{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T10:09:54Z","timestamp":1784196594903,"version":"3.55.0"},"reference-count":304,"publisher":"Portland Press Ltd.","issue":"8","license":[{"start":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T00:00:00Z","timestamp":1784160000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","award":["RN493731-487577"],"award-info":[{"award-number":["RN493731-487577"]}],"id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009326","name":"Cancer Research Society","doi-asserted-by":"publisher","award":["1281853"],"award-info":[{"award-number":["1281853"]}],"id":[{"id":"10.13039\/100009326","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["portlandpress.com"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2026,8,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Cellular processes are controlled by interconnected networks of protein\u2013protein interactions that can be dynamically regulated by post-translational modifications such as phosphorylation. Dysregulation of signaling pathways can drive cellular transformation and contribute to cancer treatment resistance. Mass spectrometry (MS)-based approaches have emerged as key technologies to study both protein function and their dynamic regulation at a network level. Modern proteomics allows investigators to study how signaling networks are rewired in response to genetic lesions, external cues, and targeted therapies, enabling the comparison of baseline (steady-state) networks to perturbed states. Here, we briefly describe key advancements in proteomics to study signaling dynamics, including affinity-purification combined with MS, proximity proteomics (e.g., BioID, APEX), and phosphoproteomics. We highlight how proteomics has led to the identification of comprehensive protein\u2013protein interaction networks, to the delineation of protein subcellular localization maps and to discoveries regarding their dynamics and rewiring in disease. Finally, we comment on the future directions of proteomics to study signaling dynamics, enabled by next-generation MS instruments and AI-driven data analysis, and discuss how these developments are paving the way for clinical translation by bringing quantitative network biology into patient-relevant contexts.<\/jats:p>","DOI":"10.1042\/bsr20250116","type":"journal-article","created":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T09:45:47Z","timestamp":1784195147000},"update-policy":"https:\/\/doi.org\/10.1042\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Proteomic investigation of signaling dynamics: from static maps to network rewiring"],"prefix":"10.1042","volume":"46","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9797-7923","authenticated-orcid":false,"given":"Ugo","family":"Dionne","sequence":"first","affiliation":[{"name":"1Lunenfeld-Tanenbaum Research Institute, Sinai Health, Mount Sinai Hospital, Toronto, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-6709-0859","authenticated-orcid":false,"given":"Kosar","family":"Vafaee","sequence":"additional","affiliation":[{"name":"1Lunenfeld-Tanenbaum Research Institute, Sinai Health, Mount Sinai Hospital, Toronto, Ontario, Canada"},{"name":"2Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5570-7615","authenticated-orcid":false,"given":"Geoffrey\u00a0G.","family":"Hesketh","sequence":"additional","affiliation":[{"name":"1Lunenfeld-Tanenbaum Research Institute, Sinai Health, Mount Sinai Hospital, Toronto, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6090-4437","authenticated-orcid":false,"given":"Anne-Claude","family":"Gingras","sequence":"additional","affiliation":[{"name":"1Lunenfeld-Tanenbaum Research Institute, Sinai Health, Mount Sinai Hospital, Toronto, Ontario, Canada"},{"name":"2Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"288","published-online":{"date-parts":[[2026,7,16]]},"reference":[{"key":"2026071605453995200_B1","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1038\/nchembio.2576","article-title":"How many human proteoforms are there?","volume":"14","author":"Aebersold","year":"2018","journal-title":"Nat. Chem. Biol."},{"key":"2026071605453995200_B2","doi-asserted-by":"publisher","first-page":"6501","DOI":"10.1016\/j.cell.2024.10.038","article-title":"Discovery and significance of protein\u2013protein interactions in health and disease","volume":"187","author":"Greenblatt","year":"2024","journal-title":"Cell"},{"key":"2026071605453995200_B3","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1038\/nrm3970","article-title":"Multidimensional proteomics for cell biology","volume":"16","author":"Larance","year":"2015","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"2026071605453995200_B4","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1038\/s41580-018-0094-y","article-title":"Spatial proteomics: a powerful discovery tool for cell biology","volume":"20","author":"Lundberg","year":"2019","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"2026071605453995200_B5","doi-asserted-by":"publisher","first-page":"188","DOI":"10.1038\/nchembio.2572","article-title":"The ABCs of PTMs","volume":"14","author":"Barber","year":"2018","journal-title":"Nat. Chem. Biol."},{"key":"2026071605453995200_B6","doi-asserted-by":"publisher","first-page":"1868","DOI":"10.1016\/j.molcel.2021.03.015","article-title":"Discovering the landscape of protein modifications","volume":"81","author":"Keenan","year":"2021","journal-title":"Mol. Cell."},{"key":"2026071605453995200_B7","doi-asserted-by":"publisher","first-page":"1117","DOI":"10.1016\/j.cell.2010.06.011","article-title":"Cell signaling by receptor tyrosine kinases","volume":"141","author":"Lemmon","year":"2010","journal-title":"Cell"},{"key":"2026071605453995200_B8","doi-asserted-by":"publisher","first-page":"1220","DOI":"10.1126\/science.1175668","article-title":"Cell signaling in space and time: where proteins come together and when they\u2019re apart","volume":"326","author":"Scott","year":"2009","journal-title":"Science"},{"key":"2026071605453995200_B9","doi-asserted-by":"publisher","first-page":"666","DOI":"10.1038\/nsmb.1842","article-title":"Post-translational modifications in signal integration","volume":"17","author":"Deribe","year":"2010","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2026071605453995200_B10","doi-asserted-by":"publisher","first-page":"945","DOI":"10.1016\/j.cell.2013.02.005","article-title":"Encoding and decoding cellular information through signaling dynamics","volume":"152","author":"Purvis","year":"2013","journal-title":"Cell"},{"key":"2026071605453995200_B11","doi-asserted-by":"publisher","first-page":"986","DOI":"10.1016\/j.tibs.2024.08.004","article-title":"The expanding landscape of canonical and non-canonical protein phosphorylation","volume":"49","author":"Houles","year":"2024","journal-title":"Trends Biochem. Sci."},{"key":"2026071605453995200_B12","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1016\/j.molcel.2019.09.016","article-title":"The control centers of biomolecular phase separation: how membrane surfaces, PTMs, and active processes regulate condensation","volume":"76","author":"Snead","year":"2019","journal-title":"Mol. Cell."},{"key":"2026071605453995200_B13","doi-asserted-by":"publisher","first-page":"4137","DOI":"10.1016\/j.molcel.2021.09.010","article-title":"Liquid\u2013liquid phase separation: orchestrating cell signaling through time and space","volume":"81","author":"Su","year":"2021","journal-title":"Mol. Cell."},{"key":"2026071605453995200_B14","doi-asserted-by":"publisher","first-page":"845","DOI":"10.1016\/j.tips.2021.07.003","article-title":"Liquid\u2013liquid phase separation: a principal organizer of the cell\u2019s biochemical activity architecture","volume":"42","author":"Zhang","year":"2021","journal-title":"Trends Pharmacol. Sci."},{"key":"2026071605453995200_B15","doi-asserted-by":"publisher","first-page":"1093","DOI":"10.1126\/science.aau6313","article-title":"Stoichiometry controls activity of phase-separated clusters of actin signaling proteins","volume":"363","author":"Case","year":"2019","journal-title":"Science"},{"key":"2026071605453995200_B16","doi-asserted-by":"publisher","first-page":"1098","DOI":"10.1126\/science.aau5721","article-title":"A molecular assembly phase transition and kinetic proofreading modulate Ras activation by SOS","volume":"363","author":"Huang","year":"2019","journal-title":"Science"},{"key":"2026071605453995200_B17","doi-asserted-by":"publisher","first-page":"710","DOI":"10.1038\/s41589-023-01516-x","article-title":"LATS2 condensates organize signalosomes for Hippo pathway signal transduction","volume":"20","author":"Qin","year":"2024","journal-title":"Nat. Chem. Biol."},{"key":"2026071605453995200_B18","doi-asserted-by":"publisher","first-page":"1226","DOI":"10.1038\/s41589-024-01826-8","article-title":"Plasma membrane-associated ARAF condensates fuel RAS-related cancer drug resistance","volume":"21","author":"Li","year":"2025","journal-title":"Nat. Chem. Biol."},{"key":"2026071605453995200_B19","doi-asserted-by":"publisher","first-page":"1570.e7","DOI":"10.1016\/j.molcel.2024.03.002","article-title":"Molecular determinants and signaling effects of PKA RI\u03b1 phase separation","volume":"84","author":"Hardy","year":"2024","journal-title":"Mol. Cell."},{"key":"2026071605453995200_B20","doi-asserted-by":"publisher","first-page":"490.e18","DOI":"10.1016\/j.cell.2020.09.002","article-title":"Phase separation of disease-associated SHP2 mutants underlies MAPK hyperactivation","volume":"183","author":"Zhu","year":"2020","journal-title":"Cell"},{"key":"2026071605453995200_B21","doi-asserted-by":"publisher","first-page":"eaau8645","DOI":"10.1126\/scisignal.aau8645","article-title":"Illuminating the dark phosphoproteome","volume":"12","author":"Needham","year":"2019","journal-title":"Sci. Signal."},{"key":"2026071605453995200_B22","doi-asserted-by":"publisher","first-page":"2649.e18","DOI":"10.1016\/j.cell.2021.03.031","article-title":"Kinase-mediated RAS signaling via membraneless cytoplasmic protein granules","volume":"184","author":"Tulpule","year":"2021","journal-title":"Cell"},{"key":"2026071605453995200_B23","doi-asserted-by":"publisher","first-page":"e53693","DOI":"10.15252\/embr.202153693","article-title":"Phase-separated foci of EML4-ALK facilitate signalling and depend upon an active kinase conformation","volume":"22","author":"Sampson","year":"2021","journal-title":"EMBO Rep."},{"key":"2026071605453995200_B24","doi-asserted-by":"publisher","first-page":"986","DOI":"10.1016\/j.cell.2011.02.016","article-title":"Interactome networks and human disease","volume":"144","author":"Vidal","year":"2011","journal-title":"Cell"},{"key":"2026071605453995200_B25","doi-asserted-by":"publisher","first-page":"e8792","DOI":"10.15252\/msb.20188792","article-title":"Mass spectrometry-based protein\u2013protein interaction networks for the study of human diseases","volume":"17","author":"Richards","year":"2021","journal-title":"Mol. Syst. Biol."},{"key":"2026071605453995200_B26","doi-asserted-by":"publisher","first-page":"1706","DOI":"10.1002\/pmic.201100594","article-title":"Protein interaction networks in medicine and disease","volume":"12","author":"Taylor","year":"2012","journal-title":"Proteomics"},{"key":"2026071605453995200_B27","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1038\/s41588-020-00774-y","article-title":"Comprehensive characterization of protein\u2013protein interactions perturbed by disease mutations","volume":"53","author":"Cheng","year":"2021","journal-title":"Nat. Genet."},{"key":"2026071605453995200_B28","doi-asserted-by":"publisher","first-page":"637","DOI":"10.1038\/s41571-022-00671-9","article-title":"The current state of the art and future trends in RAS-targeted cancer therapies","volume":"19","author":"Punekar","year":"2022","journal-title":"Nat. Rev. Clin. Oncol."