EN |  中文
Current Location:Home / Scientists&Research / Core Facilities / Text

ProteomicsFacility

Proteomics Facility

She Chen, Ph.D.

Associate Investigator and Director of Proteomics Center, NIBS,BeijingChina
Phone: 010-80726688-8370
E-mail: chenshe@nibs.ac.cn

Introduction Of PI:

She Chen, Ph.D., received bachelor's degree in biochemistry in 1995 at Wuhan University, master's degree in Institute of Biophysics, Chinese Academy of Sciences in 1998 and master's degree in food science in 2000 in Iowa University in the United States and obtained a biological PhD in chemistry and molecular biology in 2009 in Beijing Normal University. From 2001 to 2004, he was engaged in biological mass spectrometry of proteins work in University of Texas Southwestern Medical Center at Dallas in the United States and the American MDS Proteomics Inc. company. In 2004, he returned back to NIBS to establish proteomics facilities, NIBS, Beijing. He is currently a senior investigator, doctoral tutor and director of proteomics facilities at NIBS.

Over the past decade, She Chen, Ph.D. has been dedicated on the development and application of bio-mass spectrometry of proteins. He has made a series of important researches by applying biological mass spectrometry technology to the fields including pathogen and host interactions, transmission of epigenetic information in eukaryotic cells, the regulation of circadian rhythms, program cell death, cell autophagy and many basic areas of RNAi biology, etc. She Chen, Ph.D. has published more than 60 papers in international journals such as Nature, Science and Cell.


Proteomics Facilities at NIBS

Proteomics Facilities, NIBS established in 2004. The core components of the center is the biological mass spectrometry laboratory which has LTQ Orbitrap Velos, Q Exactive and other large-scale bio-mass spectrometer, providing high-quality MS analysis Services to other laboratories at NIBS. Services here are including molecular weight determination of proteins and peptides, further analysis and identification, a complex mix of protein samples after protein identification, protein translational modifications, as well as comparative quantitative research proteome.

On the basis of the positive development and improvement of advanced biological mass spectrometry technology, our center is committed to the effective use of these technologies to basic biological research to help solve various biological problems. According to each specific biological problems, we continuously develop and improve relevant biological mass spectrometry technology to solve these biological problems and promote the development of basic research in the field of biology.


Contact:Proteomics Facilities at NIBS

Tel:010-80726688 to 8372

Fax:010-80727513

Address:7 Science Park Road ZGC Life Science Park, Beijing

Code:102206

You can download the sample table of MS analysis in our homepage:the sample table of MS analysis


MS Analysis Equipments:


Representative Publications:

1.

Li, S., Zhang, L., Yao, Q., Li, L., Dong, N., Rong, J., Gao, W., Ding, X., Sun, L., Chen, X., Chen, S.#, and Shao, F.# (2013). Pathogen blocks host death receptor signalling by arginine GlcNAcylation of death domains. Nature501(7466): 242-246.( #共同通讯作者).

2.

Sun, L., Wang, H., Wang, Z., He, S., Chen, S., Liao, D., Wang, L., Yan, J., Liu, W., Lei, X., and Wang, X. (2012). Mixed Lineage Kinase Domain-like Protein Mediates Necrosis Signaling Downstream of RIP3 Kinase. Cell 148(1-2): 213-227

3.

Xu, M., Wang, W., Chen, S.#, and Zhu, B.# (2012). A model for mitotic inheritance of histone lysine methylation. EMBO reports 13(1): 60-67.(#共同通讯作者).

4.

Xu, M., Chen, S.#, and Zhu, B.# (2012). Investigating the cell cycle-associated dynamics of histone modifications using quantitative mass spectrometry.Methods Enzymol. 512: 29-55.(#共同通讯作者).

5.

Zhang, L., Ding, X., Cui, J., Xu, H., Chen, J., Gong, Y. N., Hu, L., Zhou, Y., Ge, J., Lu, Q., Liu, L., Chen, S., and Shao, F. (2011). Cysteine methylation disrupts ubiquitin-chain sensing in NF-kappaB activation. Nature 481(7380): 204-208

6.

Shang, L., Chen, S., Du, F., Li, S., Zhao, L., and Wang, X. (2011). Nutrient starvation elicits an acute autophagic response mediated by Ulk1 dephosphorylation and its subsequent dissociation from AMPK. Proc. Natl. Acad. Sci. U. S. A. 108(12): 4788-4793

7.

Xu, M., Long, C., Chen, X., Huang, C., Chen, S.#, and Zhu, B.# (2010). Partitioning of histone H3-H4 tetramers during DNA replication-dependent chromatin assembly. Science 328(5974): 94-98.(#共同通讯作者).

8.

Cui, J., Yao, Q., Li, S., Ding, X., Lu, Q., Mao, H., Liu, L., Zheng, N., Chen, S., and Shao, F. (2010). Glutamine deamidation and dysfunction of ubiquitin/NEDD8 induced by a bacterial effector family. Science 329(5996): 1215-1218

9.

Tang, C. T., Li, S., Long, C., Cha, J., Huang, G., Li, L., Chen, S.#, and Liu, Y.#(2009). Setting the pace of the Neurospora circadian clock by multiple independent FRQ phosphorylation events. Proc. Natl. Acad. Sci. U. S. A.106(26): 10722-10727.(#共同通讯作者).

10.

Huang, G.*, Chen, S.*, Li, S., Cha, J., Long, C., Li, L., He, Q., and Liu, Y. (2007). Protein kinase A and casein kinases mediate sequential phosphorylation events in the circadian negative feedback loop. Genes Dev. 21(24): 3283-3295.(*共同第一作者).


Publications:

1.

Zhou, H., Lin, H., Chen, S., Becker, K., Yang, Y., Zhao, J., Kudla, J., Schumaker, K. S., and Guo, Y. (2014). Inhibition of the Arabidopsis Salt Overly Sensitive Pathway by 14-3-3 Proteins. Plant Cell

2.

Liu, Z. W., Shao, C. R., Zhang, C. J., Zhou, J. X., Zhang, S. W., Li, L., Chen, S., Huang, H. W., Cai, T., and He, X. J. (2014). The SET domain proteins SUVH2 and SUVH9 are required for Pol V occupancy at RNA-directed DNA methylation loci.PLoS Genet. 10(1): e1003948

3.

Zhou, M., Guo, J., Cha, J., Chae, M., Chen, S., Barral, J. M., Sachs, M. S., and Liu, Y. (2013). Non-optimal codon usage affects expression, structure and function of clock protein FRQ. Nature 495(7439): 111-115

4.

Yuan, G., Ma, B., Yuan, W., Zhang, Z., Chen, P., Ding, X., Feng, L., Shen, X.,Chen, S., Li, G., and Zhu, B. (2013). Histone H2A ubiquitination inhibits the enzymatic activity of H3 lysine 36 methyltransferases. J. Biol. Chem. 288(43): 30832-30842

5.

Xia, S., Cheng, Y. T., Huang, S., Win, J., Soards, A., Jinn, T. L., Jones, J. D., Kamoun, S., Chen, S., Zhang, Y., and Li, X. (2013). Regulation of transcription of nucleotide-binding leucine-rich repeat-encoding genes SNC1 and RPP4 via H3K4 trimethylation. Plant Physiol. 162(3): 1694-1705

6.

Wang, G., Wang, X., Yu, H., Wei, S., Williams, N., Holmes, D. L., Halfmann, R., Naidoo, J., Wang, L., Li, L., Chen, S.Harran, P., and Lei, X. (2013). Small-molecule activation of the TRAIL receptor DR5 in human cancer cells. Nat. Chem. Biol. 9(2): 84-89

7.

Tang, Z., Lin, M. G., Stowe, T. R., Chen, S., Zhu, M., Stearns, T., Franco, B., and Zhong, Q. (2013). Autophagy promotes primary ciliogenesis by removing OFD1 from centriolar satellites. Nature 502(7470): 254-257

8.

Liu, Z., Wu, Y., Yang, F., Zhang, Y., Chen, S., Xie, Q., Tian, X., and Zhou, J. M. (2013). BIK1 interacts with PEPRs to mediate ethylene-induced immunity. Proc. Natl. Acad. Sci. U. S. A. 110(15): 6205-6210

9.

