rtificial 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.
Publication: NATURE METHODS
http://dx.doi.org/10.1038/s41592-026-03085-y
Author:Yingying Sun, Affiliated Hangzhou First People’s Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, School of Future Biomedicine, Westlake University, Hangzhou, China., Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
Jun A, Affiliated Hangzhou First People’s Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, School of Future Biomedicine, Westlake University, Hangzhou, China.Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
Zhiwei Liu, Affiliated Hangzhou First People’s Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, School of Future Biomedicine, Westlake University, Hangzhou, China. Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
Rui Sun, Affiliated Hangzhou First People’s Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, School of Future Biomedicine, Westlake University, Hangzhou, China.Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
Liujia Qian, Affiliated Hangzhou First People’s Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, School of Future Biomedicine, Westlake University, Hangzhou, China. Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
Samuel H. Payne, Biology Department, Brigham Young University, Provo, UT, USA.
Wout Bittremieux, Department of Computer Science, University of Antwerp, Antwerp, Belgium.
Markus Ralser, Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany.
Chen Li, Department of Biochemistry and Molecular Biology, Immunity and Cancer Programs, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. Department of Medicine, School of Clinical Sciences, Monash University, Clayton, Victoria, Australia.
Yi Chen, Affiliated Hangzhou First People’s Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, School of Future Biomedicine, Westlake University, Hangzhou, China. Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
Zhen Dong, Affiliated Hangzhou First People’s Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, School of Future Biomedicine, Westlake University, Hangzhou, China. Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
Yasset Perez-Riverol, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK.
Asif Khan, Harvard Medical School, Ludwig Center at Harvard, Boston, MA, USA.
Chris Sander, Harvard Medical School, Broad Institute, Ludwig Center at Harvard, DF/HCC Cancer Center, Boston, MA, USA.
Ruedi Aebersold, Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland.
Juan Antonio Vizcaíno, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK.
Jonathan R. Krieger, Bruker Ltd., Milton, Ontario, Canada.
Jianhua Yao, AI for Life Sciences Lab, Tencent, Shenzhen, China.
Wen Han, State Key Laboratory of Medical Proteomics, AI for Science Institute, Beijing, China.
Linfeng Zhang, State Key Laboratory of Medical Proteomics, AI for Science Institute, Beijing, China.
Yunping Zhu, State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing, China.
Yue Xuan, Thermo Fisher Scientific GmbH, Bremen, Germany.
Benjamin Boyang Sun, Informatics and Predictive Sciences Research, Bristol Myers Squibb, Cambridge, MA, USA.
Liang Qiao, Department of Chemistry, Fudan University, Shanghai, China.
Henning Hermjakob, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK.
Haixu Tang, Department of Computer Science, Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA.
Huanhuan Gao, Affiliated Hangzhou First People’s Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, School of Future Biomedicine, Westlake University, Hangzhou, China.
Yamin Deng, Affiliated Hangzhou First People’s Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, School of Future Biomedicine, Westlake University, Hangzhou, China.
Qing Zhong, Children’s Medical Research Institute, The University of Sydney, Westmead, New South Wales, Australia.
Cheng Chang, State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing, China.
Nuno Bandeira, Center 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 Li, Peng Cheng Laboratory, Shenzhen, China. Bioinformatics Solutions Inc, Waterloo, Ontario, Canada.University of Waterloo, Waterloo, Ontario, Canada.
Weinan E, AI for Science Institute, Center for Machine Learning Research, School of Mathematical Sciences, Peking University, Beijing, P. R. China.
Siqi Sun, Research Institute of Intelligent Complex Systems, Fudan University, Shanghai, China.
Yuedong Yang, School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China.
Gilbert S. Omenn, Departments of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics & Genomics, and Environmental Health, University of Michigan, Ann Arbor, MI, USA.
Yue Zhang, Department of Materials Science and Engineering, Westlake University, Hangzhou, China.
Ping Xu, State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing, China.
Yan Fu, State Key Laboratory of Mathematical Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China.
Xiaowen Liu, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, USA.
Christopher M. Overall, Department of Oral Biological and Medical Sciences, Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada.
Yu Wang, Peng Cheng Laboratory, Shenzhen, China.
Eric W. Deutsch, Institute for Systems Biology (ISB), Seattle, WA, USA.
Luonan Chen, School of Mathematical Sciences and School of AI, Shanghai Jiao Tong University, Shanghai, China.
Jürgen Cox, Computational Systems Biochemistry Research Group, Max Planck Institute of Biochemistry, Martinsried, Germany.
Vadim Demichev, Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany.
Fuchu He, State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing, China.International Academy of Phronesis Medicine (Guang Dong), Guangzhou International Bio Island, Guangzhou, China.
Jiaxing Huang, Department of Materials Science and Engineering, Westlake University, Hangzhou, China.
Huilin Jin, School of Big Data, Anhui University, Hefei, China.
Chao Liu, School of Biological Science and Medical Engineering & School of Engineering Medicine, Beihang University, Beijing, China.
Nan Li, Westlake University High-Performance Computing Center, Westlake University, Hangzhou, China.
Zhongzhi Luan, School of Computer Science and Engineering, Beihang University, Beijing, China.
Jiangning Song, Department of Biochemistry and Molecular Biology, Immunity and Cancer Programs, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
Kaicheng Yu, Department of Materials Science and Engineering, Westlake University, Hangzhou, China.
Wanggen Wan, School of Communication and Information Engineering, Institute of Smart City, Shanghai University, Shanghai, China.
Tai Wang, Bristol Myers Squibb, Cambridge, MA, USA.
Kang Zhang, Eye Hospital and Institute for Advanced Study on Eye Health and Diseases, Institute for clinical Data Science, Wenzhou Medical University, Wenzhou, China.
Le Zhang, Department of Computer Science, Sichuan University, Chengdu, China.
Peter A. Bell, Department of Oral Biological and Medical Sciences, Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada.
Matthias Mann, Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
mmann@biochem.mpg.de
Bing Zhang, Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA.
Bing.Zhang@bcm.edu
Tiannan Guo, Affiliated Hangzhou First People’s Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, School of Future Biomedicine, Westlake University, Hangzhou, China.Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
guotiannan@westlake.edu.cn
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