Xlink-Identifier: An Automated Data Analysis Platform for Confident Identifications of Chemically Cross-linked Peptides using Tandem Mass Spectrometry
Identifieur interne : 000638 ( Main/Merge ); précédent : 000637; suivant : 000639Xlink-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
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PMC:3048902Le document en format XML
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<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>
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