孙瑞毕业于中国药科大学药理学专业，获学士、硕士学位(2011-2018)。硕士期间，主要研究方向为阐明肿瘤干细胞和肿瘤发生过程中炎症功能的分子机制。2016-2017年，她作为交换生访问了国家蛋白质科学中心(北京)，并在杨靖博士实验室主要利用化学蛋白质组学技术发现药物靶点。2018年，孙瑞作为博士研究生加入guomics团队，在这期间，主要工作是分析以前列腺癌、乳腺癌、脑胶质瘤和新冠等疾病为主的蛋白质组学研究，发现更准确的预后预测地分子生物标志物以及治疗靶点。在蛋白质组学流程的样本前处理，质谱方法开发和优化，生物信息学分析方面均有创新性贡献。2022年获得博士学位，在西湖智能生物标记物核心实验室作为博士后研究员，主导微扰蛋白质组学技术开发和应用，建立了大规模自动化的细胞微扰平台，采集微扰蛋白质组学数据，建立动态网络模型。2024年以助理研究员身份加入西湖大学蛋白质组复杂科学实验室主要从事AI大数据相关工作。是医学蛋白质组全国重点实验室、一带一路浙江-瑞士临床蛋白质组学联合实验室的主要成员之一。
Oral talks / posters / conferences (International)
1. Oral talk: 2025.10.10-14 CNHUPO rising star (China) title: “ProteinTalks: An AI virtual cell foundation model extended to clinical application.”
2. Oral talk: 2025.11.9-15 HUPO (Canada) title: “ProteinTalks: An AI virtual cell foundation model extended to clinical application.” (Unable to attend due to visa issues)
3. Oral talk: 2023.09.17-22 HUPO (Busan, South Korea) title: “Perturbation proteomics: insights from 16,000 perturbated triple-negative breast cancer proteomes.”
4. Poster: 2019.06.02-06 ASMS (Atlanta, America) “Microflow DIA Using 15min Gradients Analyzes 40 Tumor Proteomes per Day and Effectively Detects Promising Protein Biomarkers.”
Representative Publications
[Note: *, co-corresponding; #, co-first author]
1 Perturbation proteomics
1.1 Rui Sun#, Liujia Qian#, Yongge Li#, Honghan Cheng, Xuedong Zhang, Xueya Zhou, Yuecheng Zhan, Guangmei Zhang, Zhengchao Luo, Kunpeng Ma, Chunlong Wu, Dongchen Ji, Zhangzhi Xue, Hongxue Meng, Yuhang Xiang, Dingwei Lei, Qianhe Zhou, Wenbin Hu, Yuhan Deng, Lingling Tan, Qi Xiao, Zhiwei Liu, Lei Zeng, Liqin Qian, Xuan Zheng, Qiong Hu, Nianzi Luo, Weinan E, Peijie Zhou*, Han Wen*, Yi Zhu*, Tiannan Guo* An operational perturbation proteomics-based virtual cell model. Nature. Online (ProteinTalks modeling)
1.2 Mengge Lyu, Pingping Hu, Pingping Hu, Guangmei Zhang, Kunpeng Ma, Xuedong Zhang, Pu Liu, Sai Zhang, Xiangqing Li, Rui Sun*, Yi Chen*, Tiannan Guo* ProteoAutoNet: high-throughput co-eluted protein analysis with robotics and machine learning. Nature Communications. 2026 Jan 22;17(1):1949. doi: 10.1038/s41467-026-68686-9. PMID: 41571643. (Automated technology-assisted high-throughput proteomics)
1.3 Rui Sun#, Weigang Ge#, Yi Zhu#, Azin Sayad#, Augustin Luna, Mengge Lyu, Shuang Liang, Luis Tobalina, Vinodh N. Rajapakse, Chenhuan Yu, Huanhuan Zhang, Jie Fang, Fang Wu, Hui Xie, Julio Saez-Rodriguez, Huazhong Ying, William C. Reinhold, Chris Sander, Yves Pommier, Benjamin G. Neel*, Ruedi Aebersold*, Tiannan Guo* Proteomic dynamics of breast cancer cell lines identifies potential therapeutic protein targets. Molecular & Cellular Proteomics.2023 Aug; 22(8):100602. doi.org/10.1016/j.mcpro.2023.100602. PMID: 37343696. (Prototype study for ProteinTalks)