},{"key":"2026071605453995200_B29","doi-asserted-by":"publisher","first-page":"224","DOI":"10.1038\/s41571-023-00852-0","article-title":"BRAF\u2014a tumour-agnostic drug target with lineage-specific dependencies","volume":"21","author":"Hanrahan","year":"2024","journal-title":"Nat. Rev. Clin. Oncol."},{"key":"2026071605453995200_B30","doi-asserted-by":"publisher","first-page":"140","DOI":"10.1038\/nrd4204","article-title":"PI3K and cancer: lessons, challenges and opportunities","volume":"13","author":"Fruman","year":"2014","journal-title":"Nat. Rev. Drug Discov."},{"key":"2026071605453995200_B31","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1038\/nrclinonc.2018.28","article-title":"Targeting the PI3K pathway in cancer: are we making headway?","volume":"15","author":"Janku","year":"2018","journal-title":"Nat. Rev. Clin. Oncol."},{"key":"2026071605453995200_B32","doi-asserted-by":"publisher","first-page":"107723","DOI":"10.1016\/j.phrs.2025.107723","article-title":"Properties of FDA-approved small molecule protein kinase inhibitors: a 2025 update","volume":"216","author":"Roskoski","year":"2025","journal-title":"Pharmacol. Res."},{"key":"2026071605453995200_B33","doi-asserted-by":"publisher","first-page":"839","DOI":"10.1038\/s41573-021-00252-y","article-title":"Trends in kinase drug discovery: targets, indications and inhibitor design","volume":"20","author":"Attwood","year":"2021","journal-title":"Nat. Rev. Drug Discov."},{"key":"2026071605453995200_B34","doi-asserted-by":"publisher","first-page":"108107","DOI":"10.1016\/j.phrs.2026.108107","article-title":"Properties of FDA-approved small molecule protein kinase inhibitors: a 2026 update","volume":"224","author":"Roskoski","year":"2026","journal-title":"Pharmacol. Res."},{"key":"2026071605453995200_B35","doi-asserted-by":"publisher","first-page":"101128","DOI":"10.1016\/j.jbc.2021.101128","article-title":"New strategies for targeting kinase networks in cancer","volume":"297","author":"Yesilkanal","year":"2021","journal-title":"J. Biol. Chem."},{"key":"2026071605453995200_B36","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1038\/s41392-022-01168-8","article-title":"Protein tyrosine kinase inhibitor resistance in malignant tumors: molecular mechanisms and future perspective","volume":"7","author":"Yang","year":"2022","journal-title":"Signal Transduct. Target Ther."},{"key":"2026071605453995200_B37","doi-asserted-by":"publisher","first-page":"613","DOI":"10.1038\/s41568-025-00824-9","article-title":"Acquired resistance in cancer: towards targeted therapeutic strategies","volume":"25","author":"Soragni","year":"2025","journal-title":"Nat. Rev. Cancer"},{"key":"2026071605453995200_B38","doi-asserted-by":"publisher","first-page":"551","DOI":"10.1038\/s41573-021-00195-4","article-title":"Kinase drug discovery 20\u00a0years after imatinib: progress and future directions","volume":"20","author":"Cohen","year":"2021","journal-title":"Nat. Rev. Drug Discov."},{"key":"2026071605453995200_B39","doi-asserted-by":"publisher","first-page":"565","DOI":"10.1038\/msb.2011.99","article-title":"Differential network biology","volume":"8","author":"Ideker","year":"2012","journal-title":"Mol. Syst. Biol."},{"key":"2026071605453995200_B40","doi-asserted-by":"publisher","first-page":"617","DOI":"10.1038\/nrg2633","article-title":"Applying mass spectrometry-based proteomics to genetics, genomics and network biology","volume":"10","author":"Gstaiger","year":"2009","journal-title":"Nat. Rev. Genet."},{"key":"2026071605453995200_B41","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1038\/nature19949","article-title":"Mass-spectrometric exploration of proteome structure and function","volume":"537","author":"Aebersold","year":"2016","journal-title":"Nature"},{"key":"2026071605453995200_B42","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1146\/annurev-anchem-071015-041542","article-title":"Methods for the analysis of protein phosphorylation-mediated cellular signaling networks","volume":"9","author":"White","year":"2016","journal-title":"Annu. Rev. Anal. Chem. (Palo Alto Calif)"},{"key":"2026071605453995200_B43","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1016\/j.gde.2009.12.005","article-title":"Quantifying oncogenic phosphotyrosine signaling networks through systems biology","volume":"20","author":"Del Rosario","year":"2010","journal-title":"Curr. Opin. Genet. Dev."},{"key":"2026071605453995200_B44","doi-asserted-by":"publisher","first-page":"102260","DOI":"10.1016\/j.cbpa.2022.102260","article-title":"Recent advances in kinase signaling network profiling by mass spectrometry","volume":"73","author":"Franciosa","year":"2023","journal-title":"Curr. Opin. Chem. Biol."},{"key":"2026071605453995200_B45","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1016\/j.jprot.2018.02.004","article-title":"Targeted proteomics analyses of phosphorylation-dependent signalling networks","volume":"189","author":"Banerjee","year":"2018","journal-title":"J. Proteomics"},{"key":"2026071605453995200_B46","doi-asserted-by":"publisher","first-page":"1328.e8","DOI":"10.1016\/j.ccell.2025.05.003","article-title":"The pan-cancer proteome atlas, a mass spectrometry-based landscape for discovering tumor biology, biomarkers, and therapeutic targets","volume":"43","author":"Knol","year":"2025","journal-title":"Cancer Cell."},{"key":"2026071605453995200_B47","doi-asserted-by":"publisher","first-page":"1465","DOI":"10.1126\/science.1153878","article-title":"An in vivo map of the yeast protein interactome","volume":"320","author":"Tarassov","year":"2008","journal-title":"Science"},{"key":"2026071605453995200_B48","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1126\/science.1158684","article-title":"High-quality binary protein interaction map of the yeast interactome network","volume":"322","author":"Yu","year":"2008","journal-title":"Science"},{"key":"2026071605453995200_B49","doi-asserted-by":"publisher","first-page":"623","DOI":"10.1038\/35001009","article-title":"A comprehensive analysis of protein\u2013protein interactions Saccharomyces cerevisiae","volume":"403","author":"Uetz","year":"2000","journal-title":"Nature"},{"key":"2026071605453995200_B50","doi-asserted-by":"publisher","first-page":"4569","DOI":"10.1073\/pnas.061034498","article-title":"A comprehensive two-hybrid analysis to explore the yeast protein interactome","volume":"98","author":"Ito","year":"2001","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2026071605453995200_B51","doi-asserted-by":"publisher","first-page":"1621","DOI":"10.1126\/science.1105776","article-title":"High-throughput mapping of a dynamic signaling network in mammalian cells","volume":"307","author":"Barrios-Rodiles","year":"2005","journal-title":"Science"},{"key":"2026071605453995200_B52","doi-asserted-by":"publisher","first-page":"1030","DOI":"10.1038\/13732","article-title":"A generic protein purification method for protein complex characterization and proteome exploration","volume":"17","author":"Rigaut","year":"1999","journal-title":"Nat. Biotechnol."},{"key":"2026071605453995200_B53","doi-asserted-by":"publisher","first-page":"645","DOI":"10.1038\/nrm2208","article-title":"Analysis of protein complexes using mass spectrometry","volume":"8","author":"Gingras","year":"2007","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"2026071605453995200_B54","doi-asserted-by":"publisher","first-page":"1068","DOI":"10.1016\/j.cell.2012.08.011","article-title":"A census of human soluble protein complexes","volume":"150","author":"Havugimana","year":"2012","journal-title":"Cell"},{"key":"2026071605453995200_B55","doi-asserted-by":"publisher","first-page":"907","DOI":"10.1038\/nmeth.2131","article-title":"A high-throughput approach for measuring temporal changes in the interactome","volume":"9","author":"Kristensen","year":"2012","journal-title":"Nat. Methods"},{"key":"2026071605453995200_B56","doi-asserted-by":"publisher","first-page":"4073.e17","DOI":"10.1016\/j.cell.2021.06.003","article-title":"An atlas of protein\u2013protein interactions across mouse tissues","volume":"184","author":"Skinnider","year":"2021","journal-title":"Cell"},{"key":"2026071605453995200_B57","doi-asserted-by":"publisher","first-page":"570","DOI":"10.1038\/nature02166","article-title":"Proteomic characterization of the human centrosome by protein correlation profiling","volume":"426","author":"Andersen","year":"2003","journal-title":"Nature"},{"key":"2026071605453995200_B58","doi-asserted-by":"publisher","first-page":"8992","DOI":"10.1038\/ncomms9992","article-title":"A draft map of the mouse pluripotent stem cell spatial proteome","volume":"7","author":"Christoforou","year":"2016","journal-title":"Nat. Commun."},{"key":"2026071605453995200_B59","doi-asserted-by":"publisher","first-page":"1110","DOI":"10.1038\/nprot.2017.026","article-title":"Using hyperLOPIT to perform high-resolution mapping of the spatial proteome","volume":"12","author":"Mulvey","year":"2017","journal-title":"Nat. Protoc."},{"key":"2026071605453995200_B60","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1038\/s41467-018-08191-w","article-title":"Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics","volume":"10","author":"Geladaki","year":"2019","journal-title":"Nat. Commun."},{"key":"2026071605453995200_B61","doi-asserted-by":"publisher","first-page":"166.e7","DOI":"10.1016\/j.molcel.2018.11.035","article-title":"SubCellBarCode: proteome-wide mapping of protein localization and relocalization","volume":"73","author":"Orre","year":"2019","journal-title":"Mol. Cell."},{"key":"2026071605453995200_B62","doi-asserted-by":"publisher","first-page":"1137.e20","DOI":"10.1016\/j.cell.2024.11.028","article-title":"Global organelle profiling reveals subcellular localization and remodeling at proteome scale","volume":"188","author":"Hein","year":"2025","journal-title":"Cell"},{"key":"2026071605453995200_B63","doi-asserted-by":"publisher","first-page":"531","DOI":"10.1038\/nature03239","article-title":"Interaction network containing conserved and essential protein complexes Escherichia coli","volume":"433","author":"Butland","year":"2005","journal-title":"Nature"},{"key":"2026071605453995200_B64","doi-asserted-by":"publisher","first-page":"631","DOI":"10.1038\/nature04532","article-title":"Proteome survey reveals modularity of the yeast cell machinery","volume":"440","author":"Gavin","year":"2006","journal-title":"Nature"},{"key":"2026071605453995200_B65","doi-asserted-by":"publisher","first-page":"637","DOI":"10.1038\/nature04670","article-title":"Global landscape of protein complexes in the yeast Saccharomyces cerevisiae","volume":"440","author":"Krogan","year":"2006","journal-title":"Nature"},{"key":"2026071605453995200_B66","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1126\/science.1176495","article-title":"A global protein kinase and phosphatase interaction network in yeast","volume":"328","author":"Breitkreutz","year":"2010","journal-title":"Science"},{"key":"2026071605453995200_B67","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1074\/mcp.R100001-MCP200","article-title":"Charting the protein complexome in yeast by mass spectrometry","volume":"1","author":"Deshaies","year":"2002","journal-title":"Mol. Cell. Proteomics"},{"key":"2026071605453995200_B68","doi-asserted-by":"publisher","first-page":"180","DOI":"10.1038\/415180a","article-title":"Systematic identification of protein complexes Saccharomyces cerevisiae by mass spectrometry","volume":"415","author":"Ho","year":"2002","journal-title":"Nature"},{"key":"2026071605453995200_B69","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1038\/415141a","article-title":"Functional organization of the yeast proteome by systematic analysis of protein complexes","volume":"415","author":"Gavin","year":"2002","journal-title":"Nature"},{"key":"2026071605453995200_B70","doi-asserted-by":"publisher","first-page":"585","DOI":"10.1038\/nature11354","article-title":"Interaction landscape of membrane-protein complexes Saccharomyces cerevisiae","volume":"489","author":"Babu","year":"2012","journal-title":"Nature"},{"key":"2026071605453995200_B71","doi-asserted-by":"publisher","first-page":"690","DOI":"10.1016\/j.cell.2011.08.047","article-title":"A protein complex network of Drosophila melanogaster","volume":"147","author":"Guruharsha","year":"2011","journal-title":"Cell"},{"key":"2026071605453995200_B72","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1038\/msb4100134","article-title":"Large-scale mapping of human protein\u2013protein interactions by mass spectrometry","volume":"3","author":"Ewing","year":"2007","journal-title":"Mol. Syst. Biol."},{"key":"2026071605453995200_B73","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1038\/msb.2008.75","article-title":"An integrated workflow for charting the human interaction proteome: insights into the PP2A system","volume":"5","author":"Glatter","year":"2009","journal-title":"Mol. Syst. Biol."},{"key":"2026071605453995200_B74","doi-asserted-by":"publisher","first-page":"425","DOI":"10.1016\/j.cell.2015.06.043","article-title":"The BioPlex network: a systematic exploration of the human interactome","volume":"162","author":"Huttlin","year":"2015","journal-title":"Cell"},{"key":"2026071605453995200_B75","doi-asserted-by":"publisher","first-page":"712","DOI":"10.1016\/j.cell.2015.09.053","article-title":"A human interactome in three quantitative dimensions organized by stoichiometries and abundances","volume":"163","author":"Hein","year":"2015","journal-title":"Cell"},{"key":"2026071605453995200_B76","doi-asserted-by":"publisher","first-page":"505","DOI":"10.1038\/nature22366","article-title":"Architecture of the human interactome defines protein communities and disease networks","volume":"545","author":"Huttlin","year":"2017","journal-title":"Nature"},{"key":"2026071605453995200_B77","doi-asserted-by":"publisher","first-page":"3022.e28","DOI":"10.1016\/j.cell.2021.04.011","article-title":"Dual proteome-scale networks reveal cell-specific remodeling of the human interactome","volume":"184","author":"Huttlin","year":"2021","journal-title":"Cell"},{"key":"2026071605453995200_B78","doi-asserted-by":"publisher","first-page":"eabi6983","DOI":"10.1126\/science.abi6983","article-title":"OpenCell: endogenous tagging for the cartography of human cellular organization","volume":"375","author":"Cho","year":"2022","journal-title":"Science"},{"key":"2026071605453995200_B79","doi-asserted-by":"publisher","first-page":"635","DOI":"10.1038\/s41592-024-02211-y","article-title":"DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes","volume":"21","author":"Frommelt","year":"2024","journal-title":"Nat. Methods"},{"key":"2026071605453995200_B80","doi-asserted-by":"publisher","first-page":"13283","DOI":"10.1073\/pnas.0702654104","article-title":"The Btk tyrosine kinase is a major target of the Bcr-Abl inhibitor dasatinib","volume":"104","author":"Hantschel","year":"2007","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2026071605453995200_B81","doi-asserted-by":"publisher","first-page":"1035","DOI":"10.1038\/nbt1328","article-title":"Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors","volume":"25","author":"Bantscheff","year":"2007","journal-title":"Nat. Biotechnol."},{"key":"2026071605453995200_B82","doi-asserted-by":"publisher","first-page":"eaan4368","DOI":"10.1126\/science.aan4368","article-title":"The target landscape of clinical kinase drugs","volume":"358","author":"Klaeger","year":"2017","journal-title":"Science"},{"key":"2026071605453995200_B83","doi-asserted-by":"publisher","first-page":"577","DOI":"10.1038\/s41589-023-01459-3","article-title":"Chemical proteomics reveals the target landscape of 1,000 kinase inhibitors","volume":"20","author":"Reinecke","year":"2024","journal-title":"Nat. Chem. Biol."},{"key":"2026071605453995200_B84","doi-asserted-by":"publisher","first-page":"585","DOI":"10.1038\/nmeth.2895","article-title":"The mammalian-membrane two-hybrid assay (MaMTH) for probing membrane\u2013protein interactions in human cells","volume":"11","author":"Petschnigg","year":"2014","journal-title":"Nat. Methods"},{"key":"2026071605453995200_B85","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1002\/cpch.15","article-title":"Detecting membrane protein\u2013protein interactions using the mammalian membrane two-hybrid (MaMTH) assay","volume":"9","author":"Saraon","year":"2017","journal-title":"Curr. Protoc. Chem. Biol."},{"key":"2026071605453995200_B86","doi-asserted-by":"publisher","first-page":"848","DOI":"10.15252\/msb.20156351","article-title":"Fundamentals of protein interaction network mapping","volume":"11","author":"Snider","year":"2015","journal-title":"Mol. Syst. Biol."},{"key":"2026071605453995200_B87","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1007\/978-1-62703-601-6_2","article-title":"Analysis of protein\u2013protein interactions using LUMIER assays","volume":"1064","author":"Blasche","year":"2013","journal-title":"Methods Mol. Biol."},{"key":"2026071605453995200_B88","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1007\/978-1-4939-6747-6_10","article-title":"Parallel exploration of interaction space by BioID and affinity purification coupled to mass spectrometry","volume":"1550","author":"Hesketh","year":"2017","journal-title":"Methods Mol. Biol."},{"key":"2026071605453995200_B89","doi-asserted-by":"publisher","first-page":"801","DOI":"10.1083\/jcb.201112098","article-title":"A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells","volume":"196","author":"Roux","year":"2012","journal-title":"J. Cell Biol."},{"key":"2026071605453995200_B90","doi-asserted-by":"publisher","first-page":"1328","DOI":"10.1126\/science.1230593","article-title":"Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging","volume":"339","author":"Rhee","year":"2013","journal-title":"Science"},{"key":"2026071605453995200_B91","doi-asserted-by":"publisher","first-page":"1143","DOI":"10.1038\/nbt.2375","article-title":"Engineered ascorbate peroxidase as a genetically encoded reporter for electron microscopy","volume":"30","author":"Martell","year":"2012","journal-title":"Nat. Biotechnol."},{"key":"2026071605453995200_B92","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1038\/nmeth.3179","article-title":"Directed evolution of APEX2 for electron microscopy and proximity labeling","volume":"12","author":"Lam","year":"2015","journal-title":"Nat. Methods"},{"key":"2026071605453995200_B93","doi-asserted-by":"publisher","first-page":"1188","DOI":"10.1038\/s41467-018-03523-2","article-title":"An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations","volume":"9","author":"Liu","year":"2018","journal-title":"Nat. Commun."},{"key":"2026071605453995200_B94","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1038\/s43586-021-00029-y","article-title":"Subcellular proteomics","volume":"1","author":"Christopher","year":"2021","journal-title":"Nat. Rev. Methods Primers"},{"key":"2026071605453995200_B95","doi-asserted-by":"publisher","first-page":"852911","DOI":"10.3389\/fmolb.2022.852911","article-title":"Proximity-dependent biotinylation approaches to explore the dynamic compartmentalized proteome","volume":"9","author":"Dionne","year":"2022","journal-title":"Front. Mol. Biosci."},{"key":"2026071605453995200_B96","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1016\/j.cbpa.2018.10.017","article-title":"Getting to know the neighborhood: using proximity-dependent biotinylation to characterize protein complexes and map organelles","volume":"48","author":"Gingras","year":"2019","journal-title":"Curr. Opin. Chem. Biol."},{"key":"2026071605453995200_B97","doi-asserted-by":"publisher","first-page":"E2453","DOI":"10.1073\/pnas.1406459111","article-title":"Probing nuclear pore complex architecture with proximity-dependent biotinylation","volume":"111","author":"Kim","year":"2014","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2026071605453995200_B98","doi-asserted-by":"publisher","first-page":"332","DOI":"10.1016\/j.molcel.2014.06.003","article-title":"Proteomic mapping of the human mitochondrial intermembrane space in live cells via ratiometric APEX tagging","volume":"55","author":"Hung","year":"2014","journal-title":"Mol. Cell."},{"key":"2026071605453995200_B99","doi-asserted-by":"publisher","first-page":"479.e9","DOI":"10.1016\/j.cmet.2020.07.017","article-title":"A high-density human mitochondrial proximity interaction network","volume":"32","author":"Antonicka","year":"2020","journal-title":"Cell Metab."},{"key":"2026071605453995200_B100","doi-asserted-by":"publisher","first-page":"757","DOI":"10.1074\/mcp.R120.001941","article-title":"Proximity dependent biotinylation: key enzymes and adaptation to proteomics approaches","volume":"19","author":"Samavarchi-Tehrani","year":"2020","journal-title":"Mol. Cell. Proteomics"},{"key":"2026071605453995200_B101","doi-asserted-by":"publisher","first-page":"590.e13","DOI":"10.1016\/j.cell.2017.12.032","article-title":"Context-dependent and disease-specific diversity in protein interactions within stress granules","volume":"172","author":"Markmiller","year":"2018","journal-title":"Cell"},{"key":"2026071605453995200_B102","doi-asserted-by":"publisher","first-page":"286","DOI":"10.1016\/j.molcel.2019.09.014","article-title":"Properties of stress granule and P-body proteomes","volume":"76","author":"Youn","year":"2019","journal-title":"Mol. Cell."},{"key":"2026071605453995200_B103","doi-asserted-by":"publisher","first-page":"517.e11","DOI":"10.1016\/j.molcel.2017.12.020","article-title":"High-density proximity mapping reveals the subcellular organization of mRNA-associated granules and bodies","volume":"69","author":"Youn","year":"2018","journal-title":"Mol. Cell."},{"key":"2026071605453995200_B104","doi-asserted-by":"publisher","first-page":"1484","DOI":"10.1016\/j.cell.2015.10.065","article-title":"A dynamic protein interaction landscape of the human centrosome\u2013cilium interface","volume":"163","author":"Gupta","year":"2015","journal-title":"Cell"},{"key":"2026071605453995200_B105","doi-asserted-by":"publisher","first-page":"2198","DOI":"10.1038\/s41556-025-01809-4","article-title":"Proximal proteomics reveals a landscape of human nuclear condensates","volume":"27","author":"Li","year":"2025","journal-title":"Nat. Cell Biol."},{"key":"2026071605453995200_B106","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1038\/s41586-021-03592-2","article-title":"A proximity-dependent biotinylation map of a human cell","volume":"595","author":"Go","year":"2021","journal-title":"Nature"},{"key":"2026071605453995200_B107","doi-asserted-by":"publisher","first-page":"497","DOI":"10.1016\/j.devcel.2015.10.015","article-title":"Proteomics of primary cilia by proximity labeling","volume":"35","author":"Mick","year":"2015","journal-title":"Dev. Cell."},{"key":"2026071605453995200_B108","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1038\/s41556-019-0438-7","article-title":"Mapping the proximity interaction network of the Rho-family GTPases reveals signalling pathways and regulatory mechanisms","volume":"22","author":"Bagci","year":"2020","journal-title":"Nat. Cell Biol."},{"key":"2026071605453995200_B109","doi-asserted-by":"publisher","first-page":"1717","DOI":"10.1038\/s42003-025-09121-5","article-title":"A proximity map of RAB GTPases delineates roles for RAB14 in EARP complex and UHRF1BP1 endosomal recruitments","volume":"8","author":"Gaudreault","year":"2025","journal-title":"Commun. Biol."},{"key":"2026071605453995200_B110","doi-asserted-by":"publisher","first-page":"6671","DOI":"10.1038\/s41467-021-26807-6","article-title":"Identification of proximal SUMO-dependent interactors using SUMO-ID","volume":"12","author":"Barroso-Gomila","year":"2021","journal-title":"Nat. Commun."},{"key":"2026071605453995200_B111","doi-asserted-by":"publisher","first-page":"15690","DOI":"10.1038\/ncomms15690","article-title":"Split-BioID a conditional proteomics approach to monitor the composition of spatiotemporally defined protein complexes","volume":"8","author":"Schopp","year":"2017","journal-title":"Nat. Commun."},{"key":"2026071605453995200_B112","doi-asserted-by":"publisher","first-page":"12109","DOI":"10.1073\/pnas.1916584117","article-title":"Contact-ID, a tool for profiling organelle contact sites, reveals regulatory proteins of mitochondrial-associated membrane formation","volume":"117","author":"Kwak","year":"2020","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2026071605453995200_B113","doi-asserted-by":"publisher","first-page":"12143","DOI":"10.1073\/pnas.1919528117","article-title":"Split-TurboID enables contact-dependent proximity labeling in cells","volume":"117","author":"Cho","year":"2020","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2026071605453995200_B114","doi-asserted-by":"publisher","first-page":"974.e15","DOI":"10.1016\/j.molcel.2023.02.018","article-title":"A central chaperone-like role for 14-3-3 proteins in human cells","volume":"83","author":"Segal","year":"2023","journal-title":"Mol. Cell."},{"key":"2026071605453995200_B115","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1038\/nmeth.1541","article-title":"SAINT: probabilistic scoring of affinity purification-mass spectrometry data","volume":"8","author":"Choi","year":"2011","journal-title":"Nat. Methods"},{"key":"2026071605453995200_B116","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1016\/j.jprot.2013.10.023","article-title":"SAINTexpress: improvements and additional features in Significance Analysis of INTeractome software","volume":"100","author":"Teo","year":"2014","journal-title":"J. Proteomics"},{"key":"2026071605453995200_B117","first-page":"8.15.1","article-title":"Analyzing protein\u2013protein interactions from affinity purification-mass spectrometry data with SAINT","volume":"Chapter 8","author":"Choi","year":"2012","journal-title":"Curr. Protoc. Bioinformatics"},{"key":"2026071605453995200_B118","doi-asserted-by":"publisher","first-page":"2238","DOI":"10.1002\/pmic.201500499","article-title":"SAINTq: scoring protein\u2013protein interactions in affinity purification-mass spectrometry experiments with fragment or peptide intensity data","volume":"16","author":"Teo","year":"2016","journal-title":"Proteomics"},{"key":"2026071605453995200_B119","doi-asserted-by":"publisher","first-page":"730","DOI":"10.1038\/nmeth.2557","article-title":"The CRAPome: a contaminant repository for affinity purification-mass spectrometry data","volume":"10","author":"Mellacheruvu","year":"2013","journal-title":"Nat. Methods"},{"key":"2026071605453995200_B120","doi-asserted-by":"publisher","first-page":"389","DOI":"10.1016\/j.cell.2009.04.042","article-title":"Defining the human deubiquitinating enzyme interaction landscape","volume":"138","author":"Sowa","year":"2009","journal-title":"Cell"},{"key":"2026071605453995200_B121","doi-asserted-by":"publisher","first-page":"D559","DOI":"10.1093\/nar\/gky973","article-title":"CORUM: the comprehensive resource of mammalian protein complexes-2019","volume":"47","author":"Giurgiu","year":"2019","journal-title":"Nucleic. Acids Res."},{"key":"2026071605453995200_B122","doi-asserted-by":"publisher","first-page":"3442","DOI":"10.1093\/nar\/28.18.3442","article-title":"STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene","volume":"28","author":"Snel","year":"2000","journal-title":"Nucleic. Acids Res."},{"key":"2026071605453995200_B123","doi-asserted-by":"publisher","first-page":"258","DOI":"10.1093\/nar\/gkg034","article-title":"STRING: a database of predicted functional associations between proteins","volume":"31","author":"von Mering","year":"2003","journal-title":"Nucleic. Acids Res."},{"key":"2026071605453995200_B124","doi-asserted-by":"publisher","first-page":"D433","DOI":"10.1093\/nar\/gki005","article-title":"STRING: known and predicted protein\u2013protein associations, integrated and transferred across organisms","volume":"33","author":"von Mering","year":"2005","journal-title":"Nucleic. Acids Res."},{"key":"2026071605453995200_B125","doi-asserted-by":"publisher","first-page":"D638","DOI":"10.1093\/nar\/gkac1000","article-title":"The STRING database in 2023: protein\u2013protein association networks and functional enrichment analyses for any sequenced genome of interest","volume":"51","author":"Szklarczyk","year":"2023","journal-title":"Nucleic. Acids Res."},{"key":"2026071605453995200_B126","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1002\/pro.3978","article-title":"The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions","volume":"30","author":"Oughtred","year":"2021","journal-title":"Protein Sci."},{"key":"2026071605453995200_B127","doi-asserted-by":"publisher","first-page":"D535","DOI":"10.1093\/nar\/gkj109","article-title":"BioGRID: a general repository for interaction datasets","volume":"34","author":"Stark","year":"2006","journal-title":"Nucleic. Acids Res."},{"key":"2026071605453995200_B128","doi-asserted-by":"publisher","first-page":"D358","DOI":"10.1093\/nar\/gkt1115","article-title":"The MIntAct project\u2013IntAct as a common curation platform for 11 molecular interaction databases","volume":"42","author":"Orchard","year":"2014","journal-title":"Nucleic. Acids Res."},{"key":"2026071605453995200_B129","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s44320-024-00077-y","article-title":"State of the interactomes: an evaluation of molecular networks for generating biological insights","volume":"21","author":"Wright","year":"2025","journal-title":"Mol. Syst. Biol."},{"key":"2026071605453995200_B130","doi-asserted-by":"publisher","first-page":"7866","DOI":"10.1038\/s41467-024-51771-2","article-title":"Modelling protein complexes with crosslinking mass spectrometry and deep learning","volume":"15","author":"Stahl","year":"2024","journal-title":"Nat. Commun."},{"key":"2026071605453995200_B131","doi-asserted-by":"publisher","first-page":"1810","DOI":"10.1038\/s41587-023-01704-z","article-title":"Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning","volume":"41","author":"Stahl","year":"2023","journal-title":"Nat. Biotechnol."},{"key":"2026071605453995200_B132","doi-asserted-by":"publisher","first-page":"1451","DOI":"10.1002\/pmic.200800454","article-title":"Analytical strategies for phosphoproteomics","volume":"9","author":"Thingholm","year":"2009","journal-title":"Proteomics"},{"key":"2026071605453995200_B133","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1038\/nbt0302-301","article-title":"Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae","volume":"20","author":"Ficarro","year":"2002","journal-title":"Nat. Biotechnol."},{"key":"2026071605453995200_B134","doi-asserted-by":"publisher","first-page":"250","DOI":"10.1016\/0003-2697(86)90523-3","article-title":"Isolation of phosphoproteins by immobilized metal (Fe3+) affinity chromatography","volume":"154","author":"Andersson","year":"1986","journal-title":"Anal. Biochem."},{"key":"2026071605453995200_B135","doi-asserted-by":"publisher","first-page":"1123","DOI":"10.1016\/S0021-9258(19)57275-1","article-title":"Tandem mass spectrometry reveals that three photosystem II proteins of spinach chloroplasts contain N-acetyl-O-phosphothreonine at their NH2 termini","volume":"263","author":"Michel","year":"1988","journal-title":"J. Biol. Chem."},{"key":"2026071605453995200_B136","doi-asserted-by":"publisher","first-page":"1234","DOI":"10.1074\/mcp.T300006-MCP200","article-title":"Large-scale analysis of in vivo hosphorylated membrane proteins by immobilized metal ion affinity chromatography and mass spectrometry","volume":"2","author":"N\u00fchse","year":"2003","journal-title":"Mol. Cell. Proteomics"},{"key":"2026071605453995200_B137","doi-asserted-by":"publisher","first-page":"310","DOI":"10.1074\/mcp.M400219-MCP200","article-title":"Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway","volume":"4","author":"Gruhler","year":"2005","journal-title":"Mol. Cell. Proteomics"},{"key":"2026071605453995200_B138","doi-asserted-by":"publisher","first-page":"635","DOI":"10.1016\/j.cell.2006.09.026","article-title":"Global, in vivo, and site-specific phosphorylation dynamics in signaling networks","volume":"127","author":"Olsen","year":"2006","journal-title":"Cell"},{"key":"2026071605453995200_B139","doi-asserted-by":"publisher","first-page":"1630","DOI":"10.1038\/nprot.2008.150","article-title":"The SCX\/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry","volume":"3","author":"Vill\u00e9n","year":"2008","journal-title":"Nat. Protoc."},{"key":"2026071605453995200_B140","doi-asserted-by":"publisher","first-page":"1093","DOI":"10.1074\/mcp.M400085-MCP200","article-title":"Phosphoproteomic analysis of the developing mouse brain","volume":"3","author":"Ballif","year":"2004","journal-title":"Mol. Cell. Proteomics"},{"key":"2026071605453995200_B141","doi-asserted-by":"publisher","first-page":"1285","DOI":"10.1038\/nbt1240","article-title":"A probability-based approach for high-throughput protein phosphorylation analysis and site localization","volume":"24","author":"Beausoleil","year":"2006","journal-title":"Nat. Biotechnol."},{"key":"2026071605453995200_B142","doi-asserted-by":"publisher","first-page":"5354","DOI":"10.1021\/pr200611n","article-title":"Universal and confident phosphorylation site localization using phosphoRS","volume":"10","author":"Taus","year":"2011","journal-title":"J. Proteome Res."},{"key":"2026071605453995200_B143","doi-asserted-by":"publisher","first-page":"5860","DOI":"10.1073\/pnas.0608638104","article-title":"Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks","volume":"104","author":"Wolf-Yadlin","year":"2007","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2026071605453995200_B144","doi-asserted-by":"publisher","first-page":"1139","DOI":"10.1038\/nbt1005","article-title":"Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics","volume":"22","author":"Blagoev","year":"2004","journal-title":"Nat. Biotechnol."},{"key":"2026071605453995200_B145","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1038\/nbt1046","article-title":"Immunoaffinity profiling of tyrosine phosphorylation in cancer cells","volume":"23","author":"Rush","year":"2005","journal-title":"Nat. Biotechnol."},{"key":"2026071605453995200_B146","doi-asserted-by":"publisher","first-page":"2171","DOI":"10.2337\/db06-0148","article-title":"Temporal dynamics of tyrosine phosphorylation in insulin signaling","volume":"55","author":"Schmelzle","year":"2006","journal-title":"Diabetes"},{"key":"2026071605453995200_B147","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1073\/pnas.2436191100","article-title":"Profiling of tyrosine phosphorylation pathways in human cells using mass spectrometry","volume":"100","author":"Salomon","year":"2003","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2026071605453995200_B148","doi-asserted-by":"publisher","first-page":"1868","DOI":"10.1021\/acs.jproteome.2c00850","article-title":"Automated enrichment of phosphotyrosine peptides for high-throughput proteomics","volume":"22","author":"Chang","year":"2023","journal-title":"J. Proteome Res."},{"key":"2026071605453995200_B149","doi-asserted-by":"publisher","first-page":"ra68","DOI":"10.1126\/scisignal.2003021","article-title":"Superbinder SH2 domains act as antagonists of cell signaling","volume":"5","author":"Kaneko","year":"2012","journal-title":"Sci. Signal."