Skip to main content


Link to all publications


  • Feltcher Meghan E, Gunawardena Harsha P, Zulauf Kate E, Malik Seidu, Griffin JE, Sassetti CM, Chen X, Braunstein M.Label-free quantitative proteomics reveals a role for the Mycobacterium tuberculosis SecA2 pathway in exporting solute binding proteins and Mce transporters to the cell wall. Molecular & Cellular Proteomics, 2015, March 26.


  • Cui Liu, Yanbao Yu, Feng Liu, John A. Wrobel, Li Zhou, Xin Wei, Harsha P. Gunawardena, Jian Jin, and Xian Chen* (2014) A chromatin activity-based chemoproteomic approach reveals a transcriptional repressome for gene-specific silencing. Nature Communications, Dec.15th, 2014, In press.
  • Guy Aaron Hobbs, Lauren E Mitchell, Megan E. Arrington, Harsha P Gunarwardena, Molly J DeCristo, Xian Chen, Adrienne D Cox, Sharon L Campbell (2014) Redox Regulation of Rac1 by Thiol Oxidation. Free Radical Biology & Medicine. In press.
  • Tadashi Nakagawa, Lei Lv, Makiko Nakagawa, Yanbao Yu, Chao Yu, Ana C. D’Alessio, Keiko Nakayama, Heng-Yu Fan, Xian Chen, (2014) CRL4VprBP E3 ligase promotes monoubiquitylation and chromatin binding of TET dioxygenases. Molecular Cell, in press.
  • Whiteaker JR, Halusa GN, Hoofnagle AN, Sharma V, MacLean B, Yan P, Wrobel JA, Kennedy J,…Contributing authors of NCI Clinical Proteomic Tumor Analysis Consortium (CPTAC), Paulovich AG*. (2014) CPTAC Assay Portal: a repository of targeted proteomic assays. Nature Methods.11(7):703-4.
  • Zhang, B., Wang, J., …Liebler, DC.*, Contributing authors of the NCI CPTAC (2014) Proteogenomic characterization of human colon and rectal cancer. Nature, 513:382-7.
  • Yunlong Li, Xiaofeng Liao, Xiaoxi Zhang, Guicen Ma, Shuai Zuo , Liping Xiao, Galen D. Stucky, Zhugang Wang, Xian Chen, Xiaoqiang Shang, Jie Fan “In-situ Generated Thrombin in the Protein Corona of Zeolite: Relevance of the Functional Proteins to Its Biological Impact”. Nano Research, 2014, 7(10) 1457-1465.
  • Xingnan Zhen, Bo Zhai, Peppi Koivunen, Sandra Shin, Gang Lu, Jiayun Liu, Christoph Geisen, Abhishek Chakraborty, Javid Moslehi, David Smalley, Xin Wei, Xian Chen, Zhengming Chen, Justine Beres, Jing Zhang, Jen Lan Tsao, Mitchell Brenner, Yuqing Zhang, Cheng Fan, Ronald DePinho, Jihye Park, Steven Gygi, William Kaelin, and Qing Zhang “Prolyl Hydroxylation by EglN2 Destabilizes FOXO3a by Blocking its Interaction with the USP9x Deubiquitinase”. Genes & Development, 2014, 28, 1429-1444.
  • Jun Yan, Feng Yan, Zhijun Li, Becky Sinnott, Kathryn M. Cappell, Yanbao Yu, Jinyao Mo, Joseph A. Duncan, Xian Chen, Valerie Cormier-Daire, Angelique W. Whitehurst, “The 3M complex maintains microtubule and genome integrity” Molecular Cell, 2014, 54(5) 791-804.


