Center for Molecular and Cellular Biology of Aquatic Organisms

Research Group of Functional Proteomics




PI: Prof. GE Feng, PhD

Members: Assistant Professor: Qian Xiong; Senior Technician: Mingkun Yang, Technician: Jia Zhang;  

Contact Us: Prof Feng Ge ( 

Laboratory of Functional Proteomics, Institute of Hydrobiology, the Chinese Academy of Sciences 

7# South Donghu Road, Wuhan, Hubei, China, 430072 

Tel: +86-27-87680500 

General Introduction:   

The Research Group of Functional Proteomics uses the state-of-the-art mass spectrometric methods to identify proteins and characterize post-translational modifications in signal transduction pathways and in the analysis of human and several different hydrobiontes. They use different techniques that help quantitate levels of protein as well as post-translational modifications.  

They also develop computational methods that allow them to extract annotated information from existing databases including genomic databases while performing searches using mass spectrometry-derived data.  

Current research interests:  

* Proteomic and functional analysis of protein post-translational modifications based on the mass spectrometry 

* Functional proteomic analysis of non-coding-RNA targets 

* Proteogenomics analysis of several important model organisms 

Recent Publications:

1. Chen, Zhuo; Zhang, Guiying; Yang, Mingkun; Li, Tao*; Ge, Feng*; Zhao, Jindong. Lysine Acetylome Analysis Reveals Photosystem II Manganese-stabilizing Protein Acetylation is Involved in Negative Regulation of Oxygen Evolution in Model Cyanobacterium Synechococcus sp. PCC 7002. Molecular & Cellular Proteomics. 2017;16(7):1297-1311. (*Corresponding Author) 

2. Ma, Yanyan; Yang, Mingkun; Lin, Xiaohuang; Liu, Xin; Huang, Hui; Feng Ge*. Malonylome Analysis Reveals the Involvement of Lysine Malonylation in Metabolism and Photosynthesis in Cyanobacteria. Journal of Proteome Research. 2017;16(5):2030-2043. (*Corresponding Author) 

3. Jia Zhang, Ming-kun Yang, Honghui Zeng, and Feng Ge*. GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes. Molecular & Cellular Proteomics. 2016;15(11):3529-3539. (*Corresponding Author) 

4. 吴英; 熊倩; 葛峰*. 长链非编码RNA HOTAIR在细胞增殖中的作用机制. 生命科学. 2016, 28: 6; 680-685. (*Corresponding Author) 

5: Wu Y, Lou QY, Ge F, Xiong Q.*. Quantitative Proteomics Analysis Reveals Novel Targets of miR-21 in Zebrafish Embryos. Scientific Reports. 2017; 7(1):4022. (*Corresponding Author) 

6: Ren S, Yang M, Li Y, Zhang F, Chen Z, Zhang J, Yang G, Yue Y, Li S, Ge F*, Wang S.*. Global Phosphoproteomic Analysis Reveals the Involvement of Phosphorylation in Aflatoxins Biosynthesis in the Pathogenic Fungus Aspergillus flavus. Scientific Reports. 2016; 6: 34078. (*Corresponding Author) 

7. Siting Li, Minghai Chen, Qian Xiong, Jia Zhang, Zongqiang Cui, Feng Ge*. Characterization of the Translationally Controlled Tumor Protein (TCTP) Interactome Reveals Novel Binding Partners in Human Cancer Cells. Journal of Proteome Research. 2016, 7;15(10):3741-3751. (*Corresponding Author) 

8. 杨明坤;林小煌;马炎炎;王炎;葛峰*. 蓝藻的蛋白质翻译后修饰研究进展. 水生生物学报,2016 (05)1056-1067. (*Corresponding Author) 

9: Ming-kun Yang, Yao-hua Yang, Zhuo Chen, Jia Zhang, Yan Lin, Yan Wang, Qian Xiong, Tao Li*, Feng Ge*, Donald A. Bryant, and Jin-dong Zhao. Proteogenomic analysis and global discovery of post-translational modifications in prokaryotes. Proceedings of the National Academy of Sciences of the United States of America201411152):E5633-E5642(*Corresponding Author) 

