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.

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