Identification of cross-linked peptides from large sequence databases

Nat Methods. 2008 Apr;5(4):315-8. doi: 10.1038/nmeth.1192. Epub 2008 Mar 9.


We describe a method to identify cross-linked peptides from complex samples and large protein sequence databases by combining isotopically tagged cross-linkers, chromatographic enrichment, targeted proteomics and a new search engine called xQuest. This software reduces the search space by an upstream candidate-peptide search before the recombination step. We showed that xQuest can identify cross-linked peptides from a total Escherichia coli lysate with an unrestricted database search.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods*
  • Cross-Linking Reagents / analysis*
  • Cross-Linking Reagents / chemistry
  • Databases, Protein*
  • Escherichia coli / metabolism
  • Mass Spectrometry
  • Models, Molecular
  • Peptides / analysis*
  • Peptides / chemistry
  • Protein Conformation
  • Sensitivity and Specificity


  • Cross-Linking Reagents
  • Peptides