Principal Investigator, Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences.

Postdoctoral Fellow, The Scripps Research Institute

Ph.D., Max Planck Institute of Psychiatry / Ludwig Maximilian University of Munich

B.S., Beijing Institute of Technology

Our research focuses on mass spectrometry based multidimensional proteomics and its application to a variety of chemical and biological questions, and their interfaces. We are particularly interested in 1) developing new strategies to analyze minor proteome and protein modifications; 2) using chemical proteomics-centered integrated approach to understand how small molecules interact with proteins and signaling pathways, revealing new mechanisms and therapeutic targets; 3) characterization of selenoproteome and exploration of new selenoproteins; 4) discovering aging- and disease- associated protein dynamics and modifications. 

Selected publications

1.        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.

2.        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.

3.        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.

4.        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.

5.        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.

6.        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.

7.        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.

8.        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.

9.        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.

10.    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.

11.    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.

12.    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.

13.    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.

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.