{"doi":"10.1016/j.xpro.2024.103286","title":"Protocol for mapping differential protein-protein interaction networks using affinity purification-mass spectrometry","abstract":"Proteins congregate into complexes to perform diverse cellular functions. Protein complexes are remodeled by protein-coding mutations or cellular signaling changes, driving phenotypic outcomes in health and disease. We present an affinity purification-mass spectrometry (AP-MS) proteomics protocol to express affinity-tagged “bait” proteins in mammalian cells, identify and quantify purified protein interactors, and visualize differential protein-protein interaction networks between pairwise conditions. Our protocol possesses general applicability to various cell types and biological areas. For complete details on the use and execution of this protocol, please refer to Bouhaddou et al. 1 • Steps for construct design, transfection, APMS, and data quality control • Approach for protein-protein interaction (PPI) scoring to remove background • Cross-run normalization and statistical comparison between pairwise conditions • Visualization of quantitative changes in PPI networks Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. Proteins congregate into complexes to perform diverse cellular functions. Protein complexes are remodeled by protein-coding mutations or cellular signaling changes, driving phenotypic outcomes in health and disease. We present an affinity purification-mass spectrometry (APMS) proteomics protocol to express affinity-tagged “bait” proteins in mammalian cells, identify and quantify purified protein interactors, and visualize differential protein-protein interaction networks between pairwise conditions. Our protocol possesses general applicability to various cell types and biological areas.","journal":"STAR Protocols","year":2024,"id":472320,"datarank":0.18965405563564564,"base_score":1.0986122886681096,"endowment":1.0986122886681096,"self_citation_contribution":0.16479184330021646,"citation_network_contribution":0.024862212335429172,"self_endowment_contribution":0.16479184330021646,"citer_contribution":0.024862212335429172,"corpus_percentile":null,"corpus_rank":null,"citation_count":2,"citer_count":2,"citers_with_citation_signal":2,"citers_with_endowment":2,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.956,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1494,"name":"Manisha R. Ummadi","orcid":"0000-0001-9575-9025","position":1,"is_corresponding":false},{"id":1341,"name":"Gwendolyn M. Jang","orcid":"0000-0001-7806-9874","position":2,"is_corresponding":false},{"id":1119229,"name":"Yennifer Delgado","orcid":"0000-0002-7582-8545","position":3,"is_corresponding":false},{"id":713751,"name":"Sara K. Makanani","orcid":null,"position":4,"is_corresponding":false},{"id":1307781,"name":"Kareem Alba","orcid":null,"position":5,"is_corresponding":false},{"id":1307782,"name":"Doug Winters","orcid":null,"position":6,"is_corresponding":false},{"id":627584,"name":"Sophie F. Blanc","orcid":"0000-0002-9550-1590","position":7,"is_corresponding":false},{"id":2362,"name":"Jiewei Xu","orcid":"0000-0002-8647-4172","position":8,"is_corresponding":false},{"id":1458,"name":"Benjamin J. Polacco","orcid":"0000-0003-1570-9234","position":9,"is_corresponding":false},{"id":2365,"name":"Yuan Zhou","orcid":"0000-0001-6378-1711","position":10,"is_corresponding":false},{"id":2366,"name":"Erica Stevenson","orcid":"0000-0001-7853-1854","position":11,"is_corresponding":false},{"id":1359,"name":"Manon Eckhardt","orcid":"0000-0001-8143-6129","position":12,"is_corresponding":false},{"id":1457,"name":"Lorena Zuliani-Alvarez","orcid":null,"position":13,"is_corresponding":false},{"id":103631,"name":"Robyn M. Kaake","orcid":"0000-0002-8341-3067","position":14,"is_corresponding":false},{"id":1356,"name":"Danielle L. Swaney","orcid":"0000-0001-6119-6084","position":15,"is_corresponding":false},{"id":1363,"name":"Nevan J. Krogan","orcid":"0000-0003-4902-337X","position":16,"is_corresponding":false},{"id":1455,"name":"Mehdi Bouhaddou","orcid":"0000-0002-9526-1427","position":17,"is_corresponding":false},{"id":1202022,"name":"Prashant Kaushal","orcid":null,"position":0,"is_corresponding":true}],"reference_count":22,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T02:05:53.032464Z","pmid":"39488835","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}