Chuanqi Zhong

Research Areas:
1. Development of proteomics methods: Proteomics is the discipline that studies the functional states of all proteins in biological samples. It consists of three parts: sample preprocessing, mass spectrometry data acquisition, and mass spectrometry data bioinformatics analysis. We developed an algorithm for data-independent acquisition mass spectrometry (DIA-MS) data (Nature Methods, 2015), which can directly analyze DIA-MS data without relying on data-dependent acquisition mass spectrometry (DDA-MS). Additionally, we developed the SDS-based proteomics sample preparation method SCASP (MCP, 2021) and the desalting-free post-translational modification enrichment method SCASP-PTM (Cell Reports, 2025).
2. Molecular mechanism research on innate immunity and tumor immunity signaling pathways: We integrate self-developed proteomics technologies with high-throughput CRISPR/Cas9 screening tools to systematically analyze key regulatory mechanisms in signaling pathways. Using the SCASP-PTM method, we analyzed changes in proteins, ubiquitination, phosphorylation, and glycosylation in HeLa-S3 cells stimulated by RNA analog poly(I:C), discovering that poly(I:C) induces GSK3B-mediated phosphorylation at position 28 of p62 protein, which triggers TNFAIP1-mediated ubiquitination at lysine 420, ultimately leading to p62 degradation and weakened autophagy (Cell Reports, 2025). Furthermore, using the SCASP-PTM method to analyze total proteins, ubiquitination, acetylation, phosphorylation, and glycosylation in clinical lung cancer and adjacent tissues, we revealed that acetylation and ubiquitination of ALDOA at K330 promotes tumor development (Cell Reports, 2025).

Selected Publications:
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)