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PMID: 21175198 Published · ppublish English Evaluation Study Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Xlink-identifier: an automated data analysis platform for confident identifications of chemically cross-linked peptides using tandem mass spectrometry.

Journal of proteome research ·Vol. 10 ·No. 3 ·2011-03-04 ·Pages 923-31

Du X, Chowdhury SM, Manes NP, Wu S, Mayer MU, Adkins JN, Anderson GA, Smith RD

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.

MeSH Terms
Amino Acid Sequence Cross-Linking Reagents/chemistry Molecular Sequence Data Molecular Structure Peptides/chemistry,genetics,metabolism Protein Binding Software Tandem Mass Spectrometry/instrumentation,methods Ubiquitin/chemistry,genetics,metabolism
Chemicals
Cross-Linking Reagents Peptides Ubiquitin
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Du Xiuxia
Department of Bioinformatics & Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina 28023, USA. xiuxia.du@uncc.edu
Chowdhury Saiful M
Manes Nathan P
Wu Si
Mayer M Uljana
Adkins Joshua N
Anderson Gordon A
Smith Richard D
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Article Info
Journal
Journal of proteome research
Abbr.
J Proteome Res
ISSN
1535-3907
DOI
10.1021/pr100848a
Email
xiuxia.du@uncc.edu
Published
2011-03-04
Epub
2011-00-16
Pages
923-31
Language
English
Region
United States
NLM ID
101128775
PMCID
PMC3048902
Subset
IM
Grants
NCRR NIH HHS · P41 RR018522 · United States
NCRR NIH HHS · P41 RR018522-09 · United States
NCRR NIH HHS · RR18522 · United States
External Links
PubMed source DOI: 10.1021/pr100848a PMC Full Text View journal details
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