10: Peng ZhengQian XiongYing WuYing ChenZhuo ChenJoy FlemingDing GaoLijun Bi,Feng Ge*Quantitative Proteomics Analysis Reveals Novel Insights into Mechanisms of Action of Long Non-coding RNA HOTAIR in HeLa CellsMolecular & Cellular Proteomics, 2015, 14 (5) :1447-63. (*Corresponding Author) 

11: Feng Ge, Weichao Huang, Zhuo Chen, Chunye Zhang, Qian Xiong, Chris Bowler, Juan Yang, Jin Xu, and Hanhua Hu. Methylcrotonyl-CoA Carboxylase Regulates Triacylglycerol Accumulation in the Model Diatom Phaeodactylum tricornutum Plant Cell 2014; 26(4):1681-1697. (*Corresponding Author) 

12: Ziyad Tariq Muhseen, Qian Xiong, Zhuo Chen and Feng Ge*. Proteomics studies on stress responses in diatoms. Proteomics. 2015; 15(23-24):3943-53. (*Corresponding Author) 

13: Zhuo Chen, Jiao Zhan, Ying Chen, Mingkun Yang, Chenliu He, Feng Ge*, Qiang Wang*. Effects of Phosphorylation of β Subunits of Phycocyanins on State Transition in the Model Cyanobacterium Synechocystis sp. PCC 6803. Plant and Cell Physiology. 2015, 56 (10): 1997-2013. (*Corresponding Author) 

14: Qian Xiong, Zhuo Chen, Feng Ge*. Proteomic analysis of post translational modifications in cyanobacteria. Journal of Proteomics. 2016; 134:57-64. (*Corresponding Author) 

15: Mingkun Yang, Yan Wang, Ying Chen, Zhongyi Cheng, Jing Gu, Jiaoyu Deng, Lijun Bi, Chuangbin Chen, Ran Mo, Xude Wang, and Feng Ge*. Succinylome Analysis Reveals the Involvement of Lysine Succinylation in Metabolism in Pathogenic Mycobacterium tuberculosis H37Rv. Molecular & Cellular Proteomics201514 (4): 796-811(*Corresponding Author) 

16: Qian XiongJie FengSi-ting LiGui-ying ZhangZhi-xian QiaoZhuo ChenYing WuHui HuangYan LinTao Li*,Feng Ge*Jin-dong Zhao*. Integrated Transcriptomic and Proteomic Analysis of the Global Response of Synechococcus sp. PCC 7002 to High Light Stress. Molecular & Cellular Proteomics2015; 14(4): 1038-53(*Corresponding Author) 

17: Yang, YaohuaFeng, JieLi, Tao*,Feng Ge*Zhao, Jindong. CyanOmics: an integrated database of omics for the model cyanobacterium Synechococcus sp. PCC 7002. Database (Oxford)2015 Jan 28;2015. pii: bau127. doi: 10.1093/database/bau127. (*Corresponding Author) 

18: Ran Mo, Mingkun Yang, Zhuo Chen, Zhongyi Cheng, Xingling Yi, Chongyang Li, Chenliu He, Qian Xiong, Hui Chen, Qiang Wang*, and Feng Ge*. Acetylome Analysis Reveals the Involvement of Lysine Acetylation in Photosynthesis and Carbon Metabolism in the Model Cyanobacterium Synechocystis sp. PCC 6803. Journal of Proteome Research 2015142: 1275-1286(*Corresponding Author) 

19: Fengying Liu, Mingkun Yang, Xude Wang, Shanshan Yang, Jing Gu, Jie Zhou, Xian-En Zhang*, Jiaoyu Deng*, and Feng Ge*. Acetylome analysis reveals diverse functions of lysine acetylation in Mycobacterium tuberculosis. Molecular & Cellular Proteomics 2014; 13(12):3352-66 (*Corresponding Author) 

20: Zhuo Chen, Ming-kun Yang, Chong-yang Li, Yan Wang, Jia Zhang, Dian-bing Wang, Xian-en Zhang*, and Feng Ge*. Phosphoproteomic Analysis Provides Novel Insights into Stress Responses in Phaeodactylum tricornutum, a Model Diatom. Journal of Proteome Research 2014; 13(5): 2511-23 (*Corresponding Author) 

