title: Analyzing protein-protein interactions from affinity purification-mass spectrometry data with SAINT.
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.
authors.affiliation: Saw Swee Hock School of Public Health, National University of Singapore, Singapore.
authors.forename: Hyungwon
authors.initials: H
authors.lastname: Choi
authors.affiliation: Center for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto, Ontario, Canada.
authors.forename: Guomin
authors.initials: G
authors.lastname: Liu
authors.affiliation: Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan.
authors.forename: Dattatreya
authors.initials: D
authors.lastname: Mellacheruvu
authors.affiliation: Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada and Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom.
authors.forename: Mike
authors.initials: M
authors.lastname: Tyers
authors.affiliation: Center for Systems Biology, Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto, Ontario, Canada.|Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Anne-Claude
authors.initials: AC
authors.lastname: Gingras
authors.affiliation: Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan.|Department of Pathology, University of Michigan, Ann Arbor, Michigan.
authors.forename: Alexey I
authors.initials: AI
authors.lastname: Nesvizhskii
mesh_terms: D001665:Binding Sites; D002846:Chromatography, Affinity / Q000379:methods; D030562:Databases, Protein; D013058:Mass Spectrometry / Q000379:methods; D025941:Protein Interaction Mapping / Q000379:methods; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins