Cross-linking applications in structural proteomics

Evgeniy V. Petrotchenko, Jason J. Serpa, Christoph H. Borchers

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review


The overall design of a mass spectrometry (MS) cross-linking experiment needs to take into account the complexity of the protein system studied, the desired level of structural information that needs to be obtained, the mutual compatibility of each successive step, and the feasibility of the MS and data analysis of the processed sample. The initial step in a cross-linking experiment involves performing a cross-linking reaction on the protein(s) of interest, and several factors need to be taken into consideration. The goal of MS analysis of the cross-links is a confident identification of the cross- linked peptides and it therefore relies on accurate determination of which pairs of sites are cross-linked. Applications of cross-linking for the structural analyses of proteins can vary depending on the level of the protein system studied and structural questions asked. Single proteins, protein complexes, and whole protein-protein interaction networks can be the subject of cross-linking analyses.

Original languageEnglish
Title of host publicationProteomics for Biological Discovery
Number of pages22
ISBN (Electronic)9781119081661
ISBN (Print)9781118279243
Publication statusPublished - 1 Jan 2019
Externally publishedYes


  • Confident identification
  • Cross-linked peptides
  • Cross-linking applications
  • Mass spectrometry cross-linking experiment
  • Protei-protein interaction networks
  • Protein system
  • Structural information
  • Structural proteomics


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