21: Miao Tian, Xiulan Chen, Qian Xiong, Jie Xiong, Chuanle Xiao, Feng Ge*, Fuquan Yang*, and Wei Miao*. Phosphoproteomic analysis of protein phosphorylation networks in Tetrahymena thermophila, a Model Single-Celled Organism. Molecular & Cellular Proteomics 2014;13(2):503-19. (*Corresponding Author) 

22: Ying Chen, Li-Na Yang, Li Cheng, Shun Tu, Shu-Juan Guo, Huang-Ying Le, Qian Xiong, Ran Mo, Chong-Yang Li, Jun-Seop Jeong, Lizhi Jiang, Seth Blackshaw, Li-Jun Bi, Heng Zhu*, Sheng-Ce Tao*, and Feng Ge*. BAG3 Interactome Analysis Reveals a New Role in Modulating Proteasome Activity. Molecular & Cellular Proteomics 2013;12(10):2804-19. (*Corresponding Author) 

23: Ming-kun Yang, Zhi-xian Qiao, Wan-yi Zhang, Qian Xiong, Jia Zhang, Tao Li*, Feng Ge*, and Jin-dong Zhao*. Global phosphoproteomic analysis reveals diverse functions of Serine/Threonine/Tyrosine phosphorylation in the model cyanobacterium synechococcus sp. strain PCC 7002. Journal of Proteome Research 2013, 12 (4), 1909–1923. (*Corresponding Author) 

24: Chongyang Li, Qian Xiong, Jia Zhang, Feng Ge* and Li-Jun Bi. Quantitative Proteomic Strategies for the Identification of MicroRNA Targets. Expert Review of Proteomics 2012;9(5):549-59 (*Corresponding Author) 

25: Qian Xiong, Qiu Zhong, Jia Zhang, Mingkun Yang, Chongyang Li, Peng Zheng, Li-Jun Bi*, and Feng Ge*. Identification of Novel miR-21 Target Proteins in Multiple Myeloma Cells by Quantitative Proteomics. Journal of Proteome Research 2012; 11(4):2078-90 (*Corresponding Author) 

26: Peng Zheng, Qiu Zhong, Qian Xiong, Mingkun Yang, Jia Zhang, Chongyang Li, Li-Jun Bi*, Feng Ge*. QUICK identification and SPR validation of signal transducers and activators of transcription 3 (Stat3) interacting proteins. Journal of Proteomics 2012; 75(3):1055-66. (*Corresponding Author) 

27: Jia Zhang, Fangjin Chen, Wenliang Li, Qian Xiong, Mingkun Yang, Peng Zheng, Chongyang Li, Jianfeng Pei*, Feng Ge*. 14-3-3ζ interacts with stat3 and regulates its constitutive activation in multiple myeloma cells. PLoS One 2012;7(1):e29554. (*Corresponding Author) 

28: Qian Xiong, Feng Ge*. Identification and evaluation of a panel of serum biomarkers for predicting response to thalidomide in multiple myeloma patients. Expert Review of Proteomics 2011;8(4):439-42 (*Corresponding Author) 

29: Feng Ge*, Li-Jun Bi, Sheng-Ce Tao, Xudong Xu, Zhi-Ping Zhang, Kaio Kitazato and Xian-En Zhang*. Proteomic analysis of multiple myeloma: current status and future perspectives. Proteomics Clin Appl 2011; 5:30-37. (*Corresponding Author) 

30: Feng Ge*, Shengce Tao, Lijun Bi, Zhiping Zhang, and Xianen Zhang*. Proteomics: addressing the challenges of multiple myeloma. Acta Biochim Biophys Sin (Shanghai) 2011; 43:89-95. (*Corresponding Author) 

31: Feng Ge*, Liang Zhang, Sheng-Ce Tao, Kaio Kitazato, Zhi-Ping Zhang, Xian-En Zhang, and Li-Jun Bi*. Quantitative proteomic analysis of tumor reversion in multiple myeloma cells. Journal of Proteome Research 2011;10(2):845-55. (*Corresponding Author) 

32: Feng Ge*, Wen-Liang Li, Li-Jun Bi, Sheng-Ce Tao, Zhi-Ping Zhang, and Xian-En Zhang. Identification of novel 14-3-3ζ interacting proteins by quantitative immunoprecipitation combined with knockdown (QUICK). Journal of Proteome Research 2010 Nov 5;9(11):5848-58. (*Corresponding Author)