  • Harsha P. Gunawardena, Meghan E. Feltcher, John A. wrobel, Sheng Gu, Miriam Braunstein, Xian Chen Comparison of the Membrane Proteome of Virulent Mycobacterium tuberculosis and the Attenuated Mycobacterium bovis BCG Vaccine Strain by Label-free Quantitative Proteomics” J. Proteome Research 2013, 12(12), 5463-5474 Web-link to article
  • Hayden JD, Brown LR, Gunawardena HP, Perkowski EF, Chen X, Braunstein M. Reversible acetylation regulates acetate and propionate metabolism in Mycobacterium smegmatis. Microbiology. 2013 Sep;159(Pt 9):1986-99. Web-link to article
  • Tang S, Bai C, Yang P, Chen X. 14-3-3ε boosts bleomycin-induced DNA damage response by inhibiting the drug-resistant activity of MVP. J. Proteome Research. 2013 Jun 7;12(6):2511-24. Web-link to article
  • G. Aaron Hobbs, Marcelo G. Bonini, Harsha P. Gunawardena, Xian Chen, Sharon L. Campbell Free Radical Bio. and Med., 2013, 57, 221-229 “Glutathiolated Ras: Characterization and Implications for Ras Activation” Web-link to article
  • Jainab Khatun, Yanbao Yu, John Wrobel, Christoph, Brian Risk, Harsha P. Gunawardena, Ashley Secrest, Wendy Spitzer, Dennis Crenshaw, Xian Chen and Morgan C. Giddings. BMC Genomics 2013, 14, 141 “Whole human genome proteogenomic mapping for ENCODE cell-line data: identifying protein-coding regions” web-link to article
  • Hui Wang, Dandan Dong, Siwei Tang, Xian Chen* and Qian Gao* (2013) “PPE38 of Mycobacterium marinum triggers the cross-talk of multiple pathways involved in the host response, as revealed by subcellular quantitative proteomics”.J Proteome Research 2013, 12(5) 2055-2066 web-link to article
  • Karen R. Lane, Yanbao Yu, Patrick E. Lackey, Xian Chen, William F. Marzluff, and Jean Cook (2013) “Cell cycle-regulated protein abundance changes in synchronously proliferating HeLa cells include regulation of pre-mRNA splicing proteins.” PLoS One, 8 (3), e58456. web-link to article
  • Ling Xie, Cui Liu, Li Wang, Harsha P. Gunawardena, Yanbao Yu, Ruyun Du, Debra J.Taxman, Penggao Dai, Zhen Yan, Jing Yu, Stephen P. Holly, Leslie V. Parise, Yisong Wan, Jenny P. Ting, and Xian Chen, Cell Reports 2013, 3, 1-11 “Protein Phosphatase 2A Catalytic Subunit C (PP2Ac) Plays a MyD88-dependent, Central Role in the Gene-specific Regulation of Endotoxin Tolerance” Web-link to article
  • Cui Liu, Lin-Chen Li, Wen-Qian Chen, Xian Chen, Zhi-Hong Xu and Shu-Nong Bai (2013) HDA18 Affects Cell Fate in the Arabidopsis Root Epidermis via Histone Acetylation at Four Kinase Genes. Plant Cell, 2013, 112, 107045. web-link to article


  • Siwei Tang, Huimin Bao, Yang Zhang, Jun Yao, Pengyuan Yang, and Xian Chen* “14-3-3ε Mediates the Cell Fate Decision-making Pathways in Response of Hepatocellular Carcinoma to Bleomycin-induced DNA Damage” PloS One, 2012 8(3), e55268
  • G. Aaron Hobbs, Marcelo G. Bonini, Harsha P. Gunawardena, Xian Chen, Sharon L. Campbell Free Radical Bio. and Med., Oct 2012 In Press “Glutathiolated Ras: Characterization and Implications for Ras Activation” Web-link to article
  • Yanbao Yu, Ling Xie, Harsha P.Gunawardena, Christorpher Maier, Maarten Lerkes, Jainab Khatun, Morgan C. Giddings, Xian Chen Anal. Chem, 2012, 84, 9008-9014 “GOFAST: An Integrated Approach for Efficient and Comprehensive Membrane Proteome Analysis” Web-link to article
  • Djebali, S., Davis, C.A.,… Harsha P. Gunawardena …Xian Chen, .. Yanbao Yu…Roderic Guigó*, and Thomas R. Gingeras* (2012) Landscape of transcription in human cells, Nature, 2012, 489, 101-108. Web-link to article
  • Yu Lei, Haitao Wen,Yanbao Yu, Debra J. Taxman, Lu Zhang, Douglas G. Widman, Karen V. Swanson, Kwun-Wah Wen, Blossom A. Damania, Chris B. Moore, Patrick M. Giguère, David P. Siderovski, John Hiscott, Babak Razani, Clay F. Semenkovich, Xian Chen, and Jenny P.-Y. Ting (2012) NLRX1 and TUFM form a mitochondrial complex that regulates type 1 interferon and autophagy. Immunity, 36, 933-46.
  • … Harsha P. Gunawardena, Yanbao Yu, Ling Xie, Xian Chen, …. (The ENCODE Project Consortium) (2012) An Integrated Encyclopedia of DNA Elements in the Human Genome. Nature, 2012, 489, 57-74. Web-link to article
  • Weigang Huang, Wei Sun, Zhiquan Song, Yanbao Yu, Xian Chen, and Qisheng Zhang (2012) Incorporation of a Fluorous Diazirine Group into Phosphatidylinositol 4,5-Bisphosphate to Illustrate its Interaction with ADP-ribosylation Factor 1. Organic and Biomolecular Chemistry. In press.
  • Schroeder GK, Zhou L, Snider MJ, Chen X, Wolfenden R. Flight of a Cytidine Deaminase Complex with an Imperfect Transition State Analogue Inhibitor: Mass Spectrometric Evidence for the Presence of a Trapped Water Molecule. Biochemistry 51(32):6476-86

