Label-free visual proteomics: Coupling MS- and EM-based approaches in structural biology

Mol Cell. 2022 Jan 20;82(2):285-303. doi: 10.1016/j.molcel.2021.12.027.


Combining diverse experimental structural and interactomic methods allows for the construction of comprehensible molecular encyclopedias of biological systems. Typically, this involves merging several independent approaches that provide complementary structural and functional information from multiple perspectives and at different resolution ranges. A particularly potent combination lies in coupling structural information from cryoelectron microscopy or tomography (cryo-EM or cryo-ET) with interactomic and structural information from mass spectrometry (MS)-based structural proteomics. Cryo-EM/ET allows for sub-nanometer visualization of biological specimens in purified and near-native states, while MS provides bioanalytical information for proteins and protein complexes without introducing additional labels. Here we highlight recent achievements in protein structure and interactome determination using cryo-EM/ET that benefit from additional MS analysis. We also give our perspective on how combining cryo-EM/ET and MS will continue bridging gaps between molecular and cellular studies by capturing and describing 3D snapshots of proteomes and interactomes.

Keywords: crosslinking MS; cryo-EM; cryo-ET; integrative structural biology; label-free visual proteomics; protein-protein interactions; structural proteomics.

Publication types

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

MeSH terms

  • Animals
  • Cryoelectron Microscopy*
  • Electron Microscope Tomography*
  • Humans
  • Mass Spectrometry*
  • Models, Molecular
  • Protein Interaction Maps
  • Proteome*
  • Proteomics*
  • Signal Transduction


  • Proteome