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Hui Zhang, M.S., Ph.