  • Jennifer Cable, Kirk Prutzman, Harsha P. Gunawardena, Michael D. Schaller, Xian Chen, Sharon Campbell “Phosphorylation of the Focal Adhesion Targeting (FAT) domain of Focal Adhesion Kinase (FAK) reveals a possible mechanism for regulation of pH” Biochemistry 2012, 51(11): 2213-2223. Web-link to article
  • Davis M. F, Zhou L, Ehrenshaft M, Ranguelova K., Gunawardena H. P., Chen, X., Mason R. P., Campbell S. L. Detection Of Ras GTPase Protein Radicals Through Immuno-Spin Trapping.”Free. Radical. Bio & Med 2012, 53, 1339-1345. web-link to article
  • Balázs Bánfai, Hui Jia, Jainab Khatun, Emily Wood, Brian Risk, Will Gundling, Anshul Kundaje, Harsha P. Gunawardena, Yanbao Yu, Ling Xie, Krzysztof Krajewski, Brian D. Strahl, Xian Chen, Peter J. Bickel, Morgan C. Giddings, James B. Brown* and Leonard Lipovich* “Long non-coding RNAs are rarely translated in two human cell lines” Genome Research 2012, 22, 1646-1657. Web-link to article
  • YuanYu Lee, YanBao Yu, Harsha P. Gunawardena, Ling Xie, and Xian Chen “BCLAF1 is a Radiation-induced H2AX-interacting Partner Involved in gH2AX-mediated Regulation of Apoptosis and DNA Repair” Accepted in Cell Death & Disease 2012, e359. Web-link to article


  • Holly SP, Chen X, and Parise LV.(2011) Abundance- and Activity-Based Proteomics in Platelet Biology.Current Proteomics. 8:216-228.
  • The Encode project consortium “A User’s guide to the Encyclopedia of DNA elements (ENCODE)” (2011) PLoS Biology, 9, 1-21. Web-link to article
  • Linhong Jing, Carol E. Parker, David Seo, Maria Warren Hines, Nedyalka Dicheva, Yanbao Yu, Debra Schwinn, Geoffrey S. Ginsburg, and Xian Chen (2011) Discovery of biomarker candidates for coronary artery disease (CAD) from an APOE-knock out mouse model using iTRAQ-based multiplex quantitative proteomics. Proteomics, in press
  • Harsha P. Gunawardena, Yi Huang, Roma Kenjale, Haiyang Wang, Ling Xie, and Xian Chen (2011) Unambiguous characterization of site-specific phosphorylation of leucine-rich repeat Fli-I-interacting protein 2 (LRRFIP2) in toll-like receptor 4 (TLR4)-mediated signaling. Journal of Biological Chemistry, 286, 10897-10910 Web-link to article
  • Yi Huang, Qihui Shi, Chia-Kuang Tsung, Harsha P. Gunawardena, Ling Xie, Yanbao Yu, Xinwen Zhou, Hongjun Liang, Pengyuan Yang, Galen D. Stucky, and Xian Chen* (2011) Optimization of a magnetite microparticle-based phosphopeptide enrichment strategy for identifying phosphorylation in a signal protein isolated by immunoprecipitation. Anal. Biochem, 408, 19-31 Web-link to article


