Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions

Mass Spectrom Rev. Jul-Aug 2006;25(4):663-82. doi: 10.1002/mas.20082.


Closely related to studying the function of a protein is the analysis of its three-dimensional structure and the identification of interaction sites with its binding partners. An alternative approach to the high-resolution methods for three-dimensional protein structure analysis, such as X-ray crystallography and NMR spectroscopy, consists of covalently connecting two functional groups of the protein(s) under investigation. The location of the created cross-links imposes a distance constraint on the location of the respective side chains and allows one to draw conclusions on the three-dimensional structure of the protein or a protein complex. Recently, chemical cross-linking of proteins has been combined with a mass spectrometric analysis of the created cross-linked products. This review article describes the most popular cross-linking reagents for protein structure analysis and gives an overview of the different available strategies that employ chemical cross-linking and different mass spectrometric techniques. The challenges for mass spectrometry caused by the enormous complexity of the cross-linking reaction mixtures are emphasized. The various approaches described in the literature to facilitate the mass spectrometric detection of cross-linked products as well as computer software for data analyses are reviewed.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Cross-Linking Reagents / chemistry*
  • Humans
  • Mass Spectrometry*
  • Protein Conformation*
  • Protein Interaction Mapping / methods*
  • Proteins / chemistry*


  • Cross-Linking Reagents
  • Proteins