{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,10]],"date-time":"2026-10-10T08:31:15Z","timestamp":1791621075864,"version":"4.3.4"},"reference-count":34,"publisher":"Elsevier BV","issue":"9","license":[{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,6,25]],"date-time":"2026-06-25T00:00:00Z","timestamp":1782345600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000051","name":"National Human Genome Research Institute","doi-asserted-by":"publisher","award":["NHGRI R21HG011855"],"award-info":[{"award-number":["NHGRI R21HG011855"]}],"id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"NIH National Cancer Institute","doi-asserted-by":"publisher","award":["U54 CA274502"],"award-info":[{"award-number":["U54 CA274502"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000052","name":"NIH Office of the Director","doi-asserted-by":"publisher","award":["OT2 OD032742"],"award-info":[{"award-number":["OT2 OD032742"]}],"id":[{"id":"10.13039\/100000052","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000052","name":"NIH Office of the Director","doi-asserted-by":"publisher","award":["DP2NS131566-01"],"award-info":[{"award-number":["DP2NS131566-01"]}],"id":[{"id":"10.13039\/100000052","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Reports Methods"],"published-print":{"date-parts":[[2026,9]]},"DOI":"10.1016\/j.crmeth.2026.101534","type":"journal-article","created":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T15:16:05Z","timestamp":1784733365000},"page":"101534","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":1,"title":["HIT-MAP: A scalable approach to multimodal mapping of subcellular organization"],"prefix":"10.1016","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5068-0399","authenticated-orcid":false,"given":"Gege","family":"Qian","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joonwon","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richa","family":"Tiwari","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin J.","family":"Polacco","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antoine","family":"Forget","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leah V.","family":"Schaffer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hark Kyun","family":"Kim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiahao","family":"Gao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuan","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gwendolyn M.","family":"Jang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcus R.","family":"Kelly","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoyu","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helene","family":"Foussard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liudeng","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nevan","family":"Krogan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Trey","family":"Ideker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alejandro","family":"Chavez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.crmeth.2026.101534_bib1","doi-asserted-by":"crossref","first-page":"3022","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":"10.1016\/j.crmeth.2026.101534_bib2","doi-asserted-by":"crossref","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":"10.1016\/j.crmeth.2026.101534_bib3","doi-asserted-by":"crossref","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":"10.1016\/j.crmeth.2026.101534_bib4","doi-asserted-by":"crossref","DOI":"10.1126\/science.aal3321","article-title":"A subcellular map of the human proteome","volume":"356","author":"Thul","year":"2017","journal-title":"Science"},{"key":"10.1016\/j.crmeth.2026.101534_bib5","doi-asserted-by":"crossref","first-page":"6501","DOI":"10.1016\/j.cell.2024.10.038","article-title":"Discovery and significance of protein-protein interactions in health and disease","volume":"187","author":"Greenblatt","year":"2024","journal-title":"Cell"},{"key":"10.1016\/j.crmeth.2026.101534_bib6","doi-asserted-by":"crossref","first-page":"8530","DOI":"10.1038\/srep08530","article-title":"Proteins interacting with cloning scars: a source of false positive protein-protein interactions","volume":"5","author":"Banks","year":"2015","journal-title":"Sci. Rep."},{"key":"10.1016\/j.crmeth.2026.101534_bib7","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2302471120","article-title":"Efficient tagging of endogenous proteins in human cell lines for structural studies by single-particle cryo-EM","volume":"120","author":"Choi","year":"2023","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.crmeth.2026.101534_bib8","doi-asserted-by":"crossref","first-page":"794","DOI":"10.1101\/gad.311936.118","article-title":"Live-cell imaging reveals the dynamics of PRC2 and recruitment to chromatin by SUZ12-associated subunits","volume":"32","author":"Youmans","year":"2018","journal-title":"Genes Dev."},{"key":"10.1016\/j.crmeth.2026.101534_bib9","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.35069","article-title":"An efficient and scalable pipeline for epitope tagging in mammalian stem cells using Cas9 ribonucleoprotein","volume":"7","author":"Dewari","year":"2018","journal-title":"eLife"},{"key":"10.1016\/j.crmeth.2026.101534_bib10","doi-asserted-by":"crossref","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":"10.1016\/j.crmeth.2026.101534_bib11","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.adg8771","article-title":"High-throughput tagging of endogenous loci for rapid characterization of protein function","volume":"10","author":"Kim","year":"2024","journal-title":"Sci. Adv."},{"key":"10.1016\/j.crmeth.2026.101534_bib12","doi-asserted-by":"crossref","first-page":"1245","DOI":"10.1038\/s41592-024-02294-7","article-title":"Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images","volume":"21","author":"Wernersson","year":"2024","journal-title":"Nat. Methods"},{"key":"10.1016\/j.crmeth.2026.101534_bib13","doi-asserted-by":"crossref","first-page":"1254","DOI":"10.1038\/s41592-019-0658-6","article-title":"Analysis of the Human Protein Atlas image classification competition","volume":"16","author":"Ouyang","year":"2019","journal-title":"Nat. Methods"},{"key":"10.1016\/j.crmeth.2026.101534_bib14","doi-asserted-by":"crossref","DOI":"10.1126\/science.1260419","article-title":"Tissue-based map of the human proteome","volume":"347","author":"Uhl\u00e9n","year":"2015","journal-title":"Science"},{"key":"10.1016\/j.crmeth.2026.101534_bib15","series-title":"Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining","first-page":"855","article-title":"node2vec: scalable feature learning for networks","author":"Grover","year":"2016"},{"key":"10.1016\/j.crmeth.2026.101534_bib16","doi-asserted-by":"crossref","first-page":"D559","DOI":"10.1093\/nar\/gky973","article-title":"CORUM: the comprehensive resource of mammalian protein complexes\u20142019","volume":"47","author":"Giurgiu","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.crmeth.2026.101534_bib17","doi-asserted-by":"crossref","first-page":"D362","DOI":"10.1093\/nar\/gkw937","article-title":"The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible","volume":"45","author":"Szklarczyk","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.crmeth.2026.101534_bib18","doi-asserted-by":"crossref","DOI":"10.15252\/msb.202010016","article-title":"hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies","volume":"17","author":"Drew","year":"2021","journal-title":"Mol. Syst. Biol."},{"key":"10.1016\/j.crmeth.2026.101534_bib19","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1038\/s41586-025-08878-3","article-title":"Multimodal cell maps as a foundation for structural and functional genomics","volume":"642","author":"Schaffer","year":"2025","journal-title":"Nature"},{"key":"10.1016\/j.crmeth.2026.101534_bib20","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1038\/s41586-021-04115-9","article-title":"A multi-scale map of cell structure fusing protein images and interactions","volume":"600","author":"Qin","year":"2021","journal-title":"Nature"},{"key":"10.1016\/j.crmeth.2026.101534_bib21","article-title":"UMAP: uniform manifold approximation and projection for dimension reduction","author":"McInnes","year":"2018","journal-title":"arXiv"},{"key":"10.1016\/j.crmeth.2026.101534_bib22","doi-asserted-by":"crossref","DOI":"10.15252\/msb.20188438","article-title":"Complex-centric proteome profiling by SEC-SWATH-MS","volume":"15","author":"Heusel","year":"2019","journal-title":"Mol. Syst. Biol."},{"key":"10.1016\/j.crmeth.2026.101534_bib23","article-title":"X-atlas\/Orion: genome-wide Perturb-seq datasets via a scalable Fix-Cryopreserve platform for training dose-dependent biological foundation models","author":"Huang","year":"2025","journal-title":"bioRxiv"},{"key":"10.1016\/j.crmeth.2026.101534_bib24","first-page":"D498","article-title":"The Reactome pathway knowledgebase","volume":"48","author":"Jassal","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.crmeth.2026.101534_bib25","doi-asserted-by":"crossref","first-page":"D650","DOI":"10.1093\/nar\/gkz813","article-title":"Alliance of Genome Resources Portal: unified model organism research platform","volume":"48","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.crmeth.2026.101534_bib26","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1038\/s41556-024-01407-w","article-title":"Pooled multicolour tagging for visualizing subcellular protein dynamics","volume":"26","author":"Reicher","year":"2024","journal-title":"Nat. Cell Biol."},{"key":"10.1016\/j.crmeth.2026.101534_bib27","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.100211","article-title":"Antibody characterization is critical to enhance reproducibility in biomedical research","volume":"13","author":"Kahn","year":"2024","journal-title":"eLife"},{"key":"10.1016\/j.crmeth.2026.101534_bib28","article-title":"Pooled endogenous protein tagging and recruitment for systematic profiling of protein function","volume":"4","author":"Serebrenik","year":"2024","journal-title":"Cell Genom."},{"key":"10.1016\/j.crmeth.2026.101534_bib29","doi-asserted-by":"crossref","first-page":"1868","DOI":"10.1016\/j.molcel.2025.04.002","article-title":"Pooled tagging and hydrophobic targeting of endogenous proteins for unbiased mapping of unfolded protein responses","volume":"85","author":"Sansbury","year":"2025","journal-title":"Mol. Cell"},{"key":"10.1016\/j.crmeth.2026.101534_bib30","doi-asserted-by":"crossref","DOI":"10.1016\/j.jmb.2022.167505","article-title":"The BioImage Archive\u2014building a home for life-sciences microscopy data","volume":"434","author":"Hartley","year":"2022","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.crmeth.2026.101534_bib31","doi-asserted-by":"crossref","first-page":"1466","DOI":"10.1021\/acs.jproteome.2c00834","article-title":"MSstats version 4.0: statistical analyses of quantitative mass spectrometry-based proteomic experiments with chromatography-based quantification at scale","volume":"22","author":"Kohler","year":"2023","journal-title":"J. Proteome Res."},{"key":"10.1016\/j.crmeth.2026.101534_bib32","doi-asserted-by":"crossref","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":"10.1016\/j.crmeth.2026.101534_bib33","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"10.1016\/j.crmeth.2026.101534_bib34","doi-asserted-by":"crossref","first-page":"1295","DOI":"10.1038\/s41587-022-01340-z","article-title":"Integrative spatial analysis of cell morphologies and transcriptional states with MUSE","volume":"40","author":"Bao","year":"2022","journal-title":"Nat. Biotechnol."}],"container-title":["Cell Reports Methods"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2667237526002353?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2667237526002353?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T21:30:32Z","timestamp":1790112632000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2667237526002353"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9]]},"references-count":34,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2026,9]]}},"alternative-id":["S2667237526002353"],"URL":"https:\/\/doi.org\/10.1016\/j.crmeth.2026.101534","relation":{},"ISSN":["2667-2375"],"issn-type":[{"value":"2667-2375","type":"print"}],"subject":[],"published":{"date-parts":[[2026,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"HIT-MAP: A scalable approach to multimodal mapping of subcellular organization","name":"articletitle","label":"Article Title"},{"value":"Cell Reports Methods","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.crmeth.2026.101534","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Authors. Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"101534"}}