title: Xlink-identifier: an automated data analysis platform for confident identifications of chemically cross-linked peptides using tandem mass spectrometry.
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 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.
authors.affiliation: Department of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina 28023, USA. xiuxia.du@uncc.edu
authors.forename: Xiuxia
authors.initials: X
authors.lastname: Du
authors.forename: Saiful M
authors.initials: SM
authors.lastname: Chowdhury
authors.forename: Nathan P
authors.initials: NP
authors.lastname: Manes
authors.forename: Si
authors.initials: S
authors.lastname: Wu
authors.forename: M Uljana
authors.initials: MU
authors.lastname: Mayer
authors.forename: Joshua N
authors.initials: JN
authors.lastname: Adkins
authors.forename: Gordon A
authors.initials: GA
authors.lastname: Anderson
authors.forename: Richard D
authors.initials: RD
authors.lastname: Smith
mesh_terms: D000595:Amino Acid Sequence; D003432:Cross-Linking Reagents / Q000737:chemistry*; D008969:Molecular Sequence Data; D015394:Molecular Structure; D010455:Peptides / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D012984:Software; D053719:Tandem Mass Spectrometry / Q000295:instrumentation / Q000379:methods*; D025801:Ubiquitin / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
chemical_list: D003432:Cross-Linking Reagents; D010455:Peptides; D025801:Ubiquitin