Cross-linking and mass spectrometry as a tool for studying the structural biology of ribonucleoproteins

Structure. 2022 Apr 7;30(4):441-461. doi: 10.1016/j.str.2022.03.003. Epub 2022 Apr 1.


Cross-linking and mass spectrometry (XL-MS) workflows represent an increasingly popular technique for low-resolution structural studies of macromolecular complexes. Cross-linking reactions take place in the solution state, capturing contact sites between components of a complex that represent the native, functionally relevant structure. Protein-protein XL-MS protocols are widely adopted, providing precise localization of cross-linking sites to single amino acid positions within a pair of cross-linked peptides. In contrast, protein-RNA XL-MS workflows are evolving rapidly and differ in their ability to localize interaction regions within the RNA sequence. Here, we review protein-protein and protein-RNA XL-MS workflows, and discuss their applications in studies of protein-RNA complexes. The examples highlight the complementary value of XL-MS in structural studies of protein-RNA complexes, where more established high-resolution techniques might be unable to produce conclusive data.

Keywords: cross-linking; distance restraint; integrative structural biology; mass spectrometry; modeling; protein-RNA complexes; protein-RNA interactions; ribonucleoproteins.

Publication types

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

MeSH terms

  • Cross-Linking Reagents / chemistry
  • Mass Spectrometry / methods
  • Molecular Biology*
  • RNA
  • Ribonucleoproteins*


  • Cross-Linking Reagents
  • Ribonucleoproteins
  • RNA