SAINT: probabilistic scoring of affinity purification-mass spectrometry data

Nat Methods. 2011 Jan;8(1):70-3. doi: 10.1038/nmeth.1541. Epub 2010 Dec 5.


We present 'significance analysis of interactome' (SAINT), a computational tool that assigns confidence scores to protein-protein interaction data generated using affinity purification-mass spectrometry (AP-MS). The method uses label-free quantitative data and constructs separate distributions for true and false interactions to derive the probability of a bona fide protein-protein interaction. We show that SAINT is applicable to data of different scales and protein connectivity and allows transparent analysis of AP-MS data.

Publication types

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

MeSH terms

  • Chromatography, Affinity / methods*
  • Computational Biology*
  • Computer Simulation
  • Mass Spectrometry
  • Probability
  • Protein Binding
  • Protein Interaction Mapping / methods*
  • Proteins / isolation & purification
  • Proteins / metabolism*


  • Proteins