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

SAINT: probabilistic scoring of affinity purification-mass spectrometry data.

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  • 1Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA.


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.

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