Next-generation Interactomics: Considerations for the Use of Co-elution to Measure Protein Interaction Networks

Mol Cell Proteomics. 2020 Jan;19(1):1-10. doi: 10.1074/mcp.R119.001803. Epub 2019 Dec 2.

Abstract

Understanding how proteins interact is crucial to understanding cellular processes. Among the available interactome mapping methods, co-elution stands out as a method that is simultaneous in nature and capable of identifying interactions between all the proteins detected in a sample. The general workflow in co-elution methods involves the mild extraction of protein complexes and their separation into several fractions, across which proteins bound together in the same complex will show similar co-elution profiles when analyzed appropriately. In this review we discuss the different separation, quantification and bioinformatic strategies used in co-elution studies, and the important considerations in designing these studies. The benefits of co-elution versus other methods makes it a valuable starting point when asking questions that involve the perturbation of the interactome.

Keywords: Protein-protein interactions; SILAC; bioinformatics; chromatography; co-elution; co-fractionation; complexes; interactome; mass spectrometry; protein complex analysis; protein correlation profiling; separation technologies.

Publication types

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

MeSH terms

  • Cells / metabolism
  • Chromatography, Gel / methods*
  • Chromatography, Ion Exchange / methods*
  • Computational Biology / methods
  • Electrophoresis, Polyacrylamide Gel / methods
  • Humans
  • Protein Interaction Mapping / methods*
  • Protein Interaction Maps*
  • Proteins / chemistry
  • Proteins / metabolism
  • Proteomics / methods
  • Tandem Mass Spectrometry / methods*

Substances

  • Proteins