1.4 Liujia Qian, Rui Sun, Christ Sandar, Ruedi Aebersold, Peter Bühlmann, Tiannan Guo* Perturbation proteomics in complex biological systems. Cell Genomics. 2024 Nov 13;4(11):100691. doi: 10.1016/j.xgen.2024.100691. PMID: 39488205. (Theoretical basis of ProteinTalks)
1.5 Rui Sun#, Christie Hunter#, Chen Chen, Weigang Ge, Nick Morrice, Shuang Liang, Tiansheng Zhu, Chunhui Yuan, Guan Ruan, Qiushi Zhang, Xue Cai, Xiaoyan Yu, Lirong Chen, Shaozheng Dai, Zhongzhi Luan, Ruedi Aebersold, Yi Zhu*, Tiannan Guo*. Accelerated Protein Biomarker Discovery from FFPE tissue samplesusing Single-shot, Short Gradient Microflow SWATH MS. Journal of Proteome Research. 2020 Jul 2;19(7):2732-2741. doi: 10.1021/acs.jproteome.9b00671. PMID: 32053377. (High-throughput mass spectrometry-based technology)
2 Clinical proteomics studies
2.1 Rui Sun#, Jun A#, Haolan Yu #, Yan Wang#, Miaoxia He#, Lingling Tan, Jili Zhang, Yingrui Wang, Xiaochen Sun, Mengge Lyu, Min Qu, Lingling Huang, Zhenyang Dong, Weigang Ge, Yun Zhang, Honghan Cheng, Xuan Ding, Bo Yang, Jianguo Hou, Chuanliang Xu, Linhui Wang, Yi Zhu, Tiannan Guo*, Xu Gao*, Chenghua Yang*. Proteomic landscape profiling of primary prostate cancer reveals a 16-ptotein panel for prognosis prediction. Cell Reports Medicine. 2024 Aug 20;5(8):101679. doi: 10.1016/j.xcrm.2024.101679. PMID: 39168102.
2.2 Jinsen Zhang#, Rui Sun#, Yingying Lyu#, Chaxian Liu#, Ying Liu, Feng Yuan, Minjie Fu, Peter Jih Cheng Wong, Zunguo Du, Tianming Qiu, Yi Zhang, Dongxiao Zhuang, Zhiyong Qin, Yu Yao, Wei Zhu, Tiannan Guo, Wei Hua#, Hui Yang#, Ying Mao# Proteomic Profiling of Gliomas Unveils Immune and Metabolism-Driven Subtypes with Implications for Anti-Nucleotide Metabolism Therapy. Nature Communications. 2024 Nov 19;15(1):10005. doi: 10.1038/s41467-024-54352-5. PMID: 39562821.
2.3 Rui Sun*#, Lingling Tan#, Xuan Ding, Jun A, Zhangzhi Xue, Xue Cai, Sainan Li, Tiannan Guo* A pathway activity-based proteomic classifier stratifies prostate tumors into two subtypes. Clinical Proteomics. 2023 Nov 11;20(1):50. doi: 10.1186/s12014-023-09441-w. PMID: 37950160.
2.4 Qing Zhong#, Rui Sun#, Adel T. Aref#, Zainab Noor#, Asim Anees#, Yi Zhu, Natasha Lucas, Rebecca C. Poulos, Mengge Lyu, Tiansheng Zhu, Guo-Bo Chen, Yingrui Wang, Xuan Ding, Dorothea Rutishauser, Niels J. Rupp, Jan H. Rueschoff, Cédric Poyet, Thomas Hermanns, Christian Fankhauser, María Rodríguez Martínez, Wenguang Shao, Marija Buljan, Janis Frederick Neumann, Andreas Beyer, Peter G. Hains, Roger R. Reddel, Phillip J. Robinson, Ruedi Aebersold*, Tiannan Guo*, Peter J. Wild*. Proteomic-based stratification of intermediate-risk prostate cancer patients. Life Science Alliance. 2023 Dec 4;7(2):e202302146. doi: 10.26508/lsa.202302146. PMID: 38052461.
2.5 Rui Sun, Mengge Lyu, Shuang Liang, Weigang Ge, Yingrui Wang, Xuan Ding, Cheng Zhang, Yan Zhou, Shanjun Chen, Lirong Chen, Tiannan Guo#. A prostate cancer tissue specific spectral library for targeted proteomic analysis. Proteomics. 2022 Apr;22(7):e2100147. doi: 10.1002/pmic.202100147. Epub 2021 Dec 1. PMID: 34799972.
2.6 Youming Wang#, Rui Sun#, Weigang Ge, Lei Xue, Qianwen Xu, Hui Xu, Sujun Li, Miaomiao Wu, Tiannan Guo*, Xingbing Wang*. Longitudinal Serum Proteomics Characterization of CD19-CAR-T Cell Therapy for B-Cell Malignancies. Journal of Proteome Research. 2023 Sep 1;22(9):2985-94. doi: 10.1021/acs.jproteome.3c00322. PMID: 37531193.
2.7 Shaohua Tang#, Rui Sun#, Weigang Ge#,Tingting Mao#, Liujia Qian#, Chongquan Huang#, Zhouyang Kang#, Qi Xiao, Meng Luo, Qiushi Zhang, Sainan Li, Hao Chen, Wei Liu, Bingjie Wang, Shufei Li, Xiaoling Lin, Xueqin Xu, Huanzheng Li, Lianpeng Wu, Jianyi Dai, Huanhuan Gao, Lu Li, Tian Lu, Xiao Liang, Xue Cai, Guan Ruan, Fei Xu, Yan Li, Yi Zhu*, Ziqing Kong*, Jianping Huang*, Tiannan Guo*. Enhanced inflammation and suppressed adaptive immunity in COVID-19 with prolonged RNA shedding. Cell Discovery. 2022 Jul 25;8(1):70. doi: 10.1038/s41421-022-00441-y. PMID: 35879274.（The first author is the chief clinician.）
2.8 Jianfeng Bao#, Rui Sun#, Jingwen Ai#, Liujia Qian#, Fang Liu#, Hongyu Wang#, Lingling Tan, Xue Cai, Yingqiu Shi, Xiao Liang, Weigang Ge, Jing Wu, Chen Chen, Wenhong Zhang*, Jinsong Huang*, Tiannan Guo*. Proteomic characterization of Omicron SARS-CoV-2 host response. Cell Discovery. 2022 May 18;8(1):46. doi: 10.1038/s41421-022-00418-x. PMID: 35581179.（The first author is the chief clinician.）
2.9 Xiu Nie#, Liujia Qian#, Rui Sun#, Bo Huang#, Xiaochuan Dong#, Qi Xiao#, Qiushi Zhang#, Tian Lu, Liang Yue, Shuo Chen, Xiang Li, Yaoting Sun, Lu Li, Luang Xu, Yan Li, Ming Yang, Zhangzhi Xue, Shuang Liang, Xuan Ding, Chunhui Yuan, Li Peng, Wei Liu, Xiao Yi, Mengge Lyu, Guixiang Xiao, Xia Xu, Weigang Ge, Jiale He, Jun Fan, Junhua Wu, Meng Luo, Xiaona Chang, Huaxiong Pan, Xue Cai, Junjie Zhou, Jing Yu, Huanhuan Gao, Mingxing Xie, Sihua Wang, Guan Ruan, Hao Chen, Hua Su, Heng Mei, Danju Luo, Dashi Zhao, Fei Xu, Yan Li, Yi Zhu*, Jiahong Xia*, Yu Hu*, Tiannan Guo*. Multi-organ proteomic landscape of COVID-19 autopsies. Cell. 2021 Feb 4;184(3): 775-791.e14. doi: 10.1016/j.cell.2021.01.004. PMID: 33503446.（The first author is the chief clinician.）
2.10 Yingrui Wang#, Qianru Zhu#, Rui Sun#, Xiao Yi#, Lingling Huang, Yifan Hu, Weigang Ge, Huanhuan Gao , Xinfu Ye , Yu Song, Li Shao, Yantao Li, Jie Li*, Tiannan Guo*, Junping Shi*. Longitudinal proteomic investigation of COVID-19 vaccination. Protein & Cell. 2023 Sep 14;14(9):668-682. doi: 10.1093/procel/pwad004. PMID: 36930526.
