu S" first="Si" last="Wu">Si Wu</name>
<affiliation><nlm:aff id="A2">Pacific Northwest National Laboratory, Richland, WA 99352, USA</nlm:aff>
</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><nlm:aff id="A2">Pacific Northwest National Laboratory, Richland, WA 99352, USA</nlm:aff>
</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><nlm:aff id="A2">Pacific Northwest National Laboratory, Richland, WA 99352, USA</nlm:aff>
</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><nlm:aff id="A2">Pacific Northwest National Laboratory, Richland, WA 99352, USA</nlm:aff>
</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><nlm:aff id="A2">Pacific Northwest National Laboratory, Richland, WA 99352, USA</nlm:aff>
</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>
</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><nlm:aff id="A1">Department of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, NC 28023, USA</nlm:aff>
</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><nlm:aff id="A4">National Institute of Environmental Health Sciences – National Institutes of Health, Research Triangle Park, NC 27709, USA</nlm:aff>
</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><nlm:aff id="A3">National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA</nlm:aff>
</affiliation>
</author>
<author><name sortKey="Wu, Si" sort="Wu, Si" uniqKey="Wu S" first="Si" last="Wu">Si Wu</name>
<affiliation><nlm:aff id="A2">Pacific Northwest National Laboratory, Richland, WA 99352, USA</nlm:aff>
</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><nlm:aff id="A2">Pacific Northwest National Laboratory, Richland, WA 99352, USA</nlm:aff>
</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><nlm:aff id="A2">Pacific Northwest National Laboratory, Richland, WA 99352, USA</nlm:aff>
</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><nlm:aff id="A2">Pacific Northwest National Laboratory, Richland, WA 99352, USA</nlm:aff>
</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><nlm:aff id="A2">Pacific Northwest National Laboratory, Richland, WA 99352, USA</nlm:aff>
</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>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Ticri/CIDE/explor/CyberinfraV1/Data/Pmc/Corpus
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000286 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Pmc/Corpus/biblio.hfd -nk 000286 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Ticri/CIDE |area= CyberinfraV1 |flux= Pmc |étape= Corpus |type= RBID |clé= |texte= }}
This area was generated with Dilib version V0.6.25. |