ReviewNature methods2026
AI proteomics: from protein identification to virtual cells.
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Review in Nature methods, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Authors and funding
62 authors.
Yingying SunAffiliated Hangzhou First People's Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, School of Future Biomedicine, Westlake University, Hangzhou, China.
Jun AAffiliated Hangzhou First People's Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, School of Future Biomedicine, Westlake University, Hangzhou, China.
Zhiwei LiuAffiliated Hangzhou First People's Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, School of Future Biomedicine, Westlake University, Hangzhou, China.ORCID http://orcid.org/0009-0002-9353-015X
Rui SunAffiliated Hangzhou First People's Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, School of Future Biomedicine, Westlake University, Hangzhou, China.
Liujia QianAffiliated Hangzhou First People's Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, School of Future Biomedicine, Westlake University, Hangzhou, China.
Samuel H PayneBiology Department, Brigham Young University, Provo, UT, USA.ORCID http://orcid.org/0000-0002-8351-1994
Wout BittremieuxDepartment of Computer Science, University of Antwerp, Antwerp, Belgium.ORCID http://orcid.org/0000-0002-3105-1359
Markus RalserDepartment of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany.ORCID http://orcid.org/0000-0001-9535-7413
Chen LiDepartment of Biochemistry and Molecular Biology, Immunity and Cancer Programs, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.ORCID http://orcid.org/0000-0002-1847-754X
Yi ChenAffiliated Hangzhou First People's Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, School of Future Biomedicine, Westlake University, Hangzhou, China.
Zhen DongAffiliated Hangzhou First People's Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, School of Future Biomedicine, Westlake University, Hangzhou, China.ORCID http://orcid.org/0000-0002-3480-3421
Yasset Perez-RiverolEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID http://orcid.org/0000-0001-6579-6941
Asif KhanHarvard Medical School, Ludwig Center at Harvard, Boston, MA, USA.ORCID http://orcid.org/0000-0003-3179-0140
Chris SanderHarvard Medical School, Broad Institute, Ludwig Center at Harvard, DF/HCC Cancer Center, Boston, MA, USA.
Ruedi AebersoldDepartment of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland.ORCID http://orcid.org/0000-0002-9576-3267
Juan Antonio VizcaínoEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID http://orcid.org/0000-0002-3905-4335
Jonathan R KriegerBruker Ltd., Milton, Ontario, Canada.
Jianhua YaoAI for Life Sciences Lab, Tencent, Shenzhen, China.ORCID http://orcid.org/0000-0001-9157-9596
Wen HanState Key Laboratory of Medical Proteomics, AI for Science Institute, Beijing, China.
Linfeng ZhangState Key Laboratory of Medical Proteomics, AI for Science Institute, Beijing, China.
Yunping ZhuState Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing, China.ORCID http://orcid.org/0000-0002-7320-7411
Yue XuanThermo Fisher Scientific GmbH, Bremen, Germany.ORCID http://orcid.org/0000-0001-9132-2643
Benjamin Boyang SunInformatics and Predictive Sciences Research, Bristol Myers Squibb, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-6347-2281
Liang QiaoDepartment of Chemistry, Fudan University, Shanghai, China.ORCID http://orcid.org/0000-0002-6233-8459
Henning HermjakobEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK.ORCID http://orcid.org/0000-0001-8479-0262
Haixu TangDepartment of Computer Science, Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA.ORCID http://orcid.org/0000-0001-8963-8155
Huanhuan GaoAffiliated Hangzhou First People's Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, School of Future Biomedicine, Westlake University, Hangzhou, China.
Yamin DengAffiliated Hangzhou First People's Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, School of Future Biomedicine, Westlake University, Hangzhou, China.
Qing ZhongProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia.ORCID http://orcid.org/0000-0002-5340-301X
Cheng ChangState Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing, China.ORCID http://orcid.org/0000-0002-0361-2438
Nuno BandeiraCenter for Computational Mass Spectrometry, Dept. Computer Science and Engineering, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego (UCSD), La Jolla, CA, USA.
Ming LiPeng Cheng Laboratory, Shenzhen, China.ORCID http://orcid.org/0000-0002-2157-2775
Weinan EAI for Science Institute, Center for Machine Learning Research, School of Mathematical Sciences, Peking University, Beijing, P. R. China.
Siqi SunResearch Institute of Intelligent Complex Systems, Fudan University, Shanghai, China.ORCID http://orcid.org/0000-0001-7240-8724
Yuedong YangSchool of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China.ORCID http://orcid.org/0000-0002-6782-2813
Gilbert S OmennDepartments of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics & Genomics, and Environmental Health, University of Michigan, Ann Arbor, MI, USA.ORCID http://orcid.org/0000-0002-8976-6074
Yue ZhangDepartment of Materials Science and Engineering, Westlake University, Hangzhou, China.
Ping XuState Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing, China.
Yan FuState Key Laboratory of Mathematical Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China.ORCID http://orcid.org/0000-0001-6896-5931
Xiaowen LiuDeming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, USA.ORCID http://orcid.org/0000-0003-4139-1127
Christopher M OverallDepartment of Oral Biological and Medical Sciences, Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada.ORCID http://orcid.org/0000-0001-5844-2731
Yu WangPeng Cheng Laboratory, Shenzhen, China.ORCID http://orcid.org/0000-0003-4976-9366
Eric W DeutschInstitute for Systems Biology (ISB), Seattle, WA, USA.ORCID http://orcid.org/0000-0001-8732-0928
Luonan ChenSchool of Mathematical Sciences and School of AI, Shanghai Jiao Tong University, Shanghai, China.ORCID http://orcid.org/0000-0002-3960-0068
Jürgen CoxComputational Systems Biochemistry Research Group, Max Planck Institute of Biochemistry, Martinsried, Germany.ORCID http://orcid.org/0000-0001-8597-205X
Vadim DemichevDepartment of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany.ORCID http://orcid.org/0000-0002-2424-9412
Fuchu HeState Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing, China.ORCID http://orcid.org/0000-0002-1094-4019
Jiaxing HuangDepartment of Materials Science and Engineering, Westlake University, Hangzhou, China.ORCID http://orcid.org/0000-0001-9176-8901
Huilin JinSchool of Big Data, Anhui University, Hefei, China.
Chao LiuSchool of Biological Science and Medical Engineering & School of Engineering Medicine, Beihang University, Beijing, China.ORCID http://orcid.org/0000-0002-5286-6944
Nan LiWestlake University High-Performance Computing Center, Westlake University, Hangzhou, China.ORCID http://orcid.org/0000-0001-7826-4688
Zhongzhi LuanSchool of Computer Science and Engineering, Beihang University, Beijing, China.ORCID http://orcid.org/0000-0002-7186-0556
Jiangning SongDepartment of Biochemistry and Molecular Biology, Immunity and Cancer Programs, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.ORCID http://orcid.org/0000-0001-8031-9086
Kaicheng YuDepartment of Materials Science and Engineering, Westlake University, Hangzhou, China.
Wanggen WanSchool of Communication and Information Engineering, Institute of Smart City, Shanghai University, Shanghai, China.
Tai WangBristol Myers Squibb, Cambridge, MA, USA.
Kang ZhangEye Hospital and Institute for Advanced Study on Eye Health and Diseases, Institute for clinical Data Science, Wenzhou Medical University, Wenzhou, China.ORCID http://orcid.org/0000-0002-4549-1697
Le ZhangDepartment of Computer Science, Sichuan University, Chengdu, China.ORCID http://orcid.org/0000-0002-3708-1727
Peter A BellDepartment of Oral Biological and Medical Sciences, Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada.ORCID http://orcid.org/0000-0001-6143-5444
Matthias MannDepartment of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany. mmann@biochem.mpg.de.ORCID http://orcid.org/0000-0003-1292-4799
Bing ZhangLester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA. Bing.Zhang@bcm.edu.ORCID http://orcid.org/0000-0001-8676-2425
Tiannan GuoAffiliated Hangzhou First People's Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, School of Future Biomedicine, Westlake University, Hangzhou, China. guotiannan@westlake.edu.cn.ORCID http://orcid.org/0000-0003-3869-7651
Funding
No grant is acknowledged in the PubMed record.
Abstract
Artificial intelligence (AI) is transforming scientific research, including proteomics. In this Perspective, we highlight key mass spectrometry (MS)-based proteomics areas where AI is driving innovation, ranging from protein identification to building AI virtual cells. These include improving peptide and protein identification and quantification; characterizing protein-protein interactions and protein complexes; advancing spatial and perturbation proteomics; integrating multi-omics data; and, ultimately, enabling AI virtual cells. Finally, we call for global collaboration among data producers, data consumers and other stakeholders to establish an AI-friendly ecosystem for MS-based proteomics, laying the foundation for transformative advancements in proteomics driven by AI.
Indexed as
Artificial IntelligenceProteinsProteomicsAnimalsHumansMass SpectrometryMultiomicsProteins
Identifiers
PMID
42521824What Socratic holds
Textmetadata
Read underepoch 390
Registered trials
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.