2004年，武汉大学生物技术专业，学士；
2009年，武汉大学微生物学专业，博士；
2010-2016年，厦门大学生命科学学院，博士后；
2016年至今，厦门大学生命科学学院，副教授。
B.S. 2004, Wuhan University, Biotechnology;
Ph.D. 2009, Wuhan University, Microbiology;
Postdoctoral Researcher, School of Life Sciences, Xiamen University, 2010-2016;
Associate professor, School of Life Sciences, Xiamen University, 2016-present.

我们实验室研究内容分为两个部分：
蛋白组学方法的开发：蛋白组学是研究生物样品中所有蛋白的功能状态的学科，它分为样品前处理，质谱数据采集和质谱数据生物信息学分析三个部分。其中，我们开发了数据不依赖质谱（Data-independent acquisition mass spectrometry, DIA-MS）数据的算法（Nature Methods, 2015）,此算法可以不依赖于数据依赖质谱（Data-dependent acquisition mass spectrometry, DDA-MS）而可直接分析DIA-MS数据。此外我们开发了基于SDS的蛋白组学样品制备方法SCASP (MCP, 2021)以及无需脱盐方法的翻译后修饰富集方法SCASP-PTM (Cell Reports, 2025).
先天免疫和肿瘤免疫信号通路分子机制研究：我们整合自主研发的蛋白组学技术与高通量CRISPR/Cas9筛选工具，系统解析信号通路中关键的调控机制。利用SCASP-PTM方法分析了RNA类似物poly(I:C)刺激HeLa-S3细胞的蛋白、泛素化修饰、磷酸化修饰和糖基化修饰的变化，发现poly(I:C)诱导GSK3B介导的p62蛋白28位磷酸化，进而诱发TNFAIP1介导的420位赖氨酸泛素化，最终导致p62降解并减弱细胞自噬 (Cell Reports, 2025)。此外，利用SCASP-PTM方法分析了临床肺癌和癌旁组织的总蛋白、泛素化修饰、乙酰化修饰、磷酸化修饰和糖基化修饰的变化，揭示了ALDOA的K330的乙酰化修饰和泛素化修饰促进了肿瘤的发展 (Cell Reports, 2025)。
Development of Proteomics Methods:
Proteomics is the study of the functional states of all proteins in biological samples, which consists of three main components: sample preparation, mass spectrometry data acquisition, and bioinformatics analysis of mass spectrometry data. In this field, we developed an algorithm for data-independent acquisition mass spectrometry (DIA-MS) (Nature Methods, 2015), which enables direct analysis of DIA-MS data without relying on data-dependent acquisition mass spectrometry (DDA-MS). Additionally, we established the SDS-based proteomics sample preparation method SCASP (MCP, 2021) and a salt-free post-translational modification (PTM) enrichment method, SCASP-PTM (Cell Reports, 2025).
Molecular Mechanisms of Innate Immunity and Tumor Immune Signaling Pathways:
By integrating our proprietary proteomics technologies with high-throughput CRISPR/Cas9 screening tools, we systematically investigated key regulatory mechanisms in signaling pathways. Using the SCASP-PTM method, we analyzed changes in proteins, ubiquitination, phosphorylation, and glycosylation modifications in HeLa-S3 cells stimulated with the RNA analog poly(I:C). We discovered that poly(I:C) induces GSK3B-mediated phosphorylation of p62 at Ser28, triggering TNFAIP1-mediated ubiquitination at Lys420, ultimately leading to p62 degradation and attenuated autophagy (Cell Reports, 2025). Furthermore, applying SCASP-PTM to clinical lung cancer and adjacent tissues, we characterized alterations in total protein levels, ubiquitination, acetylation, phosphorylation, and glycosylation modifications, revealing that acetylation and ubiquitination of ALDOA at Lys330 promote tumor progression (Cell Reports, 2025).

代表性论文(^# co-first author, ^* Corresponding author):

1. Lin ZP, Gan G, Xu X, Wen C, Ding X, Chen XY, Zhang K, Guo WY, Lin M, Wang YY, Chen X, Xie C, Wang J*, Li M*, Zhong CQ*. Comprehensive PTM profiling with SCASP-PTM uncovers mechnisms of p62 degradation and ALDOA-mediated tumor progression. Cell Rep. 2025 Apr 3;44(4):115500. Doi: 10.1016/j.celrep.2025.115500. (IF=7.5)
2. 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. 22, 2232-2245 (2023). (IF=5.3)
3. 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. 23, e2200204 (2023). (IF=3.85)
4. 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)
5. 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)
6. 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)
7. 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)
8. 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)
9. 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)
10. 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)
11. 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)
12. 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)
13. 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)
14. 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)

荣誉、奖励及参加学术团体的情况: