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Over the years, multiple techniques have been developed to characterize PPIs to elucidate roles and regulatory mechanisms of proteins. Among them, the mass spectrometry (MS)-based interactome analysis has been increasing in popularity due to its unbiased and informative manner towards understanding PPI networks. However, with MS instrumentation advancing and yielding more data than ever, the analysis of a large amount of PPI-associated proteomic data to reveal bona fide interacting proteins become challenging. Here, we review the methods and bioinformatic resources that are commonly used in analyzing large interactome-related proteomic data and propose a simple guideline for identifying novel interacting proteins for biological research.<\/jats:p>","DOI":"10.1093\/bib\/bbad010","type":"journal-article","created":{"date-parts":[[2023,1,22]],"date-time":"2023-01-22T14:10:02Z","timestamp":1674396602000},"source":"Crossref","is-referenced-by-count":9,"title":["Analysis of affinity purification-related proteomic data for studying protein\u2013protein interaction networks in cells"],"prefix":"10.1093","volume":"24","author":[{"given":"Rebecca Elizabeth","family":"Kattan","sequence":"first","affiliation":[{"name":"Department of Developmental and Cell Biology, University of California , Irvine, Irvine, CA 92697 , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deena","family":"Ayesh","sequence":"additional","affiliation":[{"name":"Department of Developmental and Cell Biology, 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