Selected publications

1

The pan-cancer proteome atlas, a mass spectrometry-based landscape for discovering tumor biology, biomarkers, and therapeutic targets

Jaco C. Knol#, Mengge Lyu#, Franziska Böttger#, Madalena Nunes Monteiro#, Thang V. Pham, Frank Rolfs, Andrea Vallés-Martí, Tim Schelfhorst, Richard R. de Goeij-de Haas, Irene V. Bijnsdorp, Shuaiyao Wang, Fangfei Zhang, Jun A, Bart A. Westerman, Barbara Sitek, Janne Lehtiö, Jan Koster, Jan N.M. IJzermans, Hanneke W.M. van Laarhoven, Maarten F. Bijlsma, Jan Paul Medema, Alex A. Henneman, Sander R. Piersma, Ruud H. Brakenhoff, Jacqueline Cloos, Valentina Cordo’, Daphne de Jong, Geert Kazemier, Danijela Koppers-Lalic, Mariette Labots, Tessa Y.S. Le Large, John W.M. Martens, Jules P.P. Meijerink, Madiha Mumtaz, Chantal Scheepbouwer, Robby E. Kibbelaar, David P. Noske, Renske D.M. Steenbergen, Nicole C.T. van Grieken, Winan van Houdt, Elisa Giovannetti, Geert J.L.H. van Leenders, Jos Jonkers, Tong Liu, Meisi Yan, Xiaolu Zhan, Tiannan Guo*, Connie R. Jimenez*.

Cancer Cell. 2025 May 29. Epub ahead of print.

2

Proteomic analysis reveals modulation of key proteins in follicular thyroid cancer progression

Xue Cai#, Rui Sun#, Liang Yang#, Nan Yao, Yaoting Sun, Guangmei Zhang, Weigang Ge5, Yan Zhou, Zhiqiang Gui, Yu Wang, Haitao Zheng, Dong Xu, Yongfu Zhao, Xiu Nie, Zhiyan Liu, Hao Zhang, Pingping Hu, Honghan Cheng, Zhangzhi Xue, Jiatong Wang, Jing Yu, Chuang Chen, Dingcun Luo, Jingqiang Zhu, Tong Liu, Yifeng Zhang, Qijun Wu, Qiaonan Guo, Wanyuan Chen, Jianbiao Wang, Wenjun Wei, Xiangfeng Lin, Jincao Yao, Guangzhi Wang, Li Peng, Shuyi Liu, Zhihong Wang, Hanqing Liu, Jiaxi Wang, Fan Wu, Zhennan Yuan, Tingting Gong, Yangfan Lv, Jingjing Xiang, Yi Zhu, Lei Xie21, Minghua Ge, Haixia Guan, Tiannan Guo*; We-TEC Investigators.

Chinese Medical Journal. 2025 May 21. doi: 10.1097/CM9.0000000000003645. Epub ahead of print. PMID: 40394764.

5

Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence

Yingying Sun, Jun A, Zhiwei Liu, Rui Sun, Liujia Qian, Samuel H. Payne, Wout Bittremieux, Markus Ralser, Chen Li, Yi Chen, Zhen Dong, Yasset Perez-Riverol, Asif Khan, Chris Sander, Ruedi Aebersold, Juan Antonio Vizcaíno, Jonathan R Krieger, Jianhua Yao, Han Wen, Linfeng Zhang, Yunping Zhu, Yue Xuan, Benjamin Boyang Sun, Liang Qiao, Henning Hermjakob, Haixu Tang, Huanhuan Gao, Yamin Deng, Qing Zhong, Cheng Chang, Nuno Bandeira, Ming Li, Weinan E, Siqi Sun, Yuedong Yang, Gilbert S. Omenn, Yue Zhang, Ping Xu, Yan Fu, Xiaowen Liu, Christopher M. Overall, Yu Wang, Eric W. Deutsch, Luonan Chen, Jürgen Cox, Vadim Demichev, Fuchu He, Jiaxing Huang, Huilin Jin, Chao Liu, Nan Li, Zhongzhi Luan, Jiangning Song, Kaicheng Yu, Wanggen Wan, Tai Wang, Kang Zhang, Le Zhang, Peter A. Bell, Matthias Mann*, Bing Zhang*, Tiannan Guo*.

arXiv preprint. 21 Feb 2025. https://doi.org/10.48550/arXiv.2502.15867

6

Spatial distribution of the proteome in human body and cancers

Liang Yue#, Wenhao Jiang#, Sainan Li#, Meng Luo#, Ning Fan, Xiaolu Zhan, Kexin Chen, Tian Lu, Fang Guo, Dongwei Li, Weigang Ge, Zongxiang Nie, Mengge Lyu, Jun A, Yingrui Wang, Yingdan Chen, Zhenhai Fu, Nan Xiang, Lu Li, Fengchao Yu, Guo Ci Teo, Alexy I Nesvizhskii, Meng Wang, Michael P. Snyder, Ben Collins, Ruedi Aebersold, Fei Xu, Yi Zhu*, Tong Liu*, Yan Li*, Tiannan Guo*.

bioRxiv preprint. 18 Feb, 2025. https://doi.org/10.1101/2025.02.14.638212

10

iDIA-QC: AI-empowered data-independent acquisition mass spectrometry-based quality control.

