Assignment of protein interactions from affinity purification/mass spectrometry data

J Proteome Res. 2012 Mar 2;11(3):1462-74. doi: 10.1021/pr2011632. Epub 2012 Feb 10.

Abstract

The combination of affinity purification with mass spectrometry analysis has become the method of choice for protein complex characterization. With the improved performance of mass spectrometry technology, the sensitivity of the analyses is increasing, probing deeper into molecular interactions and yielding longer lists of proteins. These identify not only core complex subunits but also the more inaccessible proteins that interact weakly or transiently. Alongside them, contaminant proteins, which are often abundant proteins in the cell, tend to be recovered in affinity experiments because they bind nonspecifically and with low affinity to matrix, tag, and/or antibody. The challenge now lies in discriminating nonspecific binders from true interactors, particularly at the low level and in a larger scale. This review aims to summarize the variety of methods that have been used to distinguish contaminants from specific interactions in the past few years, ranging from manual elimination using heuristic rules to more sophisticated probabilistic scoring approaches. We aim to give awareness on the processing that takes place before an interaction list is reported and on the different types of list curation approaches suited to the different experiments.

Publication types

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

MeSH terms

  • Animals
  • Chromatography, Affinity / methods
  • Humans
  • Isotope Labeling
  • Mass Spectrometry / methods
  • Models, Statistical
  • Protein Binding
  • Protein Interaction Mapping / methods*
  • Proteome / chemistry
  • Proteome / isolation & purification
  • Proteome / metabolism*
  • Staining and Labeling / methods

Substances

  • Proteome