AI proteomics: from protein identification to virtual cells – Nature Methods

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Authors and Affiliations

1. Affiliated Hangzhou First People’s Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, School of Future Biomedicine, Westlake University, Hangzhou, China

   Yingying Sun, Jun A, Zhiwei Liu, Rui Sun, Liujia Qian, Yi Chen, Zhen Dong, Huanhuan Gao, Yamin Deng & Tiannan Guo

2. Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China

   Yingying Sun, Jun A, Zhiwei Liu, Rui Sun, Liujia Qian, Yi Chen, Zhen Dong & Tiannan Guo

3. Biology Department, Brigham Young University, Provo, UT, USA

   Samuel H. Payne

4. Department of Computer Science, University of Antwerp, Antwerp, Belgium

   Wout Bittremieux

5. Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany

   Markus Ralser & Vadim Demichev

6. Department of Biochemistry and Molecular Biology, Immunity and Cancer Programs, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia

   Chen Li & Jiangning Song

7. Department of Medicine, School of Clinical Sciences, Monash University, Clayton, Victoria, Australia

   Chen Li

8. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK

   Yasset Perez-Riverol, Juan Antonio Vizcaíno & Henning Hermjakob

9. Harvard Medical School, Ludwig Center at Harvard, Boston, MA, USA

   Asif Khan

10. Harvard Medical School, Broad Institute, Ludwig Center at Harvard, DF/HCC Cancer Center, Boston, MA, USA

    Chris Sander

11. Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland

    Ruedi Aebersold

12. Bruker Ltd., Milton, Ontario, Canada

    Jonathan R. Krieger

13. AI for Life Sciences Lab, Tencent, Shenzhen, China

    Jianhua Yao

14. State Key Laboratory of Medical Proteomics, AI for Science Institute, Beijing, China

    Wen Han & Linfeng Zhang

15. State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing, China

    Yunping Zhu, Cheng Chang, Ping Xu & Fuchu He

16. Thermo Fisher Scientific GmbH, Bremen, Germany

    Yue Xuan

17. Informatics and Predictive Sciences Research, Bristol Myers Squibb, Cambridge, MA, USA

    Benjamin Boyang Sun

18. Department of Chemistry, Fudan University, Shanghai, China

    Liang Qiao

19. Department of Computer Science, Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA

    Haixu Tang

20. ProCan®, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia

    Qing Zhong

21. 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

    Nuno Bandeira

22. Peng Cheng Laboratory, Shenzhen, China

    Ming Li & Yu Wang

23. Bioinformatics Solutions Inc, Waterloo, Ontario, Canada

    Ming Li

24. University of Waterloo, Waterloo, Ontario, Canada

    Ming Li

25. AI for Science Institute, Center for Machine Learning Research, School of Mathematical Sciences, Peking University, Beijing, P. R. China

    Weinan E

26. Research Institute of Intelligent Complex Systems, Fudan University, Shanghai, China

    Siqi Sun

27. School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China

    Yuedong Yang

28. Departments of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics & Genomics, and Environmental Health, University of Michigan, Ann Arbor, MI, USA

    Gilbert S. Omenn

29. Department of Materials Science and Engineering, Westlake University, Hangzhou, China

    Yue Zhang, Jiaxing Huang & Kaicheng Yu

30. State Key Laboratory of Mathematical Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China

    Yan Fu

31. Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, USA

    Xiaowen Liu

32. Department of Oral Biological and Medical Sciences, Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada

    Christopher M. Overall & Peter A. Bell

33. Institute for Systems Biology (ISB), Seattle, WA, USA

    Eric W. Deutsch

34. School of Mathematical Sciences and School of AI, Shanghai Jiao Tong University, Shanghai, China

    Luonan Chen

35. Computational Systems Biochemistry Research Group, Max Planck Institute of Biochemistry, Martinsried, Germany

    Jürgen Cox

36. International Academy of Phronesis Medicine (Guang Dong), Guangzhou International Bio Island, Guangzhou, China

    Fuchu He

37. School of Big Data, Anhui University, Hefei, China

    Huilin Jin

38. School of Biological Science and Medical Engineering & School of Engineering Medicine, Beihang University, Beijing, China

    Chao Liu

39. Westlake University High-Performance Computing Center, Westlake University, Hangzhou, China

    Nan Li

40. School of Computer Science and Engineering, Beihang University, Beijing, China

    Zhongzhi Luan

41. School of Communication and Information Engineering, Institute of Smart City, Shanghai University, Shanghai, China

    Wanggen Wan

42. Bristol Myers Squibb, Cambridge, MA, USA

    Tai Wang

43. Eye Hospital and Institute for Advanced Study on Eye Health and Diseases, Institute for clinical Data Science, Wenzhou Medical University, Wenzhou, China

    Kang Zhang

44. Department of Computer Science, Sichuan University, Chengdu, China

    Le Zhang

45. Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany

    Matthias Mann

46. Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA

    Bing Zhang

Contributions

T.G., B.Z. and M.M. supervised the work. Y.S., J.A., Z.L., R.S., L.Q., S.H.P., Z.D., Y.C. and Y.D. wrote the original draft and created the figures. Y.S., J.A., Z.L., R.S., L.Q., S.H.P., Z.D., Y.C., Y.D., W.B., M.R., C.L., Y.P.-R., A.K., C.S., R.A., J.A.V., J.R.K., J.Y., H.W., L.Z., Y.Z., Y.X., B.B.S., L.Q., H.H., H.T., H.G., Q.Z., C.C., N.B., M.L., W.E., S.S., Y.Y., G.S.O., Y.Z., P.X., Y.F., X.L. and C.M.O., Y.W., E.W.D., L.C., J.C., V. D., F. H., J.H., H.J., C.L., N.L., Z.L., J.S., K.Y., W.W., T.W., K.Z., L.Z. and P.A.B. reviewed the draft and provided feedback on the manuscript.

Corresponding authors

Correspondence to Matthias Mann, Bing Zhang or Tiannan Guo.

Competing interests

T.G. is the founder of Westlake Omics Inc. B.Z. received research funding from AstraZeneca and consulting fees from Inotiv. M.M. is an indirect investor in Evosep. X.L. has a project contract with Bioinformatics Solutions Inc. J.R.K. is an employee of Bruker Ltd. Milton, Canada. Y.X. is an employee of Thermo Fisher Scientific. B.B.S. is currently a full-time employee of Bristol Myers Squibb. V.D. holds shares in Aptila Biotech. M.R. is the founder and shareholder of Eliptica Ltd. C.S. is a scientific advisor for Cytoreason Ltd. The remaining authors declare no competing interests.

Peer review information

Nature Methods thanks the anonymous reviewers for their contribution to the peer review of this work. Primary Handling Editor: Arunima Singh, in collaboration with the Nature Methods team.

Supplementary Table 1 (download XLSX )

The table summarizes software and tools that apply traditional machine learning or deep learning models across the six key areas of MS-based proteomics discussed in the Perspective. It includes their corresponding subsections, modules, publication year, software/outcome name, model, model type, specific tasks, last corresponding author, first author and journal article link.

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

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