Huanhuan Gao#, Yi Zhu#*, Dongxue Wang#, Zongxiang Nie#, He Wang#, Guibin Wang, Shuang Liang, Yuting Xie, Yingying Sun, Wenhao Jiang, Zhen Dong, Liqin Qian, Xufei Wang, Mengdi Liang, Min Chen, Houqi Fang, Qiufang Zeng, Jiao Tian, Zeyu Sun, Juan Xue, Shan Li, Chen Chen, Xiang Liu, Xiaolei Lyu, Zhenchang Guo, Yingzi Qi, Ruoyu Wu, Xiaoxian Du, Tingde Tong, Fengchun Kong, Liming Han, Minghui Wang, Yang Zhao, Xinhua Dai, Fuchu He#, Tiannan Guo#

Nature Communications 16, 892 (2025). https://doi.org/10.1038/s41467-024-54871-1.

15

Artificial intelligence defines protein-based classification of thyroid nodules

Yaoting Sun#, Sathiyamoorthy Selvarajan#, Zelin Zang#, Wei Liu#, Yi Zhu#, Hao Zhang#, Wanyuan Chen, Hao Chen, Lu Li, Xue Cai, Huanhuan Gao, Zhicheng Wu, Yongfu Zhao, Lirong Chen, Xiaodong Teng, Sangeeta Mantoo, Tony Kiat-Hon Lim, Bhuvaneswari Hariraman, Serene Yeow, Syed Muhammad Fahmy bin Syed Abdillah, Sze Sing Lee, Guan Ruan, Qiushi Zhang, Tiansheng Zhu, Yifan Hu, Zhen Dong, Weigang Ge, Qi Xiao, Weibin Wang, Guangzhi Wang, Junhong Xiao, Yi He, Zhihong Wang, Wei Sun, Yuan Qin, Jiang Zhu, Xu Zheng, Linyan Wang, Xi Zheng, Kailun Xu, Yingkuan Shao, Shu Zheng, Kexin Liu, Ruedi Aebersold, Haixia Guan, Xiaohong Wu, Dingcun Luo, Wen Tian, Stan Z. Li*, Oi Lian Kon*, N. Gopalakrishna Iyer*, Tiannan Guo*.

Cell Discovery. 2022 Sep 6;8(1):85. doi: 10.1038/s41421-022-00442-x. Erratum in: Cell Discov. 2022 Sep 30;8(1):100. PMID: 36068205.

18

Multi-organ Proteomic Landscape of COVID-19 Autopsies

Xiu Nie#, Liujia Qian#, Rui Sun#, Bo Huang#, Xiaochuan Dong#, Qi Xiao#, Qiushi Zhang#, Tian Lu, Liang Yue, Shuo Chen, Xiang Li, Yaoting Sun, Li Lu, Luang Xu, Li Yan, 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*.

Cell. 2021 Feb.184(3): 775-791.e14. doi: 10.1016/j.cell.2021.01.004. PMID: 33503446.

19

Proteomic and Metabolomic Characterization of COVID-19 Patient Sera

Bo Shen #, Xiao Yi #, Yaoting Sun #, Xiaojie Bi #, Juping Du #, Chao Zhang #, Sheng Quan #, Fangfei Zhang, Rui Sun, Liujia Qian, Weigang Ge, Wei Liu, Shuang Liang, Hao Chen, Ying Zhang, Jun Li, Jiaqin Xu, Zebao He, Baofu Chen, Jing Wang, Haixi Yan, Yufen Zheng, Donglian Wang, Jiansheng Zhu, Ziqing Kong, Zhouyang Kang, Xiao Liang, Xuan Ding, Guan Ruan, Nan Xiang, Xue Cai, Huanhuan Gao, Lu Li, Sainan Li, Qi Xiao, Tian Lu, Yi Zhu*, Huafen Liu*, Haixiao Chen*, Tiannan Guo*.

Cell. 2020 Jul 9;182(1):59-72.e15. doi: 10.1016/j.cell.2020.05.032. PMID: 32492406.

20

High-throughput Proteomic analysis of FFPE tissue samples facilitates tumor stratification

Yi Zhu#, Tobias Weiss#, Qiushi Zhang, Rui Sun, Bo Wang, Xiao Yi, Zhicheng Wu, Huanhuan Gao, Xue Cai, Guan Ruan, Tiansheng Zhu, Chao Xu, Sai Lou, Xiaoyan Yu, Ludovic Gillet, Peter Blattmann, Karim Saba, Christian D. Fankhauser, Michael B. Schmid, Dorothea Rutishauser, Jelena Ljubicic, Ailsa Christiansen, Christine Fritz, Niels J. Rupp, Cedric Poyet, Elisabeth Rushing, Michael Weller, Patrick Roth, Eugenia Haralambieva, Silvia Hofer, Chen Chen, Wolfram Jochum, Xiaofei Gao, Lirong Chen, Qing Zhong, Peter J. Wild*, Ruedi Aebersold*, Tiannan Guo*.

Molecular Oncology. 2019 Sep;13(11): 2305-2328. doi: 10.1002/1878-0261.12570. PMID: 31495056.

21

Rapid mass spectrometric conversion of tissue biopsy samples into permanent quantitative digital proteome maps

Tiannan Guo#, Petri Kouvonen, Ching Chiek Koh, Ludovic C Gillet, Witold E Wolski, Hannes L Röst, George Rosenberger, Ben C Collins, Lorenz C Blum, Silke Gillessen, Markus Joerger, Wolfram Jochum, Ruedi Aebersold*.

Nature Medicine. 2015 Apr;21(4):407-13. doi: 10.1038/nm.3807. PMID: 25730263.

All publications

175

A protein-based classifier for differentiating follicular thyroid adenoma and carcinoma

Sun Y#, Wang H#, Li L#, Wang J, Chen W, Peng L, Hu P, Yu J, Cai X, Yao N, Zhou Y, Wang J, Wang Y, Qian L, Ge W, Chen M, Yang F, Gui Z, Sun W, Wang Z, Ge M, He Y, Wang G, Zhao Y, Chen H, Wu X, Du Y, Wei W, Wu F, Luo D, Lin X, Zheng H, Zhu X, Wei B, Shen J, Yao J, Yuan Z, Liu T, Pan J, Zhang Y, Lv Y, Guo Q, Wu Q, Gong T, Chen T, Zheng S, Zhu J, Liu H, Chen C, Han H, Selvarajan S, Xing MM, Kakudo K, Alexander EK, Wu Y, Wang Y, Xu D, Zhang H, Nie X, Kon OL, Iyer NG, Liu Z, Zhu Y*, Guan H*, Guo T*; We-TEC Investigators.

EMBO Molecular Medicine. 2025 May 29. doi: 10.1038/s44321-025-00242-2. Epub ahead of print. PMID: 40442320.

174

The pan-cancer proteome atlas, a mass spectrometry-based landscape for discovering tumor biology, biomarkers, and therapeutic targets

Jaco C. Knol#, Mengge Lyu#, Franziska Böttger#, Madalena Nunes Monteiro#, Thang V. Pham, Frank Rolfs, Andrea Vallés-Martí, Tim Schelfhorst, Richard R. de Goeij-de Haas, Irene V. Bijnsdorp, Shuaiyao Wang, Fangfei Zhang, Jun A, Bart A. Westerman, Barbara Sitek, Janne Lehtiö, Jan Koster, Jan N.M. IJzermans, Hanneke W.M. van Laarhoven, Maarten F. Bijlsma, Jan Paul Medema, Alex A. Henneman, Sander R. Piersma, Ruud H. Brakenhoff, Jacqueline Cloos, Valentina Cordo’, Daphne de Jong, Geert Kazemier, Danijela Koppers-Lalic, Mariette Labots, Tessa Y.S. Le Large, John W.M. Martens, Jules P.P. Meijerink, Madiha Mumtaz, Chantal Scheepbouwer, Robby E. Kibbelaar, David P. Noske, Renske D.M. Steenbergen, Nicole C.T. van Grieken, Winan van Houdt, Elisa Giovannetti, Geert J.L.H. van Leenders, Jos Jonkers, Tong Liu, Meisi Yan, Xiaolu Zhan, Tiannan Guo*, Connie R. Jimenez*.

Cancer Cell. 2025 May 29. Epub ahead of print.

173

Proteomic analysis reveals modulation of key proteins in follicular thyroid cancer progression

Xue Cai#, Rui Sun#, Liang Yang#, Nan Yao, Yaoting Sun, Guangmei Zhang, Weigang Ge5, Yan Zhou, Zhiqiang Gui, Yu Wang, Haitao Zheng, Dong Xu, Yongfu Zhao, Xiu Nie, Zhiyan Liu, Hao Zhang, Pingping Hu, Honghan Cheng, Zhangzhi Xue, Jiatong Wang, Jing Yu, Chuang Chen, Dingcun Luo, Jingqiang Zhu, Tong Liu, Yifeng Zhang, Qijun Wu, Qiaonan Guo, Wanyuan Chen, Jianbiao Wang, Wenjun Wei, Xiangfeng Lin, Jincao Yao, Guangzhi Wang, Li Peng, Shuyi Liu, Zhihong Wang, Hanqing Liu, Jiaxi Wang, Fan Wu, Zhennan Yuan, Tingting Gong, Yangfan Lv, Jingjing Xiang, Yi Zhu, Lei Xie21, Minghua Ge, Haixia Guan, Tiannan Guo*; We-TEC Investigators.

Chinese Medical Journal. 2025 May 21. doi: 10.1097/CM9.0000000000003645. Epub ahead of print. PMID: 40394764.

