Analyzing protein-protein interactions from affinity purification-mass spectrometry data with SAINT
Choi, H. Liu, G. Mellacheruvu, D. Tyers, M. Gingras, A.-C. Nesvizhskii, A.I.
Liu, G.
Mellacheruvu, D.
Tyers, M.
Gingras, A.-C.
Nesvizhskii, A.I.
Citations
Altmetric:
Alternative Title
Abstract
Significance Analysis of INTeractome (SAINT) is a software package for scoring proteinprotein interactions based on label-free quantitative proteomics data (e.g., spectral count or intensity) in affinity purification-mass spectrometry (AP-MS) experiments. SAINT allows bench scientists to select bona fide interactions and remove nonspecific interactions in an unbiased manner. However, there is no 'one-size-fits-all' statistical model for every dataset, since the experimental design varies across studies. Key variables include the number of baits, the number of biological replicates per bait, and control purifications. Here we give a detailed account of input data format, control data, selection of highconfidence interactions, and visualization of filtered data. We explain additional options for customizing the statistical model for optimal filtering in specific datasets. We also discuss a graphical user interface of SAINT in connection to the LIMS system ProHits, which can be installed as a virtual machine on Mac OS X or Windows computers. © 2012 John Wiley & Sons, Inc.
Keywords
Affinity purification-mass spectrometry (AP-MS), Label-free quantitative proteomics, Protein-protein interactions, statistical model
Source Title
Current Protocols in Bioinformatics
Publisher
Series/Report No.
Collections
Rights
Date
2012-09
DOI
10.1002/0471250953.bi0815s39
Type
Article