  • Taohua Leng, Na Liu, Yanbao Yu, Chen Zhang, Ruyun Du, and Xian Chen* (2010) Quantitative dissection of progressively dys-regulated networks in coordination with diethyl nitrosamine (DEN)-induced hepato-carcinogenesis. J. Proteome Research, 9, 6207-6219. Web-link to article
  • Kathryn E. Gardner, Li Zhou, Michael A. Parra, Xian Chen, and Brian D. Strahl* (2010) Identification of Lysine 37 of Histone 1 H2B as a Novel Site of Methylation, PLoS ONE, 6 (1 ), e16244 Web-link to article
  • Shuai Zuo, Yan Xue, Shufang Liang, Siwei Tang, Jun Yao, Pengyuan Yang, and Xian Chen* (2010) TNFa-induced time course-dependent changes of NFkB activity are differentially modulated by dynamic interactions between 14-3-3 epsilon and key components in MAPK signal module. J. Proteome Research, 9, 3465–3478. Web-link to article 
  • Yanbao Yu, Taohua Leng, Dong Yun, Na Liu, Jun Yao, Ying Dai, Pengyuan Yang, and Xian Chen* (2010) Dissection of the rat and human platelet proteome: the molecular blueprint for multi-functional platelets and cross-species function evolution. Proteomics, 10, 2444-2457. Web-link to article
  • Ruyun Du, Jing Long, Jun Yao, Xiaoli Yang, Siwei Tang, Shuai Zuo, Yufei He, and Xian Chen* (2010) Subcellular quantitative proteomics reveals multiple pathway cross-talks that coordinate specific signaling and transcription regulation for early host response to LPS. J. Proteome Research, 9, 1805-1821. Web-link to article
  • Xiaoli Yang, Dong Yun, Peng Zou,Jun Yao, Taohua Leng, Huimin Yang, Ruyun Du, Jing Long, and Xian Chen* (2010) Proteomic dissection of cell type-specific H2AX-interacting complex associated with hepatocellular carcinoma. J. Proteome Research, 9, 1402-1405. Web-link to article
  • Kun Lu, Wenjie, Ye, Li Zhou, Leonard Collins, Xian Chen, Avram Gold, Louise Ball, James Swenberg (2010) Structural Characterization of Formaldehyde-induced DNA-Protein Cross-links. J. Am. Chem. Soc., 132, 3388-3399. Web-link to article
  • Shimin Zhao, Wei Xu, Wenqing Jiang, Wei Yu, Yan Lin, Tengfei Zhang, Jun Yao, Li Zhou, Hong Li, Yixue Li, Jiong Shi, Lunxiu Qin, Pengyuan Yang, Xian Chen, Qunying Lei, Kun-Liang Guan*, (2010) Protein acetylation plays an extensive role in regulating cellular metabolism, Science, 327, 1000-1004. Web-link to article