172

Systematic evaluation of blood contamination in nanoparticle-based plasma proteomics

Huanhuan Gao#, Yuecheng Zhan#, Yuanqi Liu#, Zhiyi Zhu, Yuxiu Zheng, Liqin Qian, Zhangzhi Xue, Honghan Cheng, Zongxiang Nie, Weigang Ge, Senlin Ruan, Jiaxu Liu, Jikai Zhang, Yingying Sun, Lei Zhou, Dongyue Xun, Yingrui Wang, Heyun Xu*, Huiwen Miao*, Yi Zhu*, Tiannan Guo*.

bioRxiv preprint. 26 Apr, 2025. https://www.biorxiv.org/content/10.1101/2025.04.26.650757v1

170

Proteomic profiling in cerebrospinal fluid reveal biomarkers for shunt outcome in idiopathic normal-pressure hydrocephalus

Yuqi Ying#, Jingquan Lin#, Wei Gao#, Liang Yue#, Qingze Zeng, Katrina Bartas, Dayeon Cheong, Hongjie Jiang, Zhe Zheng, Ligen Shi, An Ping, Yuanjian Fang, Feng Yan, Tiannan Guo, Jianmin Zhang*, Hemmings Wu*, Kevin Beier*, Junming Zhu*, Zhoule Zhu*.

Journal of Advanced Research. 2025 Apr 29:S2090-1232(25)00287-5. doi: 10.1016/j.jare.2025.04.043. Epub ahead of print. PMID: 40311753.

169

Integrative proteogenomic characterization reveals therapeutic targets in poorly differentiated and anaplastic thyroid cancers

Zongfu Pan#, Zhuo Tan#, Ning Xu#, Zhenmei Yao#, Chuanming Zheng, Jinbiao Shang, Lei Xie, Jiajie Xu, Jiafeng Wang, Liehao Jiang, Xuhang Zhu, Dingyi Yu, Ying Li, Yulu Che, Yingying Gong, Zhaoyu Qin, Yiwen Zhang, Xiaozhou Zou, Tong Xu, Zhenying Guo, Tiefeng Jin, Tiannan Guo, Wei Wang, Wanyuan Chen, Yaoting Sun,  Weixin Wang, Xiaojun Peng, Changtian Yin, Chen Ding*, Ping Huang*, Minghua Ge*.

Nature Communications. 2025 Apr 16;16(1):3601. doi: 10.1038/s41467-025-58910-3. PMID: 40234451; PMCID: PMC12000556.

168

The dual-targeted transcription factor BAI1 orchestrates nuclear and plastid gene transcription in land plants

Jing Qin#, Yelin Shan#, Hao Liu, Zhangzhi Xue, Yike Xie, Guoxin Yuan, Yiming Zou, Xiaonuan Hao, Yunpeng Zhu, Xuan Shen, Meng Li, Xu Wang, Puyuan Liu, Jinxiu Xu, Yuhua Wang, Peng Zhao, Yuan Chen, Yi Zhu, Min Xu, Ming Yue, Aigen Fu*, Weiguo Zhang*, Beibei Li*.

Molecular Plant. 2025 Mar 31:S1674-2052(25)00108-X. doi: 10.1016/j.molp.2025.03.018. Epub ahead of print. PMID: 40170352.

166

Spatial single-cell proteomics landscape decodes the tumor microenvironmental ecosystem of intrahepatic cholangiocarcinoma

Libing Hong#, Jie Mei#, Xuqi Sun#, Yifan Wu#, Zhen Dong#, Yuzhi Jin, Liaoliao Gao, Jinlin Cheng, Weihong Tian, Chuan Liu, Bin Li, Pingping Hu, Lulu Liu, Shan Xin, Xiaomeng Dai, Peng Zhao, Rongping Guo, Minshan Chen, Jingping Yun, Bo Lin*, Wei Wei*, Weijia Fang*, Xuanwen Bao*.

Hepatology. 2025 Feb 25. doi: 10.1097/HEP.0000000000001283. Epub ahead of print. PMID: 39999448.

163

Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence

Yingying Sun, Jun A, Zhiwei Liu, Rui Sun, Liujia Qian, Samuel H. Payne, Wout Bittremieux, Markus Ralser, Chen Li, Yi Chen, Zhen Dong, Yasset Perez-Riverol, Asif Khan, Chris Sander, Ruedi Aebersold, Juan Antonio Vizcaíno, Jonathan R Krieger, Jianhua Yao, Han Wen, Linfeng Zhang, Yunping Zhu, Yue Xuan, Benjamin Boyang Sun, Liang Qiao, Henning Hermjakob, Haixu Tang, Huanhuan Gao, Yamin Deng, Qing Zhong, Cheng Chang, Nuno Bandeira, Ming Li, Weinan E, Siqi Sun, Yuedong Yang, Gilbert S. Omenn, Yue Zhang, Ping Xu, Yan Fu, Xiaowen Liu, Christopher M. Overall, Yu Wang, Eric W. Deutsch, Luonan Chen, Jürgen Cox, Vadim Demichev, Fuchu He, Jiaxing Huang, Huilin Jin, Chao Liu, Nan Li, Zhongzhi Luan, Jiangning Song, Kaicheng Yu, Wanggen Wan, Tai Wang, Kang Zhang, Le Zhang, Peter A. Bell, Matthias Mann*, Bing Zhang*, Tiannan Guo*.

arXiv preprint. 21 Feb 2025. https://doi.org/10.48550/arXiv.2502.15867

162

Spatial distribution of the proteome in human body and cancers

Liang Yue#, Wenhao Jiang#, Sainan Li#, Meng Luo#, Ning Fan, Xiaolu Zhan, Kexin Chen, Tian Lu, Fang Guo, Dongwei Li, Weigang Ge, Zongxiang Nie, Mengge Lyu, Jun A, Yingrui Wang, Yingdan Chen, Zhenhai Fu, Nan Xiang, Lu Li, Fengchao Yu, Guo Ci Teo, Alexy I Nesvizhskii, Meng Wang, Michael P. Snyder, Ben Collins, Ruedi Aebersold, Fei Xu, Yi Zhu*, Tong Liu*, Yan Li*, Tiannan Guo*.

bioRxiv preprint. 18 Feb, 2025. https://doi.org/10.1101/2025.02.14.638212

158

Hemithyroidectomy Versus Total Thyroidectomy for Sporadic Medullary Thyroid Cancer: A Chinese Nationwide Large-Scale Cohort Study

Xiao Shi#, Cenkai Shen#, Chuqiao Liu#, Likun Zhang#, Yuxin Du#, Hao Zhang, Hongwei Liu, Jianbiao Wang, Chuang Chen, Yijun Wu, Chunyan Zhang, Zimeng Li, Haitao Tang, Min Yin, Xiaoqi Mao, Shuyi Liu, Yaoting Sun, Yan Zhou, Wenjun Wei, Naisi Huang, Zhihong Wang, Zhiqiang Gui, Hanqing Liu, Jiaxi Wang, Jian Li, Cuiwei Li, Shiyu Xiang, Liang Guo, Yan Zhang, Yi He, Tiannan Guo*, Qinghai Ji*, Zhiyan Liu*, Yu Wang*.

Journal of the National Comprehensive Cancer Network. 2025 Feb 6:1-8. doi: 10.6004/jnccn.2024.7088. Epub ahead of print. PMID: 39919373.

157

iDIA-QC: AI-empowered data-independent acquisition mass spectrometry-based quality control.

Huanhuan Gao#, Yi Zhu#*, Dongxue Wang#, Zongxiang Nie#, He Wang#, Guibin Wang, Shuang Liang, Yuting Xie, Yingying Sun, Wenhao Jiang, Zhen Dong, Liqin Qian, Xufei Wang, Mengdi Liang, Min Chen, Houqi Fang, Qiufang Zeng, Jiao Tian, Zeyu Sun, Juan Xue, Shan Li, Chen Chen, Xiang Liu, Xiaolei Lyu, Zhenchang Guo, Yingzi Qi, Ruoyu Wu, Xiaoxian Du, Tingde Tong, Fengchun Kong, Liming Han, Minghui Wang, Yang Zhao, Xinhua Dai, Fuchu He#, Tiannan Guo#

Nature Communications 16, 892 (2025). https://doi.org/10.1038/s41467-024-54871-1.

156

Longitudinal serum proteome mapping reveals biomarkers for healthy ageing and related cardiometabolic diseases

Jun Tang#, Liang Yue#, Ying Xu#, Fengzhe Xu#, Xue Cai, Yuanqing Fu, Zelei Miao, Wanglong Gou, Wei Hu, Zhangzhi Xue, Kui Deng, Luqi Shen, Zengliang Jiang, Menglei Shuai, Xinxiu Liang, Congmei Xiao, Yuting Xie, Tiannan Guo*, Yu-ming Chen* & Ju-Sheng Zheng*.

Nature Metabolism (2025). https://doi.org/10.1038/s42255-024-01185-7.

155

Comprehensive Mass Spectral Libraries of Human Thyroid Tissues and Cells

Lu Li#, Wenhao Jiang#, Wenjun Wei, Gnana P Krishnamoorthy, Pingping Hu, Mengni Chen, Vera Tiedje, Adrián Acuña-Ruiz, He Wang, Zhihong Wang, Jianbiao Wang, Hanqing Liu, Wanyuan Chen, Haixia Guan, Chuang Chen, Hao Zhang, Yu Wang, James A Fagin, Tiannan Guo, Yi Zhu, Yingrui Wang*, Jianqing Gao*, Yaoting Sun*.

Scientific Data. 2024 Dec 28;11(1):1448. doi: 10.1038/s41597-024-04322-9. PMID: 39732735; PMCID: PMC11682198.

153

π-HuB: the proteomic navigator of the human body.

