False discovery rate estimation for cross-linked peptides identified by mass spectrometry

Thomas Walzthoeni, Manfred Claassen, Alexander Leitner, Franz Herzog, Stefan Bohn, Friedrich Förster, Martin Beck, Ruedi Aebersold

Research output: Contribution to journalArticleAcademicpeer-review


The mass spectrometric identification of chemically cross-linked peptides (CXMS) specifies spatial restraints of protein complexes; these values complement data obtained from common structure-determination techniques. Generic methods for determining false discovery rates of cross-linked peptide assignments are currently lacking, thus making data sets from CXMS studies inherently incomparable. Here we describe an automated target-decoy strategy and the software tool xProphet, which solve this problem for large multicomponent protein complexes.

Original languageEnglish
Pages (from-to)901-3
Number of pages3
JournalNature Methods
Issue number9
Publication statusPublished - Sept 2012
Externally publishedYes


  • Algorithms
  • Automation
  • Cross-Linking Reagents
  • Data Interpretation, Statistical
  • Databases, Protein
  • False Positive Reactions
  • Mass Spectrometry
  • Models, Molecular
  • Peptides
  • Protein Conformation
  • Proteomics
  • Software


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