},{"key":"2026071605453995200_B150","doi-asserted-by":"publisher","first-page":"959","DOI":"10.1038\/nchembio.2178","article-title":"Ultra-deep tyrosine phosphoproteomics enabled by a phosphotyrosine superbinder","volume":"12","author":"Bian","year":"2016","journal-title":"Nat. Chem. Biol."},{"key":"2026071605453995200_B151","doi-asserted-by":"publisher","first-page":"1870","DOI":"10.1021\/acs.jproteome.9b00045","article-title":"One-step SH2 superbinder-based approach for sensitive analysis of tyrosine phosphoproteome","volume":"18","author":"Yao","year":"2019","journal-title":"J. Proteome Res."},{"key":"2026071605453995200_B152","doi-asserted-by":"publisher","first-page":"1472","DOI":"10.1021\/acschembio.2c00051","article-title":"Engineered SH2 domains for targeted phosphoproteomics","volume":"17","author":"Martyn","year":"2022","journal-title":"ACS Chem. Biol."},{"key":"2026071605453995200_B153","doi-asserted-by":"publisher","first-page":"1190","DOI":"10.1016\/j.cell.2007.11.025","article-title":"Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer","volume":"131","author":"Rikova","year":"2007","journal-title":"Cell"},{"key":"2026071605453995200_B154","doi-asserted-by":"publisher","first-page":"1583","DOI":"10.1016\/j.celrep.2014.07.036","article-title":"Ultradeep human phosphoproteome reveals a distinct regulatory nature of Tyr and Ser\/Thr-based signaling","volume":"8","author":"Sharma","year":"2014","journal-title":"Cell Rep."},{"key":"2026071605453995200_B155","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1038\/nature18003","article-title":"Proteogenomics connects somatic mutations to signalling in breast cancer","volume":"534","author":"Mertins","year":"2016","journal-title":"Nature"},{"key":"2026071605453995200_B156","doi-asserted-by":"publisher","first-page":"1632","DOI":"10.1038\/s41596-018-0006-9","article-title":"Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography-mass spectrometry","volume":"13","author":"Mertins","year":"2018","journal-title":"Nat. Protoc."},{"key":"2026071605453995200_B157","doi-asserted-by":"publisher","first-page":"3242","DOI":"10.1016\/j.celrep.2017.03.015","article-title":"Phosphoproteomics of primary cells reveals druggable kinase signatures in ovarian cancer","volume":"18","author":"Francavilla","year":"2017","journal-title":"Cell Rep."},{"key":"2026071605453995200_B158","doi-asserted-by":"publisher","first-page":"1533","DOI":"10.1182\/blood.2022016033","article-title":"Proteomic and phosphoproteomic landscapes of acute myeloid leukemia","volume":"140","author":"Kramer","year":"2022","journal-title":"Blood"},{"key":"2026071605453995200_B159","doi-asserted-by":"publisher","first-page":"e14460","DOI":"10.1002\/alz.14460","article-title":"Brain phosphoproteomic analysis identifies diabetes-related substrates in Alzheimer\u2019s disease pathology in older adults","volume":"21","author":"Capuano","year":"2025","journal-title":"Alzheimers Dement."},{"key":"2026071605453995200_B160","doi-asserted-by":"publisher","first-page":"D512","DOI":"10.1093\/nar\/gku1267","article-title":"PhosphoSitePlus, 2014: mutations, PTMs and recalibrations","volume":"43","author":"Hornbeck","year":"2015","journal-title":"Nucleic. Acids Res."},{"key":"2026071605453995200_B161","doi-asserted-by":"publisher","first-page":"759","DOI":"10.1038\/s41586-022-05575-3","article-title":"An atlas of substrate specificities for the human serine\/threonine kinome","volume":"613","author":"Johnson","year":"2023","journal-title":"Nature"},{"key":"2026071605453995200_B162","doi-asserted-by":"publisher","first-page":"1174","DOI":"10.1038\/s41586-024-07407-y","article-title":"The intrinsic substrate specificity of the human tyrosine kinome","volume":"629","author":"Yaron-Barir","year":"2024","journal-title":"Nature"},{"key":"2026071605453995200_B163","doi-asserted-by":"publisher","first-page":"1510","DOI":"10.1021\/acs.jproteome.2c00131","article-title":"Profiling the human phosphoproteome to estimate the true extent of protein phosphorylation","volume":"21","author":"Kalyuzhnyy","year":"2022","journal-title":"J. Proteome Res."},{"key":"2026071605453995200_B164","doi-asserted-by":"publisher","first-page":"510","DOI":"10.1038\/s41467-024-55533-y","article-title":"PTMNavigator: interactive visualization of differentially regulated post-translational modifications in cellular signaling pathways","volume":"16","author":"M\u00fcller","year":"2025","journal-title":"Nat. Commun."},{"key":"2026071605453995200_B165","doi-asserted-by":"publisher","first-page":"582","DOI":"10.1038\/nature13319","article-title":"Mass-spectrometry-based draft of the human proteome","volume":"509","author":"Wilhelm","year":"2014","journal-title":"Nature"},{"key":"2026071605453995200_B166","first-page":"D1153","article-title":"ProteomicsDB: a multi-omics and multi-organism resource for life science research","volume":"48","author":"Samaras","year":"2020","journal-title":"Nucleic. Acids Res."},{"key":"2026071605453995200_B167","doi-asserted-by":"publisher","first-page":"1337","DOI":"10.1042\/BST20253100","article-title":"Are you having a LaPh? Diverse roles of Labile Phosphorylation in mammalian cells","volume":"53","author":"Clarke","year":"2025","journal-title":"Biochem. Soc. Trans."},{"key":"2026071605453995200_B168","doi-asserted-by":"publisher","first-page":"2190","DOI":"10.1016\/j.molcel.2022.05.007","article-title":"A journey from phosphotyrosine to phosphohistidine and beyond","volume":"82","author":"Hunter","year":"2022","journal-title":"Mol. Cell."},{"key":"2026071605453995200_B169","doi-asserted-by":"publisher","first-page":"1562","DOI":"10.1038\/s41587-024-02432-8","article-title":"Global profiling of protein complex dynamics with an experimental library of protein interaction markers","volume":"43","author":"D\u00f6rig","year":"2025","journal-title":"Nat. Biotechnol."},{"key":"2026071605453995200_B170","doi-asserted-by":"publisher","first-page":"3564","DOI":"10.1038\/s41467-021-23666-z","article-title":"Reliable identification of protein\u2013protein interactions by crosslinking mass spectrometry","volume":"12","author":"Lenz","year":"2021","journal-title":"Nat Commun."},{"key":"2026071605453995200_B171","doi-asserted-by":"publisher","first-page":"1036","DOI":"10.1038\/nbt.2999","article-title":"Global analysis of protein structural changes in complex proteomes","volume":"32","author":"Feng","year":"2014","journal-title":"Nat. Biotechnol."},{"key":"2026071605453995200_B172","doi-asserted-by":"publisher","first-page":"651","DOI":"10.1038\/s44320-024-00037-6","article-title":"Systematic identification of structure-specific protein\u2013protein interactions","volume":"20","author":"Holfeld","year":"2024","journal-title":"Mol. Syst. Biol."},{"key":"2026071605453995200_B173","doi-asserted-by":"publisher","first-page":"659","DOI":"10.1038\/s41596-022-00771-x","article-title":"Proteome-wide structural changes measured with limited proteolysis-mass spectrometry: an advanced protocol for high-throughput applications","volume":"18","author":"Malinovska","year":"2023","journal-title":"Nat. Protoc."},{"key":"2026071605453995200_B174","doi-asserted-by":"publisher","first-page":"9811","DOI":"10.1038\/s41467-025-64888-9","article-title":"Click-linking: a cell-compatible protein crosslinking method based on click chemistry","volume":"16","author":"Amaral","year":"2025","journal-title":"Nat. Commun."},{"key":"2026071605453995200_B175","doi-asserted-by":"publisher","first-page":"4048","DOI":"10.1038\/s41467-018-06007-5","article-title":"Cell cycle-resolved chromatin proteomics reveals the extent of mitotic preservation of the genomic regulatory landscape","volume":"9","author":"Ginno","year":"2018","journal-title":"Nat. Commun."},{"key":"2026071605453995200_B176","doi-asserted-by":"publisher","first-page":"102285","DOI":"10.1016\/j.cbpa.2023.102285","article-title":"Residue selective crosslinking of proteins through photoactivatable or proximity-enabled reactivity","volume":"74","author":"Liu","year":"2023","journal-title":"Curr. Opin. Chem. Biol."},{"key":"2026071605453995200_B177","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1038\/nbt790","article-title":"A proteomics strategy to elucidate functional protein\u2013protein interactions applied to EGF signaling","volume":"21","author":"Blagoev","year":"2003","journal-title":"Nat. Biotechnol."},{"key":"2026071605453995200_B178","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1038\/ncb1086","article-title":"A physical and functional map of the human TNF-alpha\/NF-kappa B signal transduction pathway","volume":"6","author":"Bouwmeester","year":"2004","journal-title":"Nat. Cell Biol."},{"key":"2026071605453995200_B179","doi-asserted-by":"publisher","first-page":"349","DOI":"10.1038\/ng1101","article-title":"The study of macromolecular complexes by quantitative proteomics","volume":"33","author":"Ranish","year":"2003","journal-title":"Nat. Genet."},{"key":"2026071605453995200_B180","doi-asserted-by":"publisher","first-page":"653","DOI":"10.1038\/nbt.1905","article-title":"Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor","volume":"29","author":"Bisson","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"2026071605453995200_B181","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1038\/nature12308","article-title":"Temporal regulation of EGF signalling networks by the scaffold protein Shc1","volume":"499","author":"Zheng","year":"2013","journal-title":"Nature"},{"key":"2026071605453995200_B182","doi-asserted-by":"publisher","first-page":"995.e11","DOI":"10.1016\/j.molcel.2018.05.013","article-title":"Direct phosphorylation of SRC homology 3 domains by tyrosine kinase receptors disassembles ligand-induced signaling networks","volume":"70","author":"Dionne","year":"2018","journal-title":"Mol. Cell."},{"key":"2026071605453995200_B183","doi-asserted-by":"publisher","first-page":"1246","DOI":"10.1038\/nmeth.2703","article-title":"Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system","volume":"10","author":"Collins","year":"2013","journal-title":"Nat. Methods"},{"key":"2026071605453995200_B184","doi-asserted-by":"publisher","first-page":"1239","DOI":"10.1038\/nmeth.2702","article-title":"Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition","volume":"10","author":"Lambert","year":"2013","journal-title":"Nat. Methods"},{"key":"2026071605453995200_B185","doi-asserted-by":"publisher","first-page":"3219","DOI":"10.1016\/j.celrep.2017.03.019","article-title":"Precise temporal profiling of signaling complexes in primary cells using SWATH mass spectrometry","volume":"18","author":"Caron","year":"2017","journal-title":"Cell Rep."},{"key":"2026071605453995200_B186","doi-asserted-by":"publisher","first-page":"621.e17","DOI":"10.1016\/j.molcel.2018.11.006","article-title":"Interactome rewiring following pharmacological targeting of BET bromodomains","volume":"73","author":"Lambert","year":"2019","journal-title":"Mol. Cell."},{"key":"2026071605453995200_B187","doi-asserted-by":"publisher","first-page":"1597","DOI":"10.1038\/s41467-021-21873-2","article-title":"Protein context shapes the specificity of SH3 domain-mediated interactions in vivo","volume":"12","author":"Dionne","year":"2021","journal-title":"Nat. Commun."