hu.MAP3.0: atlas of human protein complexes by integration of >25,000 proteomic experiments

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• dc.contributor.author Fischer, Samantha
• dc.contributor.author Claussen, Erin R.
• dc.contributor.author Kourtis, Savvas
• dc.contributor.author Sdelci, Sara
• dc.contributor.author Orchard, Sandra
• dc.contributor.author Hermjakob, Henning
• dc.contributor.author Kustatscher, Georg
• dc.contributor.author Drew, Kevin
• dc.date.accessioned 2025-09-09T06:02:08Z
• dc.date.available 2025-09-09T06:02:08Z
• dc.date.issued 2025
• dc.description.abstract Macromolecular protein complexes carry out most cellular functions. Unfortunately, we lack the subunit composition for many human protein complexes. To address this gap we integrated >25,000 mass spectrometry experiments using a machine learning approach to identify >15,000 human protein complexes. We show our map of protein complexes is highly accurate and more comprehensive than previous maps, placing nearly 70% of human proteins into their physical contexts. We globally characterize our complexes using mass spectrometry based protein covariation data (ProteomeHD.2) and identify covarying complexes suggesting common functional associations. hu.MAP3.0 generates testable functional hypotheses for 472 uncharacterized proteins which we support using AlphaFold modeling. Additionally, we use AlphaFold modeling to identify 5871 mutually exclusive proteins in hu.MAP3.0 complexes suggesting complexes serve different functional roles depending on their subunit composition. We identify expression as the primary way cells and organisms relieve the conflict of mutually exclusive subunits. Finally, we import our complexes to EMBL-EBI's Complex Portal ( https://www.ebi.ac.uk/complexportal/home ) and provide complexes through our hu.MAP3.0 web interface ( https://humap3.proteincomplexes.org/ ). We expect our resource to be highly impactful to the broader research community.
• dc.format.mimetype application/pdf
• dc.identifier.citation Fischer SN, Claussen ER, Kourtis S, Sdelci S, Orchard S, Hermjakob H, et al. hu.MAP3.0: atlas of human protein complexes by integration of >25,000 proteomic experiments. Mol Syst Biol. 2025 Jul;21(7):911-43. DOI: 10.1038/s44320-025-00121-5
• dc.identifier.doi http://dx.doi.org/10.1038/s44320-025-00121-5
• dc.identifier.issn 1744-4292
• dc.identifier.uri http://hdl.handle.net/10230/71156
• dc.language.iso eng
• dc.publisher EMBO Press
• dc.relation.ispartof Mol Syst Biol. 2025 Jul;21(7):911-43
• dc.rights © 2025 The Author(s). Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the data associated with this article, unless otherwise stated in a credit line to the data, but does not extend to the graphical or creative elements of illustrations, charts, or figures. This waiver removes legal barriers to the re-use and mining of research data. According to standard scholarly practice, it is recommended to provide appropriate citation and attribution whenever technically possible.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword Disease candidates
• dc.subject.keyword Machine learning
• dc.subject.keyword Mutually exclusive
• dc.subject.keyword Protein complex
• dc.subject.keyword Protein interaction
• dc.title hu.MAP3.0: atlas of human protein complexes by integration of >25,000 proteomic experiments
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion