2000-2006 北京理工大学 学士和硕士
2006-2010 德国慕尼黑-路德维希-马克西米利安大学 博士
2006-2010 德国马克斯普朗克精神病研究所 博士生
2011-2013.9 美国斯克里普斯研究所 研究助理
2013.9-至今 中国科学院生物与化学交叉研究中心 研究员、课题组长

质谱和蛋白质组实验室利用生物质谱技术来研究蛋白质在生物体系中的多种特性。其研究方向主要包括：
1.质谱蛋白质组学新技术和新方法的研究
2.神经退行性疾病和衰老过程的相关蛋白质组学研究
3.质谱蛋白质组学技术在生物学问题中的广泛应用

1. Tan, J.; Hao, K.; Yuan, Y.; Xie, S.; Qi, L.; Che, Q.; Li, Y.; Wang, R.; Zhang, Y.*; Chen, Y.*, Bioorthogonal Photocatalytic Protein Labeling and Crosslinking Enabled by Stabilized Ketyl Radicals. JACS 2025.

2. Yuan, Y., Xu, Z., Si, C., Gao, Z., Liu, X., Yuan, Y., Xu, D., Shan, B. *, Zhang, Y.*, TRIM28-mediated SUMOylation of G3BP1/2 regulates stress granule dynamics. Cell Chem Biol 2025, 32(11):1336-1352.

Yuan, Y., Zhang, Y.. Meet the authors: Yi Yuan and Yaoyang Zhang. Cell Chem Biol 2025, 32(11):1303-1304.

3. Yuan, Y., Wang, Z., Si, C., Li, J., Ren, F., Yuan, Y., Shi, Z., Sun, N., Ma, X., Dai, X., Li, Y., Zhang, Y., Liu, J., Wang, H., Zhu, Z., Shan, B.*, Zhang, Y.*, CysMP reveals metal ion-specific metalloproteomes and copper-regulated PGK1 activity in glycolysis. Sci Adv 2025, 11 (42), eadx7035.

4. Wang, Z., Li, J., Duan, J.*, Shan, B.*, Zhang, Y.*, Multi-dimensional Proteomics Reveal Metformin's Impact on Interconnected Regulatory Networks of Protein Turnover, Ubiquitination, DNA Damage, and Cell Cycle. Mol Cell Proteomics 2025, 101440.

5. Si, C., Zhang, L., Gao, J., Niu, K., Li, Y., Liu, N., Shan, B.*, Zhang, Y.*, 3S-DB identifies an RNA repository facilitating stop codon readthrough for selenocysteine insertion and selenoproteome expansion. Redox Biol 2025, 87, 103888.

6. Liu, J. #, Gao, J. #, Guo, L., Ma, G., Guan, M., Xia, C., He, J., Yang, Y., Wu, Y., Xu, J., Xiong, L., Yu, CY., Pei, G., Zhao, J., He, J., Zhang, Y. *, Wang, W. *. Astrocyte Secretome Profiling via Biorthogonal Labeling Unveils Novel Factors Relevant to Neurodegenerative Diseases. Glia 2025, Epub ahead of print.

7. Si, C., Yuan, Y., Zong, Y., Qiao, L., Zeng, W., Zhang, Y. *, DeepSecMS advances DIA-based selenoproteome profiling through Cys-to-Sec proxy training. Adv. Sci. (Weinh) 2025, e04109.

8. Gao, J. #, Liu, Y. #, Si, C., Guo, R., Hou, S., Liu, X., Long, H., Liu, D., Xu, D., Zhang, Z., Liu, C., Shan, B., Turck, C.W., He, K. *, Zhang, Y. *, Aspirin inhibits proteasomal degradation and promotes α-synuclein aggregate clearance through K63 ubiquitination. Nat Commun 2025, 16(1):1438.

9. Chen, P. #, Lin, L. #, Lin, X. #, Liao, K. #, Qiang, J. #, Wang, Z., Wu, J., Li, Y., Yang, L., Yao, N., Song, H., Hong, Y., Liu, W. H. *, Zhang, Y. *, Chang, X. *, Du, D. *, Xiao, C. *, A Csde1-Strap complex regulates plasma cell differentiation by coupling mRNA translation and decay. Nat Commun 2025, 16 (1), 2906.

10. Liu, X. #,  Novak, B. #,  Namendorf, C.,  Steigenberger, B.,  Zhang, Y. *,  Turck, C. *, Long-lived proteins and DNA as candidate predictive biomarkers for tissue associated diseases. iScience 2024, 27(4): 109642.

11. Lou, R. #, Cao, Y. #, Li, S. #, Lang, X., Li, Y., Zhang, Y. *, Shui W.*, Benchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics. Nat Commun 2023, 14 (1), 94.

12. Li, J. #, Cao, Y. #, Yang, Y., Ma, H., Zhao, J., Zhang, Y. *, Liu, N. *, Quantitative Acetylomics Reveals Substrates of Lysine Acetyltransferase GCN5 in Adult and Aging Drosophila. J Proteome Res 2023, 22 (9):2909-2924.

