Beyond hairballs: The use of quantitative mass spectrometry data to understand protein-protein interactions

FEBS Lett. 2012 Aug 14;586(17):2723-31. doi: 10.1016/j.febslet.2012.03.065. Epub 2012 Apr 10.


The past 10 years have witnessed a dramatic proliferation in the availability of protein interaction data. However, for interaction mapping based on affinity purification coupled with mass spectrometry (AP-MS), there is a wealth of information present in the datasets that often goes unrecorded in public repositories, and as such remains largely unexplored. Further, how this type of data is represented and used by bioinformaticians has not been well established. Here, we point out some common mistakes in how AP-MS data are handled, and describe how protein complex organization and interaction dynamics can be inferred using quantitative AP-MS approaches.

Publication types

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

MeSH terms

  • Animals
  • Cell Line
  • Computational Biology / methods*
  • DNA, Complementary / metabolism
  • Databases, Protein
  • Humans
  • Mass Spectrometry / methods*
  • Models, Biological
  • Open Reading Frames
  • Peptides / chemistry
  • Protein Interaction Mapping / methods*
  • Proteins / chemistry
  • Proteomics / methods
  • Software


  • DNA, Complementary
  • Peptides
  • Proteins