  • Yu-Fei He, Hui-Min Bao, Xiao-Feng Xiao, Shuai Zuo, Ru-Yun Du, Si-Wei Tang, Peng-Yuan Yang, and Xian Chen* (2009) Biotin tagging coupled with amino acid-coded mass tagging (BioCAT) for efficient and precise screening of
    interaction proteome in mammalian cells. Proteomics, 9, 5414-5424.
  • Ling Xie, Linhong Jing, Yanbao Yu, Kazuhiro Nakamura, Carol E. Parker, Gary L. Johnson, and Xian Chen* (2009) In vivo Profiling Endogenous Interactions with Knock-out (iPEIK), Anal Chem. 81 (4),1411-1417.
  • Peigao Dai, Sun Yong Jeoug, Yanbao Yu, Weidong Wu, Ling Xie, and Xian Chen* (2009) Systems Modulation of TLR signaling by dynamic MyD88-interacting partners, J. of Immunology, 182, 3450-3460.
  • Shufang Liang, Yanbao Yu, Pengyuan Yang, Sheng Gu, Yan Xue, and Xian Chen* (2009) Analysis of the protein complex associated with 14-3-3 epsilon by a deuterated-leucine labeling quantitative proteomics strategy. Journal of Chromatography B, 877, 627?634.
  • Yuchun Du, Jianhong Zhou, Jinjiang Fan, Zhiyuan Shen, and Xian Chen* (2009) A streamline proteomic approach for characterizing protein-protein interaction network in a complex. J. Proteome Research, 8, 2211-2217.
  • Kyle Wilcox, Li Zhou, Joshua Jordon, Yi Huang, Yanbao Yu, Rachel L Redler, Xian Chen*, Michael Caplow, and Nikolay V. Dokholyan* (2009) Modifications of SOD1 in human erythrocytes: a possible role in ALS. Journal of Biological Chemistry, 284, 13940-13947.
  • Huimin Bao, Peiming Song, Qingping Liu, Yinkun Liu, Dong Yun, Hexige Saiyin, Ruyun Du, Yang Zhang, Huizhi Fan, Pengyuan Yang, and Xian Chen* (2009) Quantitative Proteomic Analysis of a Paired Human Liver Healthy Versus Carcinoma Cell Lines with the Same Genetic Background to Identify Potential Hepatocellular Carcinoma Markers, Proteomics (Clinic Applications), 3, 705-719.
  • Peiming Song, Huimin Bao, Yanbao Yu, Yan Xue, Dong Yun, Yang Zhang, Yufei He, Yinkun Liu, Qingping Liu, Haojie Lu, Huizhi Fan, Jianhua Luo, Pengyuan Yang, and Xian Chen* (2009) Comprehensive Profiling of Metastasis-related Proteins in Paired Hepatocelluar Carcinoma Cells with Different Metastasis Potential, Proteomics (Clinic Applications),3, 841-852.
  • Alderman, J. McKee; Flurkey, Kevin; Brooks, Natasha L.; Naik, Sneha B.; Gutierrez, Jonathan M.; Srinivas, Urmila; Ziara, Kristen B.; Jing, Linhong; Boysen, Gunnar; Bronson, Rod; Klebanov, Simon; Chen, Xian; Swenberg, James A.; Stridsberg, Mats; Parker, Carol E.; Harrison, David E.; Combs, Terry P.* (2009) Neuroendocrine inhibition of glucose production and resistance to cancer in dwarf mice. Experimental Gerontology, 44(1-2), 26-33.


  • Sheng Gu, Tianyi Wang, and Xian Chen* (2008) Quantitative Proteomic Analysis of TLR4-Mediated Immune Response by Multiplex Amino Acid Coded Mass-tagging. Proteomics, 8:3061-3070.
  • Yan Xue, Dong Yun, Alex Esmon, Peng Zou, Shuai Zuo, Yanbao Yu, Fuchu He, Pengyuan Yang, and Xian Chen* (2008) Proteomic Dissection of Agonist-specific TLR-mediated Inflammatory Responses on Macrophages at Subcellular Resolution, J. Proteome Research, 7 (8), 3180–3193.
  • Weidong Wu, Neil E. Alexis, Xian Chen, Philip A. Bromberg, and David B. Peden (2008) Involvement of Mitogen-activated Protein Kinases and NFB in LPS-induced CD40 Expression on Human Monocytes. Toxicology and Applied Pharmacology, 228(2):135-4.


  • Xian Chen*, Liwei Sun, Yubao Yu, Yue Yan, and Pengyuan Yang (2007) Amino Acid-coded Tagging-based Approaches in Quantitative Proteomics. Expert Review of Proteomics, 4:25-37.
  • Yun Liu, Yan Xue, Ji Ji, Xian Chen, Pengyuan Yang, Hubert H. Girault, Baohong Liu (2007) Au Nanoparticles-assembled Microfluidic Reactor for Efficient On-line Proteolysis. Mol. Cell. Proteomics, 8:1428-1436.