Fuchu He, Ruedi Aebersold, Mark S Baker, Xiuwu Bian, Xiaochen Bo, Daniel W Chan, Cheng Chang, Luonan Chen, Xiangmei Chen, Yu-Ju Chen, Heping Cheng, Ben C Collins, Fernando Corrales, Jürgen Cox, Weinan E, Jennifer E Van Eyk, Jia Fan, Pouya Faridi, Daniel Figeys, George Fu Gao, Wen Gao, Zu-Hua Gao, Keisuke Goda, Wilson Wen Bin Goh, Dongfeng Gu, Changjiang Guo, Tiannan Guo, Yuezhong He, Albert J R Heck, Henning Hermjakob, Tony Hunter, Narayanan Gopalakrishna Iyer, Ying Jiang, Connie R Jimenez, Lokesh Joshi, Neil L Kelleher, Ming Li, Yang Li, Qingsong Lin, Cui Hua Liu, Fan Liu, Guang-Hui Liu, Yansheng Liu, Zhihua Liu, Teck Yew Low, Ben Lu, Matthias Mann, Anming Meng, Robert L Moritz, Edouard Nice, Guang Ning, Gilbert S Omenn, Christopher M Overall, Giuseppe Palmisano, Yaojin Peng, Charles Pineau, Terence Chuen Wai Poon, Anthony W Purcell, Jie Qiao, Roger R Reddel, Phillip J Robinson, Paola Roncada, Chris Sander, Jiahao Sha, Erwei Song, Sanjeeva Srivastava, Aihua Sun, Siu Kwan Sze, Chao Tang, Liujun Tang, Ruijun Tian, Juan Antonio Vizcaíno, Chanjuan Wang, Chen Wang, Xiaowen Wang, Xinxing Wang, Yan Wang, Tobias Weiss, Mathias Wilhelm, Robert Winkler, Bernd Wollscheid, Limsoon Wong, Linhai Xie, Wei Xie, Tao Xu, Tianhao Xu, Liying Yan, Jing Yang, Xiao Yang, John Yates, Tao Yun, Qiwei Zhai, Bing Zhang, Hui Zhang, Lihua Zhang, Lingqiang Zhang, Pingwen Zhang, Yukui Zhang, Yu Zi Zheng, Qing Zhong, Yunping Zhu & π-HuB Consortium.

Nature. 2024 Dec;636(8042):322-331. doi: 10.1038/s41586-024-08280-5. Epub 2024 Dec 11. Erratum in: Nature. 2024 Dec 23. doi: 10.1038/s41586-024-08555-x. PMID: 39663494.

152

Association of the EAT-Lancet diet, serial measures of serum proteome and gut microbiome, and cardiometabolic health: a prospective study of Chinese middle-aged and elderly adults

Kui Deng#, Luqi Shen#, Zhangzhi Xue#, Bang-yan Li#, Jun Tang, Hui Zhao, Fengzhe Xu, Zelei Miao, Xue Cai, Wei Hu, Yuanqing Fu, Zengliang Jiang, Xinxiu Liang, Congmei Xiao, Menglei Shuai, Wanglong Gou, Liang Yue, Yuting Xie, Ting-yu Sun, Tiannan Guo, Yu-ming Chen*, Ju-Sheng Zheng*.

The American Journal of Clinical Nutrition. In press. https://doi.org/10.1016/j.ajcnut.2024.10.011

151

A diagnostic protein assay for differentiating follicular thyroid adenoma and carcinoma

Yaoting Sun#, He Wang#, Lu Li#, Jianbiao Wang#, Wanyuan Chen#, Li Peng#, Pingping Hu, Jing Yu, Xue Cai, Nan Yao, Yan Zhou, Jiatong Wang, Yingrui Wang, Liqin Qian, Weigang Ge, Mengni Chen, Feng Yang, Zhiqiang Gui, Wei Sun, Zhihong Wang, Minghua Ge, Yi He, Guangzhi Wang, Yongfu Zhao, Huanjie Chen, Xiaohong Wu, Yuxin Du, Wenjun Wei, Fan Wu, Dingcun Luo, Xiangfeng Lin, Haitao Zheng, Xin Zhu, Bei Wei, Jiafei Shen, Jincao Yao, Zhennan Yuan, Tong Liu, Jun Pan, Yifeng Zhang, Yangfan Lv, Qiaonan Guo, Qijun Wu, Tingting Gong, Ting Chen, Shu Zheng, Jingqiang Zhu, Hanqing Liu, Chuang Chen, Hong Han, Sathiyamoorthy Selvarajan, Mingzhao Xing, Kennichi Kakudo, Erik K. Alexander, Yijun Wu, Yu Wang, Dong Xu, Hao Zhang, Xiu Nie, Oi Lian Kon, N. Gopalakrishna Iyer, Zhiyan Liu, Yi Zhu*, Haixia Guan*, Tiannan Guo*, We-TEC Investigators.

MedRxiv, September 2024. doi: https://doi.org/10.1101/2024.09.26.24314403

148

Proteomic profiling of gliomas unveils immune and metabolism-driven subtypes with implications for anti-nucleotide metabolism therapy

Jinsen Zhang#, Rui Sun#, Yingying Lyu#, Chaxian Liu#, Ying Liu, Yuan Feng, 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*.