13. Li, J. #, Cao, Y. #, Niu, K., Qiu, J., Wang, H., You, Y., Li, D., Luo, Y., Zhu, Z., Zhang, Y. *, Liu, N. *, Quantitative Acetylomics Reveals Dynamics of Protein Lysine Acetylation in Mouse Livers During Aging and Upon the Treatment of Nicotinamide Mononucleotide. Mol Cell Proteomics 2022, 21 (9), 100276.

14. Sun, L., Yan, Y., Lv, H., Li, J., Wang, Z., Wang, K., Wang, L., Li, Y., Jiang, H., Zhang, Y. *, Rapamycin targets STAT3 and impacts c-Myc to suppress tumor growth. Cell Chem Biol 2022, 29(3):373-385.

15. Qiang, J., Xu, Z., Li, Y., Wang, H., Zhang, Y. *, Carboxypeptidase Y Assisted Disulfide-Bond Identification with Linearized Database Search. Anal Chem 2021, 93 (45), 14940-14945.

16. Zhang, K. #, Wang, Q. #, Liang, Y., Yan, Y., Wang, H., Cao, X., Shan, B., Zhang, Y. *, Li, A. *, Fang, Y. *, Quantitative Proteomic Analysis of Mouse Sciatic Nerve Reveals Post-injury Upregulation of ADP-Dependent Glucokinase Promoting Macrophage Phagocytosis. Front Mol Neurosci 2021, 14, 777621.

17. Wang, H.#, Zhang, Y. #, Zeng, K. #, Qiang, J. #, Cao, Y., Li, Y., Fang, Y., Zhang, Y. *, Chen, Y. *, Selective Mitochondrial Protein Labeling Enabled by Biocompatible Photocatalytic Reactions inside Live Cells. JACS Au 2021, 1(7):1066-1075.

18. Wang, Z., Liu, H., Yan, Y., Yang, X., Zhang, Y. *, Wu, L. *, Integrated proteomic and N-glycoproteomic analyses of human breast cancer. J Proteome Res 2020, 19(8):3499-3509.

19. Lou, R., Tang, P., Ding, K., Li, S., Tian, C., Li, Y., Zhao, S. *, Zhang, Y. *, Shui, W. *, Hybrid Spectral Library Combining DIA-MS Data and a Targeted Virtual Library Substantially Deepens the Proteome Coverage. iScience 2020, 23(3):100903.

20. Guo, L. #, Gao, J. #, Gao, Y., Zhu, Z., Zhang, Y. *, Aspirin reshapes acetylomes in inflammatory and cancer cells via CoA-dependent and -independent pathways. J Proteome Res 2020, 19(2):962-972.

21. Yang, L., Cao, Y., Zhao, J., Fang Y., Liu, N. *, Zhang, Y. *, Multidimensional Proteomics Identifies Declines in Protein Homeostasis and Mitochondria as Early Signals for Normal Aging and Age-associated Disease in Drosophila. Mol Cell Proteomics 2019, 18(10):2078-2088.

22. Yang, L., Ma, Z., Wang, H., Niu, K., Cao, Y., Sun, L., Geng, Y., Yang, B., Gao, F., Chen, Z., Wu, Z., Li, Q., Shen, Y., Zhang, X., Jiang, H., Chen, Y., Liu, R., Liu, N. *, Zhang, Y. *, Ubiquitylome study identifies increased histone 2A ubiquitylation as an evolutionarily conserved aging biomarker. Nat Commun 2019, 10(1), 2191.

23. Qiang, J., Ma, Z., Xie, X., Shi, L., Geng, Y., Hu, J., Liu, R., Liu, N., Zhang, Y. *, Multi-omic Analyses Reveal Minimal Impact of the CRISPR-Cas9 Nuclease on Cultured Human Cells. J Proteome Res 2019, 18(3), 1054-1063.

24. Guo, L., Yang, W., Huang, Q., Qiang, J., Hart, J. R., Wang, W., Hu, J., Zhu, Z. J., Liu, N., Zhang, Y. *, Selenocysteine-Specific Mass Spectrometry Reveals Tissue-Distinct Selenoproteomes and Candidate Selenoproteins. Cell Chem Biol 2018, 25(11), 1380-1388.

25. Yang, X., Wang, Z., Guo, L., Zhu, Z. J., Zhang, Y. *, Proteome-Wide Analysis of N-Glycosylation Stoichiometry Using SWATH Technology. J Proteome Res 2017, 16(10), 3830-3840.

26. Wang, H., Ma, Z., Niu, K., Xiao, Y., Wu, X., Pan, C., Zhao, Y., Wang, K., Zhang, Y. *, Liu, N. *, Antagonistic roles of Nibbler and Hen1 in modulating piRNA 3' ends in Drosophila. Development 2016, 143(3), 530-539.

27. Huang, Q., Yang, L., Luo, J., Guo, L., Wang, Z., Yang, X., Jin, W., Fang, Y., Ye, J., Shan, B., Zhang, Y. *, SWATH enables precise label-free quantification on proteome scale. Proteomics 2015, 15(7), 1215-1223.