},{"key":"2026071605453995200_B188","doi-asserted-by":"publisher","first-page":"510","DOI":"10.1038\/nature15729","article-title":"\u2206F508 CFTR interactome remodelling promotes rescue of cystic fibrosis","volume":"528","author":"Pankow","year":"2015","journal-title":"Nature"},{"key":"2026071605453995200_B189","doi-asserted-by":"publisher","first-page":"880","DOI":"10.1038\/nbt.4201","article-title":"Efficient proximity labeling in living cells and organisms with TurboID","volume":"36","author":"Branon","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"2026071605453995200_B190","doi-asserted-by":"publisher","first-page":"657","DOI":"10.1038\/s42003-022-03604-5","article-title":"Engineering of ultraID, a compact and hyperactive enzyme for proximity-dependent biotinylation in living cells","volume":"5","author":"Kubitz","year":"2022","journal-title":"Commun. Biol."},{"key":"2026071605453995200_B191","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1038\/s41422-024-00938-z","article-title":"The rapid proximity labeling system PhastID identifies ATP6AP1 as an unconventional GEF for Rheb","volume":"34","author":"Feng","year":"2024","journal-title":"Cell Res."},{"key":"2026071605453995200_B192","doi-asserted-by":"publisher","first-page":"908","DOI":"10.1038\/s41592-023-01880-5","article-title":"Engineered allostery in light-regulated LOV-Turbo enables precise spatiotemporal control of proximity labeling in living cells","volume":"20","author":"Lee","year":"2023","journal-title":"Nat. Methods"},{"key":"2026071605453995200_B193","doi-asserted-by":"publisher","first-page":"101045","DOI":"10.1016\/j.mcpro.2025.101045","article-title":"From vision to reality: a perspective on the innovative and collaborative forces that evolved proximity labeling","volume":"24","author":"Branon","year":"2025","journal-title":"Mol. Cell. Proteomics"},{"key":"2026071605453995200_B194","doi-asserted-by":"publisher","first-page":"3307.e30","DOI":"10.1016\/j.cell.2023.05.044","article-title":"Dynamic mapping of proteome trafficking within and between living cells by TransitID","volume":"186","author":"Qin","year":"2023","journal-title":"Cell"},{"key":"2026071605453995200_B195","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1038\/s41467-020-20367-x","article-title":"Spatiotemporal profiling of cytosolic signaling complexes in living cells by selective proximity proteomics","volume":"12","author":"Ke","year":"2021","journal-title":"Nat. Commun."},{"key":"2026071605453995200_B196","doi-asserted-by":"publisher","first-page":"350.e12","DOI":"10.1016\/j.cell.2017.03.022","article-title":"An approach to spatiotemporally resolve protein interaction networks in living cells","volume":"169","author":"Lobingier","year":"2017","journal-title":"Cell"},{"key":"2026071605453995200_B197","doi-asserted-by":"publisher","first-page":"338.e11","DOI":"10.1016\/j.cell.2017.03.028","article-title":"Multidimensional tracking of GPCR signaling via peroxidase-catalyzed proximity labeling","volume":"169","author":"Paek","year":"2017","journal-title":"Cell"},{"key":"2026071605453995200_B198","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1126\/science.aaz0863","article-title":"The GATOR-Rag GTPase pathway inhibits mTORC1 activation by lysosome-derived amino acids","volume":"370","author":"Hesketh","year":"2020","journal-title":"Science"},{"key":"2026071605453995200_B199","doi-asserted-by":"publisher","first-page":"1133","DOI":"10.1038\/s41589-024-01588-3","article-title":"Profiling the proximal proteome of the activated \u03bc-opioid receptor","volume":"20","author":"Polacco","year":"2024","journal-title":"Nat. Chem. Biol."},{"key":"2026071605453995200_B200","doi-asserted-by":"publisher","first-page":"eadl6164","DOI":"10.1126\/scisignal.adl6164","article-title":"Extracellular proximal interaction profiling by cell surface-targeted TurboID reveals LDLR as a partner of liganded EGFR","volume":"17","author":"Al Mismar","year":"2024","journal-title":"Sci. Signal."},{"key":"2026071605453995200_B201","doi-asserted-by":"publisher","first-page":"1091","DOI":"10.1126\/science.aay4106","article-title":"Microenvironment mapping via Dexter energy transfer on immune cells","volume":"367","author":"Geri","year":"2020","journal-title":"Science"},{"key":"2026071605453995200_B202","doi-asserted-by":"publisher","first-page":"7036","DOI":"10.1038\/s41467-021-27280-x","article-title":"Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks","volume":"12","author":"M\u00fcller","year":"2021","journal-title":"Nat. Commun."},{"key":"2026071605453995200_B203","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1038\/nmeth.4533","article-title":"Biotinylation by antibody recognition-a method for proximity labeling","volume":"15","author":"Bar","year":"2018","journal-title":"Nat. Methods"},{"key":"2026071605453995200_B204","doi-asserted-by":"publisher","first-page":"1295.e21","DOI":"10.1016\/j.cell.2016.07.041","article-title":"Proteomic analysis of unbounded cellular compartments: synaptic clefts","volume":"166","author":"Loh","year":"2016","journal-title":"Cell"},{"key":"2026071605453995200_B205","doi-asserted-by":"publisher","first-page":"373.e15","DOI":"10.1016\/j.cell.2019.12.029","article-title":"Cell-surface proteomic profiling in the fly brain uncovers wiring regulators","volume":"180","author":"Li","year":"2020","journal-title":"Cell"},{"key":"2026071605453995200_B206","doi-asserted-by":"publisher","first-page":"1240","DOI":"10.1074\/mcp.M500089-MCP200","article-title":"Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules","volume":"4","author":"Zhang","year":"2005","journal-title":"Mol. Cell. Proteomics"},{"key":"2026071605453995200_B207","doi-asserted-by":"publisher","first-page":"ra3","DOI":"10.1126\/scisignal.2000475","article-title":"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis","volume":"3","author":"Olsen","year":"2010","journal-title":"Sci. Signal."},{"key":"2026071605453995200_B208","doi-asserted-by":"publisher","first-page":"10762","DOI":"10.1073\/pnas.0805139105","article-title":"A quantitative atlas of mitotic phosphorylation","volume":"105","author":"Dephoure","year":"2008","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2026071605453995200_B209","doi-asserted-by":"publisher","first-page":"438","DOI":"10.1016\/j.molcel.2008.07.007","article-title":"Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle","volume":"31","author":"Daub","year":"2008","journal-title":"Mol. Cell."},{"key":"2026071605453995200_B210","doi-asserted-by":"publisher","first-page":"rs5","DOI":"10.1126\/scisignal.2001497","article-title":"Quantitative phosphoproteomics identifies substrates and functional modules of Aurora and Polo-like kinase activities in mitotic cells","volume":"4","author":"Kettenbach","year":"2011","journal-title":"Sci. Signal."},{"key":"2026071605453995200_B211","doi-asserted-by":"publisher","first-page":"rs4","DOI":"10.1126\/scisignal.2001182","article-title":"Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast","volume":"3","author":"Bodenmiller","year":"2010","journal-title":"Sci. Signal."},{"key":"2026071605453995200_B212","doi-asserted-by":"publisher","first-page":"2796","DOI":"10.1074\/mcp.M900285-MCP200","article-title":"Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics","volume":"8","author":"Pan","year":"2009","journal-title":"Mol. Cell. Proteomics"},{"key":"2026071605453995200_B213","doi-asserted-by":"publisher","first-page":"4888","DOI":"10.1182\/blood-2005-08-3399","article-title":"A common phosphotyrosine signature for the Bcr-Abl kinase","volume":"107","author":"Goss","year":"2006","journal-title":"Blood"},{"key":"2026071605453995200_B214","doi-asserted-by":"publisher","first-page":"1317","DOI":"10.1126\/science.1199498","article-title":"The mTOR-regulated phosphoproteome reveals a mechanism of mTORC1-mediated inhibition of growth factor signaling","volume":"332","author":"Hsu","year":"2011","journal-title":"Science"},{"key":"2026071605453995200_B215","doi-asserted-by":"publisher","first-page":"1322","DOI":"10.1126\/science.1199484","article-title":"Phosphoproteomic analysis identifies Grb10 as an mTORC1 substrate that negatively regulates insulin signaling","volume":"332","author":"Yu","year":"2011","journal-title":"Science"},{"key":"2026071605453995200_B216","doi-asserted-by":"publisher","first-page":"1009","DOI":"10.1016\/j.cmet.2013.04.010","article-title":"Dynamic adipocyte phosphoproteome reveals that Akt directly regulates mTORC2","volume":"17","author":"Humphrey","year":"2013","journal-title":"Cell. Metab."},{"key":"2026071605453995200_B217","doi-asserted-by":"publisher","first-page":"1320","DOI":"10.1126\/science.1228771","article-title":"Quantitative phosphoproteomics reveal mTORC1 activates de novo yrimidine synthesis","volume":"339","author":"Robitaille","year":"2013","journal-title":"Science"},{"key":"2026071605453995200_B218","doi-asserted-by":"publisher","first-page":"1323","DOI":"10.1126\/science.1228792","article-title":"Stimulation of de novo yrimidine synthesis by growth signaling through mTOR and S6K1","volume":"339","author":"Ben-Sahra","year":"2013","journal-title":"Science"},{"key":"2026071605453995200_B219","doi-asserted-by":"publisher","first-page":"e107911","DOI":"10.15252\/embj.2021107911","article-title":"The TOR-dependent phosphoproteome and regulation of cellular protein synthesis","volume":"40","author":"Mak","year":"2021","journal-title":"EMBO J."},{"key":"2026071605453995200_B220","doi-asserted-by":"publisher","first-page":"110149","DOI":"10.1016\/j.celrep.2021.110149","article-title":"Phosphoproteomic responses of TORC1 target kinases reveal discrete and convergent mechanisms that orchestrate the quiescence program in yeast","volume":"37","author":"Dokl\u00e1dal","year":"2021","journal-title":"Cell. Rep."},{"key":"2026071605453995200_B221","doi-asserted-by":"publisher","first-page":"e105985","DOI":"10.15252\/embj.2020105985","article-title":"Phosphoproteomic identification of ULK substrates reveals VPS15-dependent ULK\/VPS34 interplay in the regulation of autophagy","volume":"40","author":"Mercer","year":"2021","journal-title":"EMBO J."},{"key":"2026071605453995200_B222","doi-asserted-by":"publisher","first-page":"e84319","DOI":"10.7554\/eLife.84319","article-title":"Snf1\/AMPK fine-tunes TORC1 signaling in response to glucose starvation","volume":"12","author":"Caligaris","year":"2023","journal-title":"Elife"},{"key":"2026071605453995200_B223","doi-asserted-by":"publisher","first-page":"1879.e6","DOI":"10.1016\/j.molcel.2021.02.037","article-title":"Global phosphoproteomics pinpoints uncharted Gcn2-mediated mechanisms of translational control","volume":"81","author":"Dokl\u00e1dal","year":"2021","journal-title":"Mol. Cell."},{"key":"2026071605453995200_B224","doi-asserted-by":"publisher","first-page":"2784","DOI":"10.1016\/j.celrep.2018.02.038","article-title":"Large-scale phosphoproteomics reveals Shp-2 phosphatase-dependent regulators of Pdgf receptor signaling","volume":"22","author":"Batth","year":"2018","journal-title":"Cell. Rep."},{"key":"2026071605453995200_B225","doi-asserted-by":"publisher","first-page":"e64251","DOI":"10.7554\/eLife.64251","article-title":"Time-resolved phosphoproteomics reveals scaffolding and catalysis-responsive patterns of SHP2-dependent signaling","volume":"10","author":"Vemulapalli","year":"2021","journal-title":"Elife"},{"key":"2026071605453995200_B226","first-page":"424.e7","article-title":"a library of phosphoproteomic and chromatin signatures for characterizing cellular responses to drug perturbations","volume":"6","author":"Litichevskiy","year":"2018","journal-title":"Cell. Syst."},{"key":"2026071605453995200_B227","doi-asserted-by":"publisher","first-page":"2579","DOI":"10.1038\/s41467-025-57537-8","article-title":"High resolution profiling of cell cycle-dependent protein and phosphorylation abundance changes in non-transformed cells","volume":"16","author":"Rega","year":"2025","journal-title":"Nat. Commun."