Lin, S., Yan, H., Li, L., Yang, M., Peng, B., Chen, S., Li, W., and Chen, P. R. (2013). Site-specific engineering of chemical functionalities on the surface of live hepatitis D virus. Angew. Chem. Int. Ed. Engl. 52(52): 13970-13974

10.

Liang, B., Peng, P., Chen, S., Li, L., Zhang, M., Cao, D., Yang, J., Li, H., Gui, T., Li, X., and Shen, K. (2013). Characterization and proteomic analysis of ovarian cancer-derived exosomes. Journal of proteomics 80C: 171-182

11.

Li, T. M., Chen, J., Li, X., Ding, X. J., Wu, Y., Zhao, L. F., Chen, S., Lei, X., and Dong, M. Q. (2013). Absolute quantification of a steroid hormone that regulates development in Caenorhabditis elegans. Anal. Chem. 85(19): 9281-9287

12.

Li, S., Zhang, L., Yao, Q., Li, L., Dong, N., Rong, J., Gao, W., Ding, X., Sun, L., Chen, X., Chen, S.#, and Shao, F.# (2013). Pathogen blocks host death receptor signalling by arginine GlcNAcylation of death domains. Nature501(7466): 242-246.( #共同通讯作者).

13.

Zhang, C. J., Ning, Y. Q., Zhang, S. W., Chen, Q., Shao, C. R., Guo, Y. W., Zhou, J. X., Li, L., Chen, S., and He, X. J. (2012). IDN2 and its paralogs form a complex required for RNA-directed DNA methylation. PLoS Genet. 8(5): e1002693

14.

Yang, H., Han, Z., Cao, Y., Fan, D., Li, H., Mo, H., Feng, Y., Liu, L., Wang, Z., Yue, Y., Cui, S., Chen, S., Chai, J., and Ma, L. (2012). A companion cell-dominant and developmentally regulated H3K4 demethylase controls flowering time in Arabidopsis via the repression of FLC expression. PLoS Genet. 8(4): e1002664

15.

Yang, B., Wu, Y. J., Zhu, M., Fan, S. B., Lin, J., Zhang, K., Li, S., Chi, H., Li, Y. X., Chen, H. F., Luo, S. K., Ding, Y. H., Wang, L. H., Hao, Z., Xiu, L. Y., Chen, S., Ye, K., He, S. M., and Dong, M. Q. (2012). Identification of cross-linked peptides from complex samples. Nat. Methods 9(9): 904-906

16.

Xu, M., Wang, W., Chen, S.#, and Zhu, B.# (2012). A model for mitotic inheritance of histone lysine methylation. EMBO reports 13(1): 60-67.(#共同通讯作者).

17.

Xu, M., Chen, S.#, and Zhu, B.# (2012). Investigating the cell cycle-associated dynamics of histone modifications using quantitative mass spectrometry.Methods Enzymol. 512: 29-55.(#共同通讯作者).

18.

Wang, Z., Jiang, H., Chen, S., Du, F., and Wang, X. (2012). The Mitochondrial Phosphatase PGAM5 Functions at the Convergence Point of Multiple Necrotic Death Pathways. Cell 148(1-2): 228-243

19.

Sun, L., Wang, H., Wang, Z., He, S., Chen, S., Liao, D., Wang, L., Yan, J., Liu, W., Lei, X., and Wang, X. (2012). Mixed Lineage Kinase Domain-like Protein Mediates Necrosis Signaling Downstream of RIP3 Kinase. Cell 148(1-2): 213-227

20.

Rong, Y., Liu, M., Ma, L., Du, W., Zhang, H., Tian, Y., Cao, Z., Li, Y., Ren, H., Zhang, C., Li, L., Chen, S., Xi, J., and Yu, L. (2012). Clathrin and phosphatidylinositol-4,5-bisphosphate regulate autophagic lysosome reformation. Nat. Cell Biol. 14(9): 924-934

21.

Lee, A. Y., Chen, W., Stippec, S., Self, J., Yang, F., Ding, X., Chen, S., Juang, Y. C., and Cobb, M. H. (2012). Protein kinase WNK3 regulates the neuronal splicing factor Fox-1. Proc. Natl. Acad. Sci. U. S. A. 109(42): 16841-16846

22.

Kong, Q., Qu, N., Gao, M., Zhang, Z., Ding, X., Yang, F., Li, Y., Dong, O. X., Chen, S., Li, X., and Zhang, Y. (2012). The MEKK1-MKK1/MKK2-MPK4 kinase cascade negatively regulates immunity mediated by a mitogen-activated protein kinase kinase kinase in Arabidopsis. Plant Cell 24(5): 2225-2236

23.

Kato, M., Han, T. W., Xie, S., Shi, K., Du, X., Wu, L. C., Mirzaei, H., Goldsmith, E. J., Longgood, J., Pei, J., Grishin, N. V., Frantz, D. E., Schneider, J. W., Chen, S., Li, L., Sawaya, M. R., Eisenberg, D., Tycko, R., and McKnight, S. L. (2012). Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels. Cell 149(4): 753-767

24.

Feng, F., Yang, F., Rong, W., Wu, X., Zhang, J., Chen, S., He, C., and Zhou, J. M. (2012). A Xanthomonas uridine 5'-monophosphate transferase inhibits plant immune kinases. Nature 485(7396): 114-118

25.

Chen, D., Fan, W., Lu, Y., Ding, X., Chen, S., and Zhong, Q. (2012). A mammalian autophagosome maturation mechanism mediated by TECPR1 and the Atg12-Atg5 conjugate. Mol. Cell 45(5): 629-641

26.

Zhang, L., Ding, X., Cui, J., Xu, H., Chen, J., Gong, Y. N., Hu, L., Zhou, Y., Ge, J., Lu, Q., Liu, L., Chen, S., and Shao, F. (2011). Cysteine methylation disrupts ubiquitin-chain sensing in NF-kappaB activation. Nature 481(7380): 204-208

27.

Yuan, W., Xu, M., Huang, C., Liu, N., Chen, S., and Zhu, B. (2011). H3K36 methylation antagonizes PRC2-mediated H3K27 methylation. J. Biol. Chem.286(10): 7983-7989

28.

Ye, X., Huang, N., Liu, Y., Paroo, Z., Huerta, C., Li, P., Chen, S., Liu, Q., and Zhang, H. (2011). Structure of C3PO and mechanism of human RISC activation.Nat. Struct. Mol. Biol. 18(6): 650-657

29.

Yang, P., Wang, Y., Chen, J., Li, H., Kang, L., Zhang, Y., Chen, S., Zhu, B., and Gao, S. (2011). RCOR2 is a subunit of the LSD1 complex that regulates ESC property and substitutes for SOX2 in reprogramming somatic cells to pluripotency. Stem Cells 29(5): 791-801

30.

Xing, X. F., Li, H., Zhong, X. Y., Zhang, L. H., Wang, X. H., Liu, Y. Q., Jia, S. Q., Shi, T., Niu, Z. J., Peng, Y., Du, H., Zhang, G. G., Hu, Y., Lu, A. P., Li, J. Y., Chen, S., and Ji, J. F. (2011). Phospholipase A2 group IIA expression correlates with prolonged survival in gastric cancer. Histopathology 59(2): 198-206

31.

Wu, H., Chen, X., Xiong, J., Li, Y., Li, H., Ding, X., Liu, S., Chen, S., Gao, S., and Zhu, B. (2011). Histone methyltransferase G9a contributes to H3K27 methylation in vivo. Cell Res. 21(2): 365-367

32.

Wang, W., Chen, Z., Mao, Z., Zhang, H., Ding, X., Chen, S., Zhang, X., Xu, R., and Zhu, B. (2011). Nucleolar protein Spindlin1 recognizes H3K4 methylation and stimulates the expression of rRNA genes. EMBO reports 12(11): 1160-1166

33.

Sun, Q., Zhang, J., Fan, W., Wong, K. N., Ding, X., Chen, S., and Zhong, Q. (2011). The RUN domain of rubicon is important for hVps34 binding, lipid kinase inhibition, and autophagy suppression. J. Biol. Chem. 286(1): 185-191

34.

Shang, L., Chen, S., Du, F., Li, S., Zhao, L., and Wang, X. (2011). Nutrient starvation elicits an acute autophagic response mediated by Ulk1 dephosphorylation and its subsequent dissociation from AMPK. Proc. Natl. Acad. Sci. U. S. A. 108(12): 4788-4793

35.

Liu, Y., Tan, H., Tian, H., Liang, C., Chen, S., and Liu, Q. (2011). Autoantigen La Promotes Efficient RNAi, Antiviral Response, and Transposon Silencing by Facilitating Multiple-Turnover RISC Catalysis. Mol. Cell 44(3): 502-508

36.

Kar, A., Fushimi, K., Zhou, X., Ray, P., Shi, C., Chen, X., Liu, Z., Chen, S., and Wu, J. Y. (2011). RNA helicase p68 (DDX5) regulates tau exon 10 splicing by modulating a stem-loop structure at the 5' splice site. Mol. Cell. Biol. 31(9): 1812-1821

37.

Du, W., Lin, H., Chen, S., Wu, Y., Zhang, J., Fuglsang, A. T., Palmgren, M. G., Wu, W., and Guo, Y. (2011). Phosphorylation of SOS3-like calcium-binding proteins by their interacting SOS2-like protein kinases is a common regulatory mechanism in Arabidopsis. Plant Physiol. 156(4): 2235-2243

38.

Chen, X., Xiong, J., Xu, M., Chen, S.#, and Zhu, B.# (2011). Symmetrical modification within a nucleosome is not required globally for histone lysine methylation. EMBO reports 12(3): 244-251.( #共同通讯作者).

39.

Zhang, J., Li, W., Xiang, T., Liu, Z., Laluk, K., Ding, X., Zou, Y., Gao, M., Zhang, X.,Chen, S., Mengiste, T., Zhang, Y., and Zhou, J. M. (2010). Receptor-like cytoplasmic kinases integrate signaling from multiple plant immune receptors and are targeted by a Pseudomonas syringae effector. Cell host & microbe7(4): 290-301

40.

Xu, M., Long, C., Chen, X., Huang, C., Chen, S.#, and Zhu, B.# (2010). Partitioning of histone H3-H4 tetramers during DNA replication-dependent chromatin assembly. Science 328(5974): 94-98.(#共同通讯作者).

41.

Wang, Y., Li, J., Hou, S., Wang, X., Li, Y., Ren, D., Chen, S., Tang, X., and Zhou, J. M. (2010). A Pseudomonas syringae ADP-ribosyltransferase inhibits Arabidopsis mitogen-activated protein kinase kinases. Plant Cell 22(6): 2033-2044

42.

Fang, M., Shen, Z., Huang, S., Zhao, L., Chen, S., Mak, T. W., and Wang, X. (2010). The ER UDPase ENTPD5 promotes protein N-glycosylation, the Warburg effect, and proliferation in the PTEN pathway. Cell 143(5): 711-724

43.

Fan, W., Tang, Z., Chen, D., Moughon, D., Ding, X., Chen, S., Zhu, M., and Zhong, Q. (2010). Keap1 facilitates p62-mediated ubiquitin aggregate clearance via autophagy. Autophagy 6(5): 614-621

44.

Cui, J., Yao, Q., Li, S., Ding, X., Lu, Q., Mao, H., Liu, L., Zheng, N., Chen, S., and Shao, F. (2010). Glutamine deamidation and dysfunction of ubiquitin/NEDD8 induced by a bacterial effector family. Science 329(5996): 1215-1218

45.

Yuan, W., Xie, J., Long, C., Erdjument-Bromage, H., Ding, X., Zheng, Y., Tempst, P., Chen, S., Zhu, B., and Reinberg, D. (2009). Heterogeneous nuclear ribonucleoprotein L Is a subunit of human KMT3a/Set2 complex required for H3 Lys-36 trimethylation activity in vivo. J. Biol. Chem. 284(23): 15701-15707

46.

Yao, Q., Cui, J., Zhu, Y., Wang, G., Hu, L., Long, C., Cao, R., Liu, X., Huang, N.,Chen, S., Liu, L., and Shao, F. (2009). A bacterial type III effector family uses the papain-like hydrolytic activity to arrest the host cell cycle. Proc. Natl. Acad. Sci. U. S. A. 106(10): 3716-3721

47.

Yang, K., Shi, H. X., Liu, X. Y., Shan, Y. F., Wei, B., Chen, S., and Wang, C. (2009). TRIM21 is essential to sustain IFN regulatory factor 3 activation during antiviral response. J. Immunol. 182(6): 3782-3792

48.

Tang, C. T., Li, S., Long, C., Cha, J., Huang, G., Li, L., Chen, S.#, and Liu, Y.#(2009). Setting the pace of the Neurospora circadian clock by multiple independent FRQ phosphorylation events. Proc. Natl. Acad. Sci. U. S. A.106(26): 10722-10727.(#共同通讯作者).

49.

Paroo, Z., Ye, X., Chen, S., and Liu, Q. (2009). Phosphorylation of the human microRNA-generating complex mediates MAPK/Erk signaling. Cell 139(1): 112-122

50.

Monaghan, J., Xu, F., Gao, M., Zhao, Q., Palma, K., Long, C., Chen, S., Zhang, Y., and Li, X. (2009). Two Prp19-like U-box proteins in the MOS4-associated complex play redundant roles in plant innate immunity. PLoS Pathog 5(7): e1000526

51.

Jia, G., Wang, W., Li, H., Mao, Z., Cai, G., Sun, J., Wu, H., Xu, M., Yang, P., Yuan, W., Chen, S., and Zhu, B. (2009). A systematic evaluation of the compatibility of histones containing methyl-lysine analogues with biochemical reactions. Cell Res. 19(10): 1217-1220

52.

Gao, M., Wang, X., Wang, D., Xu, F., Ding, X., Zhang, Z., Bi, D., Cheng, Y. T.,Chen, S., Li, X., and Zhang, Y. (2009). Regulation of cell death and innate immunity by two receptor-like kinases in Arabidopsis. Cell host & microbe 6(1): 34-44

53.

Ganley, I. G., Lam du, H., Wang, J., Ding, X., Chen, S., and Jiang, X. (2009). ULK1.ATG13.FIP200 complex mediates mTOR signaling and is essential for autophagy. J. Biol. Chem. 284(18): 12297-12305

54.

Sun, Q., Fan, W., Chen, K., Ding, X., Chen, S., and Zhong, Q. (2008). Identification of Barkor as a mammalian autophagy-specific factor for Beclin 1 and class III phosphatidylinositol 3-kinase. Proc. Natl. Acad. Sci. U. S. A.105(49): 19211-19216

55.

Mi, S., Cai, T., Hu, Y., Chen, Y., Hodges, E., Ni, F., Wu, L., Li, S., Zhou, H., Long, C., Chen, S., Hannon, G. J., and Qi, Y. (2008). Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide. Cell133(1): 116-127

56.

Zhu, Y., Li, H., Long, C., Hu, L., Xu, H., Liu, L., Chen, S.#, Wang, D. C.#, and Shao, F.# (2007). Structural insights into the enzymatic mechanism of the pathogenic MAPK phosphothreonine lyase. Mol. Cell 28(5): 899-913.( #共同通讯作者).

57.

Zhang, J., Shao, F., Li, Y., Cui, H., Chen, L., Li, H., Zou, Y., Long, C., Lan, L., Chai, J., Chen, S., Tang, X., and Zhou, J. M. (2007). A Pseudomonas syringae effector inactivates MAPKs to suppress PAMP-induced immunity in plants. Cell host & microbe 1(3): 175-185

58.

Xing, W., Zou, Y., Liu, Q., Liu, J., Luo, X., Huang, Q., Chen, S., Zhu, L., Bi, R., Hao, Q., Wu, J. W., Zhou, J. M., and Chai, J. (2007). The structural basis for activation of plant immunity by bacterial effector protein AvrPto. Nature 449(7159): 243-247

59.

Li, H., Xu, H., Zhou, Y., Zhang, J., Long, C., Li, S., Chen, S., Zhou, J. M., and Shao, F. (2007). The phosphothreonine lyase activity of a bacterial type III effector family. Science 315(5814): 1000-1003

60.

Huang, G.*, Chen, S.*, Li, S., Cha, J., Long, C., Li, L., He, Q., and Liu, Y. (2007). Protein kinase A and casein kinases mediate sequential phosphorylation events in the circadian negative feedback loop. Genes Dev. 21(24): 3283-3295.(*共同第一作者).