Education

B.S. 2004, Wuhan University, Biotechnology;
Ph.D. 2009, Wuhan University, Microbiology;

Professional Experience

Postdoctoral Researcher, School of Life Sciences, Xiamen University, 2010-2016;
Associate professor, School of Life Sciences, Xiamen University, 2016-present.

Research Area

Our lab focuses on the study of dynamic signaling pathway using DIA-MS based quantitative proteomics. Signal transduction in cells was generally mediated by dynamic assembly and dissociation of protein complexes. To gain an in-depth insight into the signaling transduction in cells, we employed quantitative mass spectrometry to investigate assembly and dissociation of endogenous protein complexes.
We fist purified protein complexes using affinity purification, and subsequently identified and quantified protein components of protein complexes using DIA-MS, which we referred to as AP-DIA workflow. The AP-DIA workflow can be utilized to identify novel proteins in the signaling pathway and investigate the stoichiometry of protein complexes. The AP-DIA workflow has been successfully employed to study the TNF and LPS signaling pathways.

Selected Publications (*Corresponding author, #co-first author)

1. Wen C, Wu X*, Lin G, Yan W, Gan G, Xu X, Chen XY, Chen X, Liu X, Fu G*, Zhong CQ*. Evaluation of DDA Library-Free Strategies for Phosphoproteomics and Ubiquitinomics Data-Independent Acquisition Data. J Proteome Res. 2023 May 31 (IF=5.3)
2. Xu X, Yin F, Guo M, Gan G, Lin G, Wen C, Wang J, Song P, Wang J*, Qi ZQ*, Zhong CQ*. Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells. Proteomics. 2023 Jan. (IF=3.85)
3. Wen C, Gan G, Xu X, Lin G, Chen X, Wu Y, Xu Z, Wang J, Xie C, Wang HR*, Zhong C. Q.* Investigation of Effects of the Spectral Library on Analysis of diaPASEF Data. J Proteome Res. 2022 Feb 4;21(2):507-518. (IF=5.3)
4. Gan G., Xu X., Chen X., Zhang X.F., Wang J, Zhong C. Q.* SCASP: a simple and robust sodium dodecyl sulfate-aided sample preparation method for proteomic research. Mol Cell Proteomics. 2021 Feb 4 (IF=7.2)
5. Li X#, Zhong C. Q.#, Wu R#, Xu X, Yang ZH, Cai S, Wu X, Chen X, Yin Z, He Q, Li D, Xu F, Yan Y, Qi H, Xie C, Shuai J*, Han J*. RIP1-dependent linear and nonlinear recruitments of pro-caspase-8 and RIP3 respectively to necrosome specify distinct cell death outcomes. Protein Cell. 2021 Jan 2. (IF= 14.87)
6. Wang D, Gan G, Chen X, Zhong C.Q.* QuantPipe: A User-Friendly Pipeline Software Tool for DIA Data Analysis Based on the OpenSWATH-PyProphet-TRIC Workflow. J Proteome Res. 2020 Oct 22. (IF=4.0)
7. Zhong C.Q.#*, Wu J, Qiu X, Chen X, Xie C, Han J*. Generation of a murine SWATH-MS spectral library to quantify more than 11,000 proteins. Scientific Data. 2020 Mar 26;7(1):104. (IF=5.929)
8. Zhong, C.Q.#*, Wu R, Chen X, Wu S, Shuai J, Han J*. Systematic Assessment of the Effect of Internal Library in Targeted Analysis of SWATH-MS. J Proteome Res. 2020 Jan 3;19(1):477-492. (IF=3.8)
9. Wu, X. #, Yang, D., Zhao, F., Yang Z.H., Wang, D., Qiao, M., Fang, Y., Li, W., Wu, R., He P., Cong, Y., Chen, C., Hu, L., Yan, Y., Xie, C., Wu, Y., Han, J. *, Zhong, C.Q.* Quantification of dynamic protein interactions and phosphorylation in LPS signaling pathway by SWATH-MS. Mol Cell Proteomics. 2019 Jun;18(6):1054-1069 (IF=7.2)
10. Y. Li#, C.Q. Zhong#*, X. Xu, S. Cai, X. Wu, Y. Zhang, J. Chen, J. Shi, S. Lin, and J. Han* (2015). Group-DIA: analyzing multiple data-independent acquisition mass spectrometry data files. Nature methods. 2015 Dec;12(12):1105-6 (IF=23.030)
11. W.T. He, H. Wan, L. Hu, P. Chen, X. Wang, Z. Huang, Z.H. Yang, C. Q. Zhong*, J. Han*. Gasdermin D is an executor of pyroptosis and required for interleukin-1β secretion. Cell Res. 2015 Dec;25(12):1285-98. (IF=15.393)
12. Zhong, C. Q.#, Y. Li#, D. Yang, N. Zhang, X. Xu, Y. Wu, J. Chen and J. Han* (2014). Quantitative phosphoproteomic analysis of RIP3-dependent protein phosphorylation in the course of TNF-induced necroptosis. Proteomics 2014 Mar;14(6):713-24 (IF=3.060)
13. Wu, X. #, L. Tian#, J. Li, Y. Zhang, V. Han, Y. Li, X. Xu, H. Li, X. Chen, J. Chen, W. Jin, Y. Xie, J. Han* and C. Q. Zhong*. Investigation of receptor interacting protein (RIP3)-dependent protein phosphorylation by quantitative phosphoproteomics. Mol Cell Proteomics 2012 Dec;11(12):1640-51. (IF=6.830)