Open AccessAnalyzing Protein‐Protein Interactions from Affinity Purification‐Mass Spectrometry Data with SAINT
Author(s) -
Choi Hyungwon,
Liu Guomin,
Mellacheruvu Dattatreya,
Tyers Mike,
Gingras AnneClaude,
Nesvizhskii Alexey I.
Publication year - 2012
Publication title -
current protocols in bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.535
H-Index - 57
eISSN - 1934-340X
pISSN - 1934-3396
DOI - 10.1002/0471250953.bi0815s39
Subject(s) - computer science , interactome , data mining , visualization , mass spectrometry , proteomics , software , chemistry , chromatography , operating system , biochemistry , gene
Abstract Significance Analysis of INTeractome (SAINT) is a software package for scoring protein‐protein 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 high‐confidence 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. Curr. Protoc. Bioinform . 39:8.15.1‐8.15.23. © 2012 by John Wiley & Sons, Inc.