  • Tianyi Wang, Tapani Ronni, Sheng Gu, Susan Sun, Helen Yin, and Xian Chen* (2006) Fliih Negatively Modulates the MyD88-dependent Signaling Pathway. J. of Immunology, 176:1355-1362.
  • Yu-Chun Du, Sheng Gu, Jianhong Zhou, Tianyi Wang, Hong Cai, Mark A. MacInnes, E. Morton Bradbury, and Xian Chen* (2006) The Dynamic Alterations of H2AX Complex during DNA Repair Detected by a Proteomic Approach Reveal the Critical Roles of Ca2+/Calmodulin in the Ionizing Radiation-induced Cell Cycle Arrest. Mol. Cell. Proteomics, 5:1033-1044.
  • Wenqing Shui, Jie Fan, Pengyuan Yang, Jianjun Zhai, Jie Lei, Yan Yan, Dongyuan Zhao*, and Xian Chen* (2006) A Novel in situ Proteolytic Reactor for Proteomics Research, Anal. Chem., 78:4811-4819.


  • Tianyi Wang, Sheng Gu, Tapani Ronni, Yu-Chun Du, and Xian Chen* (2005) An in vivo Dual-tagging Proteomic Approach in Studying Signaling Pathways in Immune Response. J. Proteome Research, 4:941-949.
  • Kwasi G. Mawuenyega, Christian V. Forst, Karen M. Dobos, John T. Belisle, Andrew Bradbury, Jin Chen, Edwin M. Bradbury, and Xian Chen* (2005) Mycobacterium Tuberculosis Functional Network Analysis by Global Subcellular Protein Profiling. Mol. Biol. Cell, 16, 396-404.
  • Sheng Gu and Xian Chen* (2005) Determination of Comprehensive Proteomic Profiles Using Amino Acid-coded Tagging Mass Spectrometry (review article). The Analyst, 130(9), 1225-1231.
  • Wenqing Shui, Yinkun Liu, Huizhi Fan, Huimin Bao, Shufang Liang, Pengyuan Yang*, and Xian Chen* (2005) Enhancing TOF/TOF-based de novo Sequencing Capability for High Throughput Protein Identification. J. Proteome Research, 4, 83-90.
  • Zhihe Liu, Huimei Lu, Honglian Shi, Yuchun Du, Jian Yu, Xian Chen, Ke Jian J. Liu, and Chien-an A. Hu (2005) PUMA Over-Expression Induces ROS Generation and Stathmin Degradation in Colorectal Cancer Cells. Cancer Research, 65(5),1647-1654.


  • Jacob M. Rothfork, Graham Timmins, Michael N. Harris, Xian Chen, Aldons J. Lusis, Michael Otto, Ambrose L. Cheung, and Hattie D. Gresham (2004) Inactivation of a bacterial virulence pheromone by phagocyte-derived oxidants: New role for the NADPH oxidase in host defense. Proc. Natl. Acad. Sci. USA, 101(38) 13867-13872.
  • Michael N Harris, Bulent Ozpolat, Fadi Abdi, Sheng Gu, Kwasi Muwuenyega, Gabriel Lopez-Berestein*, and Xian Chen* (2004) Comparative Proteomic Analyses of ATRA Induced Acute Promyelocytic Leukemia (APL) Cells Reveals A Systematic Post-Transcriptional Control in APL. Blood, 104(5):1314-1323. (Also see editorial comments by S. Collins on 104(5) 1234-1235).
  • Sheng Gu, Yuchun Du, Jin Chen, Zhihe Liu, Chien-An A. Hu, and Xian Chen* (2004) Large-scale Quantitative Proteomic Study of PUMA-induced Apoptosis using Two-dimensional Liquid Chromatography–Mass Spectrometry Coupled with Amino Acid-coded Mass Tagging. J. Proteome Research, 3, 1191-1200.
  • Sheng Gu, Zhihe Liu, Songqin Pan, Zeyu Jiang, Huimei Lu, Or Amit,, Jian Yu, Chien-An A. Hu, Xian Chen* (2004) Global Investigation of p53-Induced Apoptosis Through Quantitative Profiling Regulatory Proteins Using Comparative Amino Acid-Coded Tagging Proteomics. Mol. Cell. Proteomics. 3(10)998-1008.
  • Weon Bae and Xian Chen* (2004) Proteomic Study for the Cellular Responses to Cadmium in Schizosaccharomyces pombe through Amino Acid-coded Mass Tagging and LC-MS/MS. Mol. Cell. Proteomics. 3(6):596-607.
  • Jianjun Zhai, Wenqing Shui, Xuejiao Yu, Yanling Yu, Huimin Bao, Xian Chen, and Pengyuan Yang (2004) A Modified Nanospray Tip Coupled to Mass Spectrometer for Analyzing Enzymatic Peptides. Rapid Comm. In Mass Spec, 18:1177-1179.


