Identification of cross-linked peptides from complex samples

Nat Methods. 2012 Sep;9(9):904-6. doi: 10.1038/nmeth.2099. Epub 2012 Jul 8.


We have developed pLink, software for data analysis of cross-linked proteins coupled with mass-spectrometry analysis. pLink reliably estimates false discovery rate in cross-link identification and is compatible with multiple homo- or hetero-bifunctional cross-linkers. We validated the program with proteins of known structures, and we further tested it on protein complexes, crude immunoprecipitates and whole-cell lysates. We show that it is a robust tool for protein-structure and protein-protein-interaction studies.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Animals
  • Caenorhabditis elegans / chemistry
  • Chromatography, High Pressure Liquid
  • Cross-Linking Reagents / chemistry*
  • Data Interpretation, Statistical
  • Databases, Protein
  • Escherichia coli / chemistry
  • False Positive Reactions
  • Humans
  • Mass Spectrometry
  • Models, Molecular
  • Peptides / analysis*
  • Peptides / chemistry*
  • Protein Binding
  • Protein Conformation
  • Proteomics / methods*
  • Reproducibility of Results
  • Software


  • Cross-Linking Reagents
  • Peptides