Nature Communications. 2024 Nov 19;15(1):10005. doi: 10.1038/s41467-024-54352-5. PMID: 39562821.

146

The 2024 Report on the Human Proteome from the HUPO Human Proteome Project.

Gilbert S. Omenn*, Sandra Orchard, Lydie Lane, Cecilia Lindskog, Charles Pineau, Christopher M. Overall, Bogdan Budnik, Jonathan M. Mudge, Nicolle H. Packer, Susan T. Weintraub, Michael H. A. Roehrl, Edouard Nice, Tiannan Guo, Jennifer E. Van Eyk, Uwe Völker, Gong Zhang, Nuno Bandeira, Ruedi Aebersold, Robert L. Moritz, Eric W. Deutsch*.

Journal of Proteome Research. 2024 Dec 6;23(12):5296-5311. doi: 10.1021/acs.jproteome.4c00776. Epub 2024 Nov 8. PMID: 39514846.

144

metaExpertPro: a computational workflow for metaproteomics spectral library construction and data-independent acquisition mass spectrometry data analysis

Yingying Sun#, Ziyuan Xing#, Shuang Liang#, Zelei Miao, Lai-Bao Zhuo, Wenhao Jiang, Hui Zhao, Huanhuan Gao, Yuting Xie, Yan Zhou, Liang Yue, Xue Cai, Yu-Ming Chen*, Ju-Sheng Zheng*, Tiannan Guo*.

Mol Cell Proteomics. 2024 Sep 13:100840. doi: 10.1016/j.mcpro.2024.100840. Epub ahead of print. PMID: 39278598.

142

Proteomic landscape profiling of primary prostate cancer reveals a 16-protein panel for prognosis prediction

Rui Sun#, Jun A#, Haolan Yu#, Yan Wang#, Miaoxia He#, Lingling Tan, Honghan Cheng, Jili Zhang, Yingrui Wang, Xiaochen Sun, Mengge Lyu, Min Qu, Lingling Huang, Zijian Li, Wenhui Zhang, Kunpeng Ma, Zhenyang Dong, Weigang Ge, Yun Zhang, Xuan Ding, Bo Yang, Jianguo Hou, Chuanliang Xu, Linhui Wang, Yi Zhu, Tiannan Guo*, Xu Gao*, Chenghua Yang*.

Cell Reports Medicine. 2024 Aug 20; 5(8):101679. Doi: https://doi.org/10.1016/j.xcrm.2024.101679. PMID: 39168102.

141

Prediction of overall survival in stage II and III colon cancer through machine learning of rapidly-acquired proteomics

Kailun Xu#, Xiaoyang Yin#, Hui Chen#, Yuhui Huang, Xi Zheng, Biting Zhou, Xue Cai, Huanhuan Gao, Miaomiao Tian, Sijun Hu, Shu Zheng, Changzheng Yuan*, Yongzhan Nie*, Tiannan Guo* & Yingkuan Shao*

Cell Discovery. 2024 Aug 13;10(1):85. doi: 10.1038/s41421-024-00707-7. PMID: 39134531.

140

Proteomic landscape of epithelial ovarian cancer

Liujia Qian#, Jianqing Zhu#, Zhangzhi Xue#, Yan Zhou#, Nan Xiang#, Hong Xu#, Rui Sun, Wangang Gong, Xue Cai, Lu Sun, Weigang Ge, Yufeng Liu, Ying Su, Wangmin Lin, Yuecheng Zhan, Junjian Wang, Shuang Song, Xiao Yi, Maowei Ni, Yi Zhu*, Yuejin Hua*, Zhiguo Zheng*, Tiannan Guo*.

Nature Communications. 2024 Jul 31;15(1):6462. doi: 10.1038/s41467-024-50786-z. PMID: 39085232.

138

Proteomic and cellular characterization of Omicron breakthrough infections and a third homologous or heterologous boosting vaccination in a longitudinal cohort

Yi Zhang#, Zhangfan Fu#, Haocheng Zhang, Ke Lin, Jieyu Song, Jingxin Guo, Qiran Zhang, Guanmin Yuan, Hongyu Wang, Mingxiang Fan, Yuanhan Zhao, Rui Sun, Tiannan Guo, Ning Jiang, Chao Qiu, Wenhong Zhang*, Jingwen Ai*

Molecular & Cellular Proteomics. doi.org/10.1016/j.mcpro.2024.100769. PMID: 38641227.

137

Proteomics-derived biomarker panel facilitates distinguishing primary lung adenocarcinomas with intestinal or mucinous differentiation (PAIM) from lung metastatic colorectal cancer (lmCRC)

Jiaying Liu#, Xiaona Chang#, Liujia Qian#, Shuo Chen#, Zhangzhi Xue, Junhua Wu, Danju Luo, Bo Huang, Jun Fan, Tiannan Guo*, Xiu Nie*

Molecular & Cellular Proteomics. doi.org/10.1016/j.mcpro.2024.100766. PMID: 38608841.

