ProteoAutoNet: high-throughput co-eluted protein analysis with robotics and machine learning

The computational framework ProteoAutoNet, including R and Python scripts and visualized files, is publicly available at: https://github.com/guomics-lab/ProteoAutoNet. The code and example files that were used in this study are publicly available on Zenodo at https://doi.org/10.5281/zenodo.18217457.

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Authors and Affiliations

1. School of Basic Medical Science, Fudan University, Shanghai, China

   Mengge Lyu & Tiannan Guo

2. Affiliated Hangzhou First People’s Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China

   Mengge Lyu, Pingping Hu, Guangmei Zhang, Kunpeng Ma, Xuedong Zhang, Rui Sun, Yi Chen & Tiannan Guo

3. Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China

   Mengge Lyu, Pingping Hu, Guangmei Zhang, Kunpeng Ma, Xuedong Zhang, Rui Sun, Yi Chen & Tiannan Guo

4. Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China

   Mengge Lyu, Pingping Hu, Guangmei Zhang, Kunpeng Ma, Xuedong Zhang, Rui Sun, Yi Chen & Tiannan Guo

5. Westlake Omics Inc., Hangzhou, Zhejiang Province, China

   Pu Liu

6. Institute of Automation, Harbin University of Science and Technology, Harbin, China

   Sai Zhang

7. College of Medical Information and Artificial Intelligence, Shandong First Medical University, Jinan, China

   Xiangqing Li

Contributions

T.G., M.L., Y.C., and R.S. conceived and designed the project. M.L., G.Z. and X.Z. performed the cell culture and harvest. M.L., X.L., and S.Z. set up the robotics-assisted platform. M.L., P.H., and K.M. did fractionation and set the robotic platform of CF-MS. M.L., Y.C., and P.L. analyzed the data. M.L. and R.S. created and designed of the figures. M.L., R.S., and T.G. co-wrote the manuscript. M.L., R.S., and T.G. revised the manuscript. T.G. supported the study. All authors reviewed and edited the manuscript.

Corresponding authors

Correspondence to Rui Sun, Yi Chen or Tiannan Guo.

Competing interests

T. G. is a shareholder of Westlake Omics Inc. P.L. is a staff of Westlake Omics Inc. The remaining authors declare no competing interests.

Peer review information

Nature Communications thanks the anonymous reviewer(s) for their contribution to the peer review of this work. A peer review file is available.

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