  • Sheng Gu, Jin Chen, Karen M. Dobos, Edwin M. Bradbury, John T. Belisle, and Xian Chen* (2003) Proteomic View of the Membrane Constituents of a Mycobacterium Tuberculosis Strain. Mol. Cell. Proteomics, 2(12):1284-1296.
  • Sheng Gu, Songqin Pan, E. Morton Bradbury, and Xian Chen* (2003) Precise Peptide Sequencing and Protein Quantification in the Human Proteome through in vivo Lysine-Specific Mass Tagging. J. of Am. Soc. for Mass Spec. 14:1-7.
  • Songqin Pan, Sheng Gu, E. Morton Bradbury, and Xian Chen* (2003) Single peptide-based protein identification in human proteome through MALDI-TOF MS Coupled with Amino Acids Coded Mass-Tagging. Anal. Chem. 75:1316-1324.


  • Fadi Abdi, E. Morton Bradbury, Norman Dogget, and Xian Chen* (2002) Validation of DNA Sequences Using Mass Spectrometry Coupled with Nucleotide Mass Tagging. Genome Research, 12:1135-1141.
  • Haining Zhu, Songqin Pan, Sheng Gu, E. Morton Bradbury, and Xian Chen* (2002) Amino Acid Residue-Specific Stable Isotope Labeling for Quantitative Proteomics. Rapid Comm. In Mass Spec, 16:1-9.
  • Sheng Gu, Songqin Pan, E. Morton Bradbury, and Xian Chen* (2002) Use of Deuterium-Labeled Lysine for Efficient Protein Identification and Peptide de novo Sequencing. Anal. Chem. 74:5774-5785.
  • Olaf Lubeck, Chris Sewell, Sheng Gu, Xian Chen, and Michael Cai (2002) New Computational Approaches for de Novo Peptide Sequencing from MS/MS Experiments. Proc. of IEEE, 90:1868-1874.
  • John R. Engen, E. Morton Bradbury, and Xian Chen* (2002) Using stable-isotope labeled proteins for hydrogen exchange studies in complex mixtures. Anal. Chem. 74:1680-1686.
  • Haining Zhu, Tom Hunter, Songqin Pan, E. Morton Bradbury, Peter Yau and Xian Chen* (2002) Residue-specific Mass Signatures for the Efficient Identification of Protein Modifications by Mass Spectrometry. Anal. Chem. 74:1687-1694.


  • Tom Hunter, E. Li Yang, Haining Zhu, Morton Bradbury, Vahid Majidi, and Xian Chen* (2001) Rapid identification of yeast complex mixtures using peptide mass mapping constrained with stable isotope-tagged peptides. Anal. Chem. 73:4891-4902.
  • Fadi Abdi, E. Morton Bradbury, Norman Dogget, and Xian Chen* (2001) Rapid identification of single nucleotide polymorphism using mass-tagged deoxynucleotide. Nuclei. Acid Res. 29:13 e61.

