Xlink-Identifier: An Automated Data Analysis Platform for Confident Identifications of Chemically Cross-Linked Peptides Using Tandem Mass Spectrometry
journal contributionposted on 04.03.2011 by Xiuxia Du, Saiful M. Chowdhury, Nathan P. Manes, Si Wu, M. Uljana Mayer, Joshua N. Adkins, Gordon A. Anderson, Richard D. Smith
Any type of content formally published in an academic journal, usually following a peer-review process.
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 labeling 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 interpeptide, intrapeptide, and deadend cross-links as well as underivatized peptides. The software streamlines data preprocessing, 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.