Detecting protein-protein interactions/complex components using mass spectrometry coupled techniques

Methods Mol Biol. 2014;1164:1-13. doi: 10.1007/978-1-4939-0805-9_1.


Proteins play important roles in biochemical processes. Most biological functions are realized through protein-protein interactions (PPI). Co-immunoprecipitation is the most straightforward method to detect PPI. With the development of modern mass spectrometry (MS), throughput, sensitivity, and confidence for the detection of PPI can be readily achieved by scaling up traditional antibody-based strategies. Herein, we describe a typical workflow for general PPI detection using mass spectrometry coupled techniques, covering from Co-immunoprecipitation (Co-IP), to gel display, in-gel digestion, liquid chromatography mass spectrometry (LC-MS) analysis, as well as result interpretation and statistic filtering. This protocol provides an overview of the technique as well as practical tips.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chromatography, Liquid / methods
  • Electrophoresis, Polyacrylamide Gel / methods
  • Humans
  • Immunoprecipitation / methods
  • Mass Spectrometry / methods*
  • Protein Interaction Mapping / methods*
  • Protein Interaction Maps
  • Proteins / analysis
  • Proteins / metabolism*
  • Proteomics / methods
  • Software


  • Proteins