A Protein-Centric Strategy Coupled with Match-Between-Run Glycoproteomics Enables Discovery of Robust Site- Specif ic Glycan Biomarkers for Hepatocellular Carcinoma

Lei Liu, Taiheng Ma, Qi Liu, He Zhu, Zheng Fang, Jiahong Ma, Ting Yu, Yan Wang, Jiahua Zhou, Xiaoyan Liu, Yaqian Li, Zhimou Guo, Xinmiao Liang, Mingming Dong, Deguang Sun, Mingliang Ye

Advanced Science, 2026, 0:e16299, 1-16

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A peptide-centric local stability assay enables proteome-scale identification of the protein targets and binding regions of diverse ligands

Kejia Li, Shijie Chen, Keyun Wang, Yan Wang, Lianji Xue, Yuying Ye,Zheng Fang , Jiawen Lyu, Haiyang Zhu, Yanan Li, Ting Yu, Feng Yang, Xiaolei Zhang, Siqi Guo, Chengfei Ruan, Jiahua Zhou, Qi Wang, Mingming Dong , Cheng Luo, Mingliang Ye 

Nature Methods, 2025, 22, 278-282

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Solvent-induced partial cellular fixation decodes proteome-wide drug targets and downstream pathways in living cells

Ting Yu, Yan Wang, Keyun Wang, Zheng Fang, Haiyang Zhu,Xiaolei Zhang, Yanan Li, Mingliang Ye

Nature Communications, 2025, 16:10475,1-16

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Library-based virtual match-between-runs quantification in GlyPep Quant improves site-specific glycan identification

He Zhu, Zheng Fang, Lei Liu, Yan Wang, Hongqiang Qin, Yongzhan Nie, Mingming Dong, Mingliang Ye

Nature Communications, 2025, 16:6483, 1-17

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Decoding Arginine Dimethylation Isomers via pH-Tuned Reactivity with Methylglyoxal: A Chemical Approach for Functional Proteomics

Jiayi Wang,Ye Liu, Qi Wang, Yanni Ma, Longrun Shi, Yan Wang, Zhouxian Li, Zheng Fang, Zhen Liu, Jiayang Yan, Xia Mu, Guohui Li, Anhui Wang, Keyun Wang, Mingliang Ye

Journal of the American Chemical Society, 2025, 147, 43773-43784

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Modulation of Core-Fucosylation Oxidation for Selective Enrichment and Characterization of Cell Surface Glycoprotein

Xin Guo, Xiaoyan Liu, Zheng Fang, Yan Wang, Lei Liu, Zhongyu Wang, Feng Tang, Wei Huang,Zhenpeng Deng, Qi Wang, Mingliang Ye, Lingyun Jia, Mingming Dong

ACS CHEMICAL BIOLOGY, 2025, 20, 2979-2990

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A Detergent-Free Grinding Sample Preparation Method Dramatically Enhances PELSA for Mapping Integral Membrane Proteins−Ligand Interaction

Ting Yu, Yan Wang, Yanan Li, Keyun Wang, Haiyang Zhu, Mingliang Ye

Analytical Chemistry, 2025, 97, 23848−23857

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Development of complementary enrichment strategies for analysis of N-linked intact glycopeptides and potential site-speciffc glycoforms in Alzheimer’s disease

Zhenpeng Deng, Yan Wang, Xiaoyan Liu, Xingfa Ren, Weibing Zhang, Mingming Dong, Yusong Ge, Yongliang Yu, Mingliang Ye

Talanta, 2025, 297,128595, 1-9

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Sequential denaturation and protein precipitation assay (SDPP) improves the sensitivity for ligand target identification at the proteome level

Yanni Ma, Xiaolei Zhang, Longrun Shi, Jiayang Yan, Keyun Wang, Mingliang Ye

Analytica Chimica Acta, 2025, 1379, 344722, 1-9

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PELSA-Decipher: A Software Tool for the Processing and Interpretation of Ligand-Protein Interaction Data Sets Acquired by PELSA

Haiyang Zhu, Keyun Wang, Kejia Li, Zheng Fang, Jiahua Zhou, Lianji Xue, Mingliang Ye

Journal of Proteome Research, 2025, 24, 4623−4630

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