Selected publications

1. 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.

2. 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.

3. 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.

4. 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.

5. 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.

6. 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.

7. 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.

8. 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.

9. 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.

10. 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.

11. 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.

12. 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.

13. 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.

14. 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.

15. 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.

16. 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.

17. 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.