2.11 Xiuqin Zhang#, Dan Li#, Rui Sun#, Xinli Hu#, Zhiqi Song#, Xiaotian Ni, Hua Zhu, Tiannan Guo*, Chuan Qin*, Rui-Ping Xiao*. sRAGE alleviates SARS-CoV-2-induced pneumonia in hamster. Signal Transduction and Targeted Therapy. 2022 Feb 2;7(1):36. doi: 10.1038/s41392-022-00883-6. PMID: 35110523.
3 Chemoproteomics studies
3.1 Rui Sun#, Ling Fu#, Keke Liu, Caiping Tian, Yong Yang, Tallman KA, Porter NA, Liebler DC, Jing Yang*. Chemoproteomics Reveals Chemical Diversity and Dynamics of 4-Oxo-2-nonenal modifications in cells. Molecular cell Proteomics. 2017. 16 (10), 1789-1800. PMID: 28814509.
3.2 Rui Sun#, Fuguo Shi#, Keke Liu, Ling Fu, Caiping Tian, Yong Yang, Tallman KA, Porter NA, Jing Yang*. Chemoproteomic platform to assess bioactivation potential of drugs. Chemical Research in Toxicology. 2017. 30 (10), 1797-1803. PMID: 28960974.
4 Others studies
4.1 Minmin Ma#, Minxia Lu#, Rui Sun#, Zhonghua Zhu#, Dorian Q. Fuller, Jianxin Guo, Guanglin He, Xiaomin Yang, Lingling Tan, Yongxiu Lu, Jiajia Dong, Ruiliang Liu, Jishuai Yang, Bo Li, Tiannan Guo, Xiaorui Li, Dongyue Zhao, Ying Zhang, Chuan-Chao Wang*, Guanghui Dong*. Forager-farmer transition at the crossroads of East and Southeast Asia 4900 years ago. Science Bulletin. 2024 Jan 15;69(1):103-113. doi: 10.1016/j.scib.2023.10.015. Epub 2023 Oct 16. PMID: 37914610.
4.2 Chunguang Guo#, Rui Sun#, Xiao Wang, Ye Yuan, Yan Xv, Shihan Li, Xueting Sun, Yuting Lu, Jue Wang, Xinli Hu, Xiao-Wei Chen, Tiannan Guo*, Rui-Ping Xiao*, Xiuqin Zhang*. Intestinal SURF4 is essential for lipid homeostasis by regulating apolipoprotein trafficking. Molecular Metabolism. 2024 Jan;79:101847. doi: 10.1016/j.molmet.2023.101847. Epub 2023 Nov 30. PMID: 38042368.
Grants
1. National Natural Science Foundation of China (Young Scientist Fund): Graph neural networks solve differential equations for protein network inference of drug combinations and analyze the therapeutic effects of drug perturbations (Grant No. 32401239 to Dr Rui Sun) 2025.01-2027.12
2. Funded by the State Key Laboratory of Medical Proteomics（SKLP-Y202403, to Dr Sun Rui) 2025.01.01-2026.12.31
3. Noncommunicable Chronic Diseases-National Science and Technology Major Project：（Grant No. 2024ZD0533300）5-2028.4
4. National Natural Science Foundation of China (Key Joint Research Program): Systematic identification and functional characterization of understudied proteins in multiple cancers using proteomics (Grant No. U24A20476) 2025.1-2028.12
5. National Natural Science Foundation of China (Major Research Plan): Exploring colorectal cancer and its microenvironment evolution and accurate molecular classification via expansion microscopy and spatial proteomics (Grant No. 92259201) 2023.01-2026.12
6. National Natural Science Foundation of China (General Program): Discovery and Verification of Novel Protein Biomarkers and Drug Targets for Triple Negative Breast Cancers using PCT-SWATH Proteomic Big Data Technology (Grant No. 81972492) 2020.01-2023.12
7. Zhejiang Provincial Natural Science Foundation of China: A sensitization study of EGFR/mTOR/AKT targeted drugs for the treatment of triple-negative breast cancer based on multi-mics network analysis (Grant No. LQ24C050002 to Dr Rui Sun) 2024.01-2026.12
Pants
1. 一种药物组合物及其用于治疗癌症的用途 专利号： ZL 2025 1 0847310.5 授权公告号： CN 120346209 B
2. 一种用于监测CAR-T治疗之后CRS进程的临床标志物及其应用 专利号：ZL 2023 1 0257282.2 授权公告号：CN 116893215 B