2000 – 1998

  • Xian Chen*, Lloyd M. Smith, and E. M. Bradbury (2000) Site-specific mass tagging with stable isotopes in proteins for accurate and efficient protein identification. Anal. Chem. 72:1134-1143.
  • Spiro, C., Pelletier, R., Rolfsmeier, M.L., Dixon, M.J., Lahue, R.S., Gupta, G., Park, M.S., Xian Chen, Mariappan, S.V.S., and McMurray, C.T. (1999) Inhibition of FEN-1 processing by DNA secondary structure at trinucleotide repeats. Molecular Cell 4:1079-1085.
  • Xian Chen*, Zhengdong Fei, Lloyd M. Smith, E. M. Bradbury, and Vahid Majidi (1999) Stable isotope-assisted MALDI-TOF mass spectrometry allows accurate determination of base compositions of PCR products. Anal. Chem. 71:3118-3125.
  • Catasti, P., Chen, X., Mariappan, S.V.S., Bradbury, E.M. and Gupta, G. (1999) DNA repeats in the human genome; Structual biology and Functional Genomics. Genetica 106:15-36.
  • Chen, X., Mariappan, S.V.S., Kelley, J.J., Bushweller, J.H., Bradbury, E. M., and Gupta, G. (1998) A PCR-based method for uniform (13C, 15N) labeling of long DNA oligomers. FEBS Lett. 436:372-376.
  • A. Marquis Gacy, Geoffrey M. Goellner, Craig Spiro, Xian Chen, Goutam Gupta, E. Morton Bradbury, Roy B. Dyer, Marci J. Mikesell, Janet Z. Yao, Aaron J. Johnson, Andrea Richter, Serge B. Melançon, and Cynthia T. McMurray (1998) GAA instability in Friedreich’s Ataxia shares a common, DNA-directed and intraallelic mechanism with other trinucleotide diseases. Molecular Cell 1 (4): 583-593.

Prior to 1998

  • Catasti, P., Chen, X., Bradbury, E. M., and Gupta, G. (1997) The C-rich strands of the insulin mini-satellite repeats (ILPR) form ordered array of C+C Paired i-motifs. J. Mol. Biol. 272:369-382.
  • Mariappan, S. V., Catasti, P., Chen, X., Bradbury, E. M., and Gupta, G. (1996) Solution structures of the individual single strands of the fragile X DNA triplets, (GCC)n•(GGC)n. Nuclei. Acid Res. 24:784.
  • Catasti, P., Chen, X., Moyzis, R. K., Bradbury, E. M., and Gupta, G. (1996) Structure-function correlations of the insulin-linked polymorphic region. J. Mol. Biol., 264:534-545.
  • Chen, X., Mariappan, S. V., Catasti, P., Ratiliff, R., Moyzis, R. K., Laayoun, A., Smith, S. S., Bradbury, E. M., and Gupta, G. (1995) Hairpins are formed by the single DNA strands of the fragile-x triplet repeats: structure and biologic implications. Proc. Natl. Acad. Sci. USA 92:5199.
  • C.K.Tu, Xian Chen, X. Ren, P.V. LoGrasso, P. L. Laipis, and D. N. Silverman (1994) Interactions of active-site residues and catalytic activity of human carbonic anhydrase III. Journal of Biological Chemistry, 269:23002-23006.
  • D.N. Silverman, T.K. Tu, Xian Chen, P.V. LoGrasso, and P. L. Laipis (1993) Rate equilibria relationships in intramolecular proton transfer in human carbonic anhydrase III. Biochemistry 32:10757-10752.
  • Xian Chen, C.K. Tu, P. V. LoGrasso, P.J. Laipis and D. N. Silverman (1993) Interaction and influence of phenylalanine-198 and threonine-199 on catalysis by human carbonic anhydrase III. Biochemistry 32:7861-7865.
  • P.V. LoGrasso, C.K. TU, Xian Chen, P.J. Laipis and D.N. Silverman (1993) Influence of amino acid replacement at position 198 on catalytic properties of zinc-bound water in human carbonic anhydrase III. Biochemistry 32:5786-5791.
  • S. Taoka, Xian Chen, R.W.Tarnuzzer, P.J. Laipis and D.N. Silverman (1992) Catalysis by mutants of HCA II – effects of replacing hydrophobic residues 198 and 204. Biochimica et Biophysica Acta 1159:274-278.
  • L. M. Jackman and Xian Chen (1992) Solvation of aggregates of lithium phenolates by hexamethylphosphoric triamide (HMPA). HMPA causes both aggregation and deaggregation. J. Am. Chem. Soc. 114:403-411.
  • L. M. Jackman and Xian Chen (1997) Degenerate transesterification of dimeric Lithium 2,4,6 trimethylphenolate and a further observation on the reaction of tetramers. J. Am. Chem. Soc. 119:8681-8684.

Schroeder GK, Zhou L, Snider MJ, Chen X, Wolfenden R. Flight of a Cytidine Deaminase Complex with an Imperfect Transition State Analogue Inhibitor: Mass Spectrometric Evidence for the Presence of a Trapped Water Molecule. Biochemistry In Press