136

Proteomic Identification of Small Extracellular Vesicle Proteins LAMB1 and Histone H4 for Prostate Cancer Diagnosis and Risk Stratification

Bairen Pang, Qi Wang, Haotian Chen, Zhihan Liu, Meng Han, Jie Gong, Liang Yue, Xuan Ding, Suying Wang, Zejun Yan, Yingzhi Chen, David Malouf, Joseph Bucci, Tiannan Guo, Cheng Zhou,* Junhui Jiang,* and Yong Li*

Advanced Science. 2024 Apr 8:e2402509. doi: 10.1002/advs.202402509. Epub ahead of print. PMID: 38590132.

135

Plasma and urine proteomics and gut microbiota analysis reveal potential factors affecting COVID-19 vaccination response

Changjiang Hu#, Weichao Hu#, Bo Tang#, Qiyu Bao#, Xingyu Jiang#, Li Tang, He Wang, Lijiao He, Moyang Lv, Yufeng Xiao, Cheng Liu, Xinzhe Li, Yunyi Liu, Jie Li, Guiping Huang, Zhen Dong*, Zhongjun Li*, Tiannan Guo* and Shiming Yang*

iScience.  2024 Jan 8;27(2):108851. doi: 10.1016/j.isci.2024.108851. PMID: 38318387.

134

Integrated multiomic profiling of breast cancer in the Chinese population reveals patient stratification and therapeutic vulnerabilities

Yi-Zhou Jiang#, Ding Ma#, Xi Jin#, Yi Xiao#, Ying Yu#, Jinxiu Shi#, Yi-Fan Zhou, Tong Fu, Cai-Jin Lin, Lei-Jie Dai, Cheng-Lin Liu, Shen Zhao, Guan-Hua Su, Wanwan Hou, Yaqing Liu, Qingwang Chen, Jingcheng Yang, Naixin Zhang, Wen-Juan Zhang, Wei Liu, Weigang Ge, Wen-Tao Yang, Chao You, Yajia Gu, Virginia Kaklamani, François Bertucci, Claire Verschraegen, Anneleen Daemen, Nakul M. Shah, Ting Wang, Tiannan Guo, Leming Shi, Charles M. Perou, Yuanting Zheng*, Wei Huang* & Zhi-Ming Shao*

Nature Cancer. 2024 Apr;5(4):673-690. doi: 10.1038/s43018-024-00725-0. Epub 2024 Feb 12. PMID: 38347143.

133

The 2023 Report on the Proteome from the HUPO Human Proteome Project

Gilbert S Omenn, Lydie Lane, Christopher M Overall, Cecilia Lindskog, Charles Pineau, Nicolle H Packer, Ileana M Cristea, Susan T Weintraub, Sandra Orchard, Michael H A Roehrl, Edouard Nice, Tiannan Guo, Jennifer E Van Eyk, Siqi Liu, Nuno Bandeira, Ruedi Aebersold, Robert L Moritz, Eric W Deutsch.

Journal of Proteome Research.  2024 Jan 17. doi: 10.1021/acs.jproteome.3c00591. Epub ahead of print. PMID: 38232391.

130

Alzheimer’s disease early diagnostic and staging biomarkers revealed by large-scale cerebrospinal fluid and serum proteomic profiling

Qing-Qing Tao#, Xue Cai#, Yan-Yan Xue#, Weigang Ge#, Liang Yue, Xiao-Yan Li, Rong-rong Lin, Guo-Ping Peng, Wenhao Jiang, Sainan Li, Kun-Mu Zheng, Bin Jiang, Jian-Ping Jia*, Tiannan Guo*, Zhi-Ying Wu*.

The Innovation. 2024 Jan 2;5(1):100544. doi: 10.1016/j.xinn.2023.100544. PMID: 38235188.

129

Risk stratification of papillary thyroid cancers using multidimensional machine learning

Li, Yuanhui#; Wu, Fan#; Ge, Weigang#; Zhang, Yu #; Hu, Yifan; Zhao, Lingqian; Gou, Wanglong; Shi, Jingjing; Ni, Yeqin; Li, Lu; Fu, Wenxin; Lin, Xiangfeng; Yu, Yunxian; Han, Zhijiang; Chen, Chuanghua; Xu, Rujun; Zhang, Shirong; Zhou, Li; Pan, Gang; Peng, You; Mao, Linlin; Zhou, Tianhan; Zheng, Jusheng; Zheng, Haitao*; Sun, Yaoting*; Guo, Tiannan*; Luo, Dingcun*

International Journal of Surgery. 2024 Jan 1;110(1):372-384. doi: 10.1097/JS9.0000000000000814. PMID: 37916932.

126

Proteomic-based stratification of intermediate-risk prostate cancer patients

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*

Life Science Alliance. 2023 Dec 4;7(2):e202302146. doi: 10.26508/lsa.202302146. PMID: 38052461.