},{"key":"2026071605453995200_B228","doi-asserted-by":"publisher","first-page":"990","DOI":"10.1038\/nbt.3327","article-title":"High-throughput phosphoproteomics reveals in vivo sulin signaling dynamics","volume":"33","author":"Humphrey","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"2026071605453995200_B229","doi-asserted-by":"publisher","first-page":"1364.e6","DOI":"10.1016\/j.cmet.2025.02.007","article-title":"Dietary timing enhances exercise by modulating fat-muscle crosstalk via adipocyte AMPK\u03b12 signaling","volume":"37","author":"Chen","year":"2025","journal-title":"Cell. Metab."},{"key":"2026071605453995200_B230","doi-asserted-by":"publisher","first-page":"118","DOI":"10.1016\/j.cmet.2016.10.004","article-title":"Phosphorylation is a central mechanism for circadian control of metabolism and physiology","volume":"25","author":"Robles","year":"2017","journal-title":"Cell. Metab."},{"key":"2026071605453995200_B231","doi-asserted-by":"publisher","first-page":"1799","DOI":"10.1038\/s41467-024-45751-9","article-title":"A spatial map of hepatic mitochondria uncovers functional heterogeneity shaped by nutrient-sensing signaling","volume":"15","author":"Kang","year":"2024","journal-title":"Nat. Commun."},{"key":"2026071605453995200_B232","doi-asserted-by":"publisher","first-page":"eaao4927","DOI":"10.1126\/science.aao4927","article-title":"In vivo brain GPCR signaling elucidated by phosphoproteomics","volume":"360","author":"Liu","year":"2018","journal-title":"Science"},{"key":"2026071605453995200_B233","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1038\/s41586-018-0218-8","article-title":"Quantitative phosphoproteomic analysis of the molecular substrates of sleep need","volume":"558","author":"Wang","year":"2018","journal-title":"Nature"},{"key":"2026071605453995200_B234","doi-asserted-by":"publisher","first-page":"7113","DOI":"10.1038\/s41467-021-27398-y","article-title":"Spatial-proteomics reveals phospho-signaling dynamics at subcellular resolution","volume":"12","author":"Martinez-Val","year":"2021","journal-title":"Nat. Commun."},{"key":"2026071605453995200_B235","doi-asserted-by":"publisher","first-page":"844.e5","DOI":"10.1016\/j.cmet.2020.08.007","article-title":"A cell-autonomous signature of dysregulated protein phosphorylation underlies muscle insulin resistance in type 2 diabetes","volume":"32","author":"Batista","year":"2020","journal-title":"Cell. Metab."},{"key":"2026071605453995200_B236","doi-asserted-by":"publisher","first-page":"114272","DOI":"10.1016\/j.celrep.2024.114272","article-title":"Decrypting lysine deacetylase inhibitor action and protein modifications by dose-resolved proteomics","volume":"43","author":"Chang","year":"2024","journal-title":"Cell. Rep."},{"key":"2026071605453995200_B237","doi-asserted-by":"publisher","first-page":"e2216479120","DOI":"10.1073\/pnas.2216479120","article-title":"ALK fusion NSCLC oncogenes promote survival and inhibit NK cell responses via expression","volume":"120","author":"Chuang","year":"2023","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2026071605453995200_B238","doi-asserted-by":"publisher","first-page":"1248.e23","DOI":"10.1016\/j.cell.2025.01.024","article-title":"GUK1 activation is a metabolic liability in lung cancer","volume":"188","author":"Schneider","year":"2025","journal-title":"Cell"},{"key":"2026071605453995200_B239","doi-asserted-by":"publisher","first-page":"1547","DOI":"10.1038\/s44320-025-00141-1","article-title":"Phosphoproteomics of osimertinib-tolerant persister cells reveals targetable kinase-substrate signatures","volume":"21","author":"Hsu","year":"2025","journal-title":"Mol. Syst. Biol."},{"key":"2026071605453995200_B240","doi-asserted-by":"publisher","first-page":"576","DOI":"10.1038\/s41587-021-01099-9","article-title":"Personalized phosphoproteomics identifies functional signaling","volume":"40","author":"Needham","year":"2022","journal-title":"Nat. Biotechnol."},{"key":"2026071605453995200_B241","doi-asserted-by":"publisher","first-page":"7016","DOI":"10.1038\/s41467-024-51274-0","article-title":"Fast and deep phosphoproteome analysis with the Orbitrap Astral mass spectrometer","volume":"15","author":"Lancaster","year":"2024","journal-title":"Nat. Commun."},{"key":"2026071605453995200_B242","doi-asserted-by":"publisher","first-page":"100754","DOI":"10.1016\/j.mcpro.2024.100754","article-title":"Systematic optimization of automated phosphopeptide enrichment for high-sensitivity phosphoproteomics","volume":"23","author":"Bortel","year":"2024","journal-title":"Mol. Cell. Proteomics"},{"key":"2026071605453995200_B243","doi-asserted-by":"publisher","first-page":"2006","DOI":"10.1021\/acs.jproteome.4c01040","article-title":"Affinity purification mass spectrometry on the orbitrap-astral mass spectrometer enables high-throughput protein\u2013protein interaction mapping","volume":"24","author":"Serrano","year":"2025","journal-title":"J. Proteome Res."},{"key":"2026071605453995200_B244","doi-asserted-by":"publisher","first-page":"901","DOI":"10.1038\/s41586-025-08584-0","article-title":"Mass-spectrometry-based proteomics: from single cells to clinical applications","volume":"638","author":"Guo","year":"2025","journal-title":"Nature"},{"key":"2026071605453995200_B245","doi-asserted-by":"publisher","first-page":"1008.e7","DOI":"10.1016\/j.molcel.2024.12.023","article-title":"Deciphering functional tumor-immune crosstalk through highly multiplexed imaging and deep visual proteomics","volume":"85","author":"Zheng","year":"2025","journal-title":"Mol. Cell."},{"key":"2026071605453995200_B246","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1038\/s41592-023-02007-6","article-title":"Spatial single-cell mass spectrometry defines zonation of the hepatocyte proteome","volume":"20","author":"Rosenberger","year":"2023","journal-title":"Nat. Methods"},{"key":"2026071605453995200_B247","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1186\/s13059-018-1547-5","article-title":"SCoPE-MS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation","volume":"19","author":"Budnik","year":"2018","journal-title":"Genome Biol."},{"key":"2026071605453995200_B248","doi-asserted-by":"publisher","first-page":"5398","DOI":"10.1038\/s41596-021-00616-z","article-title":"Multiplexed single-cell proteomics using SCoPE2","volume":"16","author":"Petelski","year":"2021","journal-title":"Nat. Protoc."},{"key":"2026071605453995200_B249","doi-asserted-by":"publisher","first-page":"3341","DOI":"10.1038\/s41467-021-23667-y","article-title":"Quantitative single-cell proteomics as a tool to characterize cellular hierarchies","volume":"12","author":"Schoof","year":"2021","journal-title":"Nat. Commun."},{"key":"2026071605453995200_B250","doi-asserted-by":"publisher","first-page":"882","DOI":"10.1038\/s41467-018-03367-w","article-title":"Nanodroplet processing platform for deep and quantitative proteome profiling of 10-100 mammalian cells","volume":"9","author":"Zhu","year":"2018","journal-title":"Nat. Commun."},{"key":"2026071605453995200_B251","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1038\/s41587-022-01389-w","article-title":"Increasing the throughput of sensitive proteomics by plexDIA","volume":"41","author":"Derks","year":"2023","journal-title":"Nat. Biotechnol."},{"key":"2026071605453995200_B252","doi-asserted-by":"publisher","first-page":"e10798","DOI":"10.15252\/msb.202110798","article-title":"Ultra-high sensitivity mass spectrometry quantifies single-cell proteome changes upon perturbation","volume":"18","author":"Brunner","year":"2022","journal-title":"Mol. Syst. Biol."},{"key":"2026071605453995200_B253","doi-asserted-by":"publisher","first-page":"1279","DOI":"10.1038\/s41467-024-45659-4","article-title":"Pick-up single-cell proteomic analysis for quantifying up to 3000 proteins in a mammalian cell","volume":"15","author":"Wang","year":"2024","journal-title":"Nat. Commun."},{"key":"2026071605453995200_B254","doi-asserted-by":"publisher","first-page":"726","DOI":"10.1038\/s41586-024-08225-y","article-title":"Clinical functional proteomics of intercellular signalling in pancreatic cancer","volume":"637","author":"Huang","year":"2025","journal-title":"Nature"},{"key":"2026071605453995200_B255","doi-asserted-by":"publisher","first-page":"5707","DOI":"10.1038\/s41467-024-49651-w","article-title":"Automated single-cell proteomics providing sufficient proteome depth to study complex biology beyond cell type classifications","volume":"15","author":"Ctortecka","year":"2024","journal-title":"Nat. Commun."},{"key":"2026071605453995200_B256","doi-asserted-by":"publisher","first-page":"10100","DOI":"10.1038\/s41467-024-54438-0","article-title":"Multimodal single cell-resolved spatial proteomics reveal pancreatic tumor heterogeneity","volume":"15","author":"Xu","year":"2024","journal-title":"Nat. Commun."},{"key":"2026071605453995200_B257","doi-asserted-by":"publisher","first-page":"5893","DOI":"10.1021\/acs.analchem.5c00661","article-title":"Trends in mass spectrometry-based single-cell proteomics","volume":"97","author":"Sanchez-Avila","year":"2025","journal-title":"Anal. Chem."},{"key":"2026071605453995200_B258","doi-asserted-by":"publisher","first-page":"714","DOI":"10.1038\/s41592-023-01830-1","article-title":"Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics","volume":"20","author":"Huffman","year":"2023","journal-title":"Nat. Methods"},{"key":"2026071605453995200_B259","doi-asserted-by":"publisher","first-page":"1001","DOI":"10.1038\/s41586-024-08061-0","article-title":"Spatial proteomics identifies JAKi as treatment for a lethal skin disease","volume":"635","author":"Nordmann","year":"2024","journal-title":"Nature"},{"key":"2026071605453995200_B260","doi-asserted-by":"publisher","first-page":"484","DOI":"10.1038\/s41586-025-08885-4","article-title":"Deep visual proteomics maps proteotoxicity in a genetic liver disease","volume":"642","author":"Rosenberger","year":"2025","journal-title":"Nature"},{"key":"2026071605453995200_B261","doi-asserted-by":"publisher","first-page":"e202400087","DOI":"10.1002\/pmic.202400087","article-title":"Advancements in global phosphoproteomics profiling: overcoming challenges in sensitivity and quantification","volume":"25","author":"Muneer","year":"2025","journal-title":"Proteomics"},{"key":"2026071605453995200_B262","doi-asserted-by":"publisher","first-page":"100790","DOI":"10.1016\/j.mcpro.2024.100790","article-title":"Fully automated workflow for integrated sample digestion and evotip loading enabling high-throughput clinical proteomics","volume":"23","author":"Kverneland","year":"2024","journal-title":"Mol. Cell. Proteomics"},{"key":"2026071605453995200_B263","doi-asserted-by":"publisher","first-page":"406","DOI":"10.1038\/s41587-024-02218-y","article-title":"Decrypting the molecular basis of cellular drug phenotypes by dose-resolved expression proteomics","volume":"43","author":"Eckert","year":"2025","journal-title":"Nat. Biotechnol."},{"key":"2026071605453995200_B264","doi-asserted-by":"publisher","first-page":"4359","DOI":"10.1021\/acs.jproteome.4c00308","article-title":"Optimized automated workflow for BioID improves reproducibility and identification of protein\u2013protein interactions","volume":"23","author":"Cirri","year":"2024","journal-title":"J. Proteome Res."},{"key":"2026071605453995200_B265","doi-asserted-by":"publisher","first-page":"22116","DOI":"10.1021\/acs.analchem.5c03829","article-title":"A flexible end-to-end automated sample preparation workflow enables standardized and scalable bottom-up proteomics","volume":"97","author":"Sch\u00e4r","year":"2025","journal-title":"Anal. Chem."},{"key":"2026071605453995200_B266","doi-asserted-by":"publisher","first-page":"6685","DOI":"10.1038\/s41467-021-26979-1","article-title":"DeepPhospho accelerates DIA phosphoproteome profiling through in silico library generation","volume":"12","author":"Lou","year":"2021","journal-title":"Nat. Commun."