MassIVEapplication/xmlftp://massive-ftp.ucsd.edu/v01/MSV000078457/primaryOK2000000Proteomicshttps://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=3ae53e1cbead4ac687e54ea529099218MassIVE50Characterizing changes in protein-protein interactions associated with sequence variants (e.g., disease-associated mutations or splice forms) or following exposure to drugs, growth factors or hormones is critical to understanding how protein complexes are built, localized and regulated. Affinity purification (AP) coupled with mass spectrometry permits the analysis of protein interactions under near-physiological conditions, yet monitoring interaction changes requires the development of a robust and sensitive quantitative approach, especially for large-scale studies in which cost and time are major considerations. We have coupled AP to data-independent mass spectrometric acquisition (sequential window acquisition of all theoretical spectra, SWATH) and implemented an automated data extraction and statistical analysis pipeline to score modulated interactions. We used AP-SWATH to characterize changes in protein-protein interactions imparted by the HSP90 inhibitor NVP-AUY922 or melanoma-associated mutations in the human kinase CDK4. We show that AP-SWATH is a robust label-free approach to characterize such changes and propose a scalable pipeline for systems biology studies.Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition.Lambert Jean-Philippe JP, Ivosev Gordana G, Couzens Amber L AL, Larsen Brett B, Taipale Mikko M, Lin Zhen-Yuan ZY, Zhong Quan Q, Lindquist Susan S, Vidal Marc M, Aebersold Ruedi R, Pawson Tony T, Bonner Ron R, Tate Stephen S, Gingras Anne-Claude ACDmelCG5520, G protein coupled receptor phosphorylating protein kinase activity, GP93, G protein-coupled receptor kinase activity, Gprk6, GPCR kinase activity, P93, p93, GPCR phosphorylating protein kinase activity, gp93, G-protein-coupled receptor kinase activity, CG5520, G-protein coupled receptor kinase activity, GRK5, GPCRK., GRK4, GRK6, STK16, G-protein-coupled receptor phosphorylating protein kinase activity, ATP:G-protein-coupled receptor phosphotransferase activity, CT17486Mass Spectrum Analysis, isolation and purification, Spectroscopy, Mass Spectrum, MS, isolation, Analyses, Mass, Mass., Spectrometry, purification, Analysis, Spectrum Analyses, Mass Spectrum Analyses, Spectrum Analysis, Mass SpectroscopyForms, l(2)k06503, scale tissue, Product, determination, postnatal development, Mbp1, cdk4/6, growth and development, protein, sci, Measure, Cost-Minimization, Long Term, Mutations, protein polypeptide chains, Readability, diseases, melanoma, cdk, Pharmaceutical Product, HOW, How, diseases and disorders, Kinase, Analysis, protein aggregate, myd, Cost Comparison, Effect, l(3)j5D5, WMS, 24B, Mass Spectrum Analysis, human disease, Man (Taxonomy), Analyses, Biology, Hormone Receptor, plant peltate hair, Cost-Minimization Analyses, stru, Mbp-1, Comparison, proteins, purification, l(3)S053606, CG10293, free, endocrine, isolation and purification, allergic reaction, l(3)j5B5, Cost Analysis, medicine, Pharmaceutical, dCdk4, Homo sapiens disease, Comparisons, associated, Affordabilities, ATP Phosphotransferases, GPHYSD2, Long-Term Effects, ATP, SGS, 0904/17, Viramune, gyltl1b-b, Modern, Longterm Effect, Receptor Agonists, Malignant Melanomas, 11-cyclopropyl-5, Spectrum Analysis, ACMICD, Spectroscopy, Melanoma, SZ1, MDDGA6, mKIAA0609, Diseases, Pharmaceutic, KIAA0609, finances, fg, Transphosphorylases, gyltl1b, growth pattern, non-developmental growth, mdc1d, Spectrometry, expanded, salaries, Cdk4/6, MASS, human, disease, MDC1D, CDK4/6, enr, enlarged, label, 2-b:2', l(2)0671, anon-EST:Liang-2.39, financial management, humans, Cost Analyses, big, other disease, localised, human being, Systems., Effects, xcdk4, P62, peltate hair, 11-dihydro-4-methyl-6H-dipyrido(3, number, FBN, Gene, Cost Comparisons, Pk?7, Spectrum Analyses, protein-containing complex, Malignant, presence, froggy, Gyltl1a, Hormone, Human, melanoma (disease), large, polypeptide chain, Cost Minimization Analysis, Homo sapiens, isolation, sensitive, ECTOL1, Gene Products, Mass, disease or disorder, Agonists, sensitivity, Man, Phosphotransferase, Mass Spectroscopy, Drugs, hormones, l(3)s2612, localized, Longterm, Cost Measures, CG5072, MDDGB6, Affordability, Naevocarcinoma, Measures, 3'-e)(1, Hormone Receptor Agonists, LARGE, PSK-J3, financing, Long-Term, Transphosphorylase, non-neoplastic, OCTD, BPFD#36, funding, cdk4, drugs, great, DmelCG10293, CMM3, disorder, Long-Term Effect, CDK4, Preparation, 4)diazepin-6-one, l(2)05428, statistical analysis, NEV, Pharmaceuticals, Products, fees, NVP, protein complex, clone 2.39, malignant, Proteins, disorders, nevirapine, medical condition, Medications, qkr, l(3)S090417, Phosphotransferases, l(2)s4639, development, count in organism, Melanomas, MS, native protein, natural protein, KH93F, Malignant Melanoma, Protein, chemical analysis, Long Term Effects, sequence, condition, MFS1, scales, DmCdk4, Mass Spectrum Analyses, WMS2, who, Costs and Cost Analyses, Mass Spectrum, Costs, scale, Pharmaceutic Preparations, Kinases, Cost, postnatal growth, Cost-Minimization Analysis, Who/How, Pricing, Crk3, Understanding, DmelCG5072, primary structure of sequence macromolecule, Longterm Effects, Protein Gene Products, Drug, 8-6, Gene Proteins, cost, Preparations, Modern Man, SSKS, qkr[93F], Pk53C, malignant melanoma, assay, Cost Measure, Pharmaceutical Products, growth, l(2)sh0671, Pharmaceutical Preparation0trueLambert_AP_SWATH_P93_VS4_GRK6Thu Jul 04 00:00:00 BST 2013MSV00007845724162924