},{"key":"2026071605453995200_B267","doi-asserted-by":"publisher","first-page":"1400","DOI":"10.1074\/mcp.M114.044305","article-title":"Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen-treated three-dimensional liver microtissues","volume":"14","author":"Bruderer","year":"2015","journal-title":"Mol. Cell. Proteomics"},{"key":"2026071605453995200_B268","doi-asserted-by":"publisher","first-page":"787","DOI":"10.1038\/s41467-020-14609-1","article-title":"Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries","volume":"11","author":"Bekker-Jensen","year":"2020","journal-title":"Nat. Commun."},{"key":"2026071605453995200_B269","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1038\/s41592-019-0638-x","article-title":"DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput","volume":"17","author":"Demichev","year":"2020","journal-title":"Nat. Methods"},{"key":"2026071605453995200_B270","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1038\/s41467-022-35740-1","article-title":"Benchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics","volume":"14","author":"Lou","year":"2023","journal-title":"Nat. Commun."},{"key":"2026071605453995200_B271","doi-asserted-by":"publisher","first-page":"100477","DOI":"10.1016\/j.mcpro.2022.100477","article-title":"MSstatsPTM: statistical relative quantification of posttranslational modifications in bottom-up mass spectrometry-based proteomics","volume":"22","author":"Kohler","year":"2023","journal-title":"Mol. Cell. Proteomics"},{"key":"2026071605453995200_B272","doi-asserted-by":"publisher","first-page":"100279","DOI":"10.1016\/j.mcpro.2022.100279","article-title":"Rapid and in-depth coverage of the (phospho-)proteome with deep libraries and optimal window design for dia-PASEF","volume":"21","author":"Skowronek","year":"2022","journal-title":"Mol. Cell. Proteomics"},{"key":"2026071605453995200_B273","doi-asserted-by":"publisher","first-page":"1414","DOI":"10.1021\/acs.jproteome.4c01107","article-title":"Isobaric tagging and data independent acquisition as complementary strategies for proteome profiling on an orbitrap astral mass spectrometer","volume":"24","author":"Liu","year":"2025","journal-title":"J. Proteome Res."},{"key":"2026071605453995200_B274","doi-asserted-by":"publisher","first-page":"e2100245","DOI":"10.1002\/pmic.202100245","article-title":"Optimal analytical strategies for sensitive and quantitative phosphoproteomics using TMT-based multiplexing","volume":"22","author":"Koenig","year":"2022","journal-title":"Proteomics"},{"key":"2026071605453995200_B275","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-025-02791-w","article-title":"AlphaDIA enables DIA transfer learning for feature-free proteomics","author":"Wallmann","year":"2025","journal-title":"Nat. Biotechnol."},{"key":"2026071605453995200_B276","doi-asserted-by":"publisher","first-page":"1387","DOI":"10.1038\/s41592-024-02324-4","article-title":"Beyond protein lists: AI-assisted interpretation of proteomic investigations in the context of evolving scientific knowledge","volume":"21","author":"Gyori","year":"2024","journal-title":"Nat. Methods"},{"key":"2026071605453995200_B277","doi-asserted-by":"publisher","first-page":"100707","DOI":"10.1016\/j.mcpro.2023.100707","article-title":"Deep learning prediction boosts phosphoproteomics-based discoveries through improved phosphopeptide identification","volume":"23","author":"Yi","year":"2024","journal-title":"Mol. Cell. Proteomics"},{"key":"2026071605453995200_B278","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1038\/s41587-019-0344-3","article-title":"The functional landscape of the human phosphoproteome","volume":"38","author":"Ochoa","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"2026071605453995200_B279","doi-asserted-by":"publisher","first-page":"iyad031","DOI":"10.1093\/genetics\/iyad031","article-title":"The Gene Ontology knowledgebase in 2023","volume":"224","author":"Gene Ontology Consortium","year":"2023","journal-title":"Genetics"},{"key":"2026071605453995200_B280","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. The Gene Ontology Consortium","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet."},{"key":"2026071605453995200_B281","doi-asserted-by":"publisher","first-page":"1523","DOI":"10.1038\/s41592-023-02011-w","article-title":"A computational framework for the inference of protein complex remodeling from whole-proteome measurements","volume":"20","author":"Buljan","year":"2023","journal-title":"Nat. Methods"},{"key":"2026071605453995200_B282","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"2026071605453995200_B283","doi-asserted-by":"publisher","first-page":"2464","DOI":"10.1038\/s41467-024-46715-9","article-title":"High-throughput prediction of protein conformational distributions with subsampled AlphaFold2","volume":"15","author":"Monteiro da Silva","year":"2024","journal-title":"Nat. Commun."},{"key":"2026071605453995200_B284","doi-asserted-by":"publisher","first-page":"216","DOI":"10.1038\/s41594-022-00910-8","article-title":"Towards a structurally resolved human protein interaction network","volume":"30","author":"Burke","year":"2023","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2026071605453995200_B285","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","article-title":"Accurate structure prediction of biomolecular interactions with AlphaFold 3","volume":"630","author":"Abramson","year":"2024","journal-title":"Nature"},{"key":"2026071605453995200_B286","article-title":"Protein complex prediction with AlphaFold-Multimer","author":"Evans","year":"2021","journal-title":"bioRxiv"},{"key":"2026071605453995200_B287","doi-asserted-by":"publisher","first-page":"e2406407121","DOI":"10.1073\/pnas.2406407121","article-title":"AlphaFold-multimer accurately captures interactions and dynamics of intrinsically disordered protein regions","volume":"121","author":"Omidi","year":"2024","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2026071605453995200_B288","doi-asserted-by":"publisher","first-page":"9407","DOI":"10.1038\/s41467-025-64116-4","article-title":"Global comparative structural analysis of responses to protein phosphorylation","volume":"16","author":"Correa Marrero","year":"2025","journal-title":"Nat. Commun."},{"key":"2026071605453995200_B289","doi-asserted-by":"publisher","first-page":"e82593","DOI":"10.7554\/eLife.82593","article-title":"Rapid protein stability prediction using deep learning representations","volume":"12","author":"Blaabjerg","year":"2023","journal-title":"Elife"},{"key":"2026071605453995200_B290","doi-asserted-by":"publisher","first-page":"eadg7492","DOI":"10.1126\/science.adg7492","article-title":"Accurate proteome-wide missense variant effect prediction with AlphaMissense","volume":"381","author":"Cheng","year":"2023","journal-title":"Science"},{"key":"2026071605453995200_B291","doi-asserted-by":"publisher","first-page":"4303","DOI":"10.1021\/acs.jproteome.4c00294","article-title":"Analysis and visualization of quantitative proteomics data using FragPipe-Analyst","volume":"23","author":"Hsiao","year":"2024","journal-title":"J. Proteome Res."},{"key":"2026071605453995200_B292","doi-asserted-by":"publisher","first-page":"4154","DOI":"10.1038\/s41467-023-39869-5","article-title":"Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform","volume":"14","author":"Yu","year":"2023","journal-title":"Nat. Commun."},{"key":"2026071605453995200_B293","doi-asserted-by":"publisher","first-page":"513","DOI":"10.1038\/nmeth.4256","article-title":"MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics","volume":"14","author":"Kong","year":"2017","journal-title":"Nat. Methods"},{"key":"2026071605453995200_B294","doi-asserted-by":"publisher","first-page":"645","DOI":"10.1038\/nmeth.4330","article-title":"ProHits-viz: a suite of web tools for visualizing interaction proteomics data","volume":"14","author":"Knight","year":"2017","journal-title":"Nat. Methods"},{"key":"2026071605453995200_B295","doi-asserted-by":"publisher","first-page":"2524","DOI":"10.1093\/bioinformatics\/btu305","article-title":"MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments","volume":"30","author":"Choi","year":"2014","journal-title":"Bioinformatics"},{"key":"2026071605453995200_B296","doi-asserted-by":"publisher","first-page":"1367","DOI":"10.1038\/nbt.1511","article-title":"MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification","volume":"26","author":"Cox","year":"2008","journal-title":"Nat. Biotechnol."},{"key":"2026071605453995200_B297","doi-asserted-by":"publisher","first-page":"2301","DOI":"10.1038\/nprot.2016.136","article-title":"The MaxQuant computational platform for mass spectrometry-based shotgun proteomics","volume":"11","author":"Tyanova","year":"2016","journal-title":"Nat. Protoc."},{"key":"2026071605453995200_B298","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1007\/978-1-4939-7493-1_7","article-title":"Perseus: a bioinformatics platform for integrative analysis of proteomics data in cancer research","volume":"1711","author":"Tyanova","year":"2018","journal-title":"Methods Mol. Biol."},{"key":"2026071605453995200_B299","doi-asserted-by":"publisher","first-page":"731","DOI":"10.1038\/nmeth.3901","article-title":"The Perseus computational platform for comprehensive analysis of (prote)omics data","volume":"13","author":"Tyanova","year":"2016","journal-title":"Nat. Methods"},{"key":"2026071605453995200_B300","doi-asserted-by":"publisher","first-page":"2890","DOI":"10.1021\/acs.jproteome.3c00186","article-title":"Phospho-Analyst: an interactive, easy-to-use web platform to analyze quantitative phosphoproteomics data","volume":"22","author":"Zhang","year":"2023","journal-title":"J. Proteome Res."},{"key":"2026071605453995200_B301","doi-asserted-by":"publisher","first-page":"D609","DOI":"10.1093\/nar\/gkae1010","article-title":"UniProt: the Universal Protein Knowledgebase in 2025","volume":"53","author":"UniProt Consortium","year":"2025","journal-title":"Nucleic. Acids Res."},{"key":"2026071605453995200_B302","doi-asserted-by":"publisher","first-page":"1188","DOI":"10.1091\/mbc.E15-12-0844","article-title":"An improved smaller biotin ligase for BioID proximity labeling","volume":"27","author":"Kim","year":"2016","journal-title":"Mol. Biol. Cell."},{"key":"2026071605453995200_B303","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/nmeth.4601","article-title":"RNA\u2013protein interaction detection in living cells","volume":"15","author":"Ramanathan","year":"2018","journal-title":"Nat. Methods"},{"key":"2026071605453995200_B304","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1038\/417463a","article-title":"The catalytic pathway of horseradish peroxidase at high resolution","volume":"417","author":"Berglund","year":"2002","journal-title":"Nature"}],"container-title":["Bioscience Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/portlandpress.com\/bioscirep\/article-pdf\/doi\/10.1042\/BSR20250116\/990206\/bsr-2025-0116c.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/portlandpress.com\/bioscirep\/article-pdf\/doi\/10.1042\/BSR20250116\/990206\/bsr-2025-0116c.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T09:45:50Z","timestamp":1784195150000},"score":1,"resource":{"primary":{"URL":"https:\/\/portlandpress.com\/bioscirep\/article\/46\/8\/BSR20250116\/237830\/Proteomic-investigation-of-signaling-dynamics-from"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,16]]},"references-count":304,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2026,8,19]]}},"URL":"https:\/\/doi.org\/10.1042\/bsr20250116","relation":{},"ISSN":["0144-8463","1573-4935"],"issn-type":[{"value":"0144-8463","type":"print"},{"value":"1573-4935","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,8]]},"published":{"date-parts":[[2026,7,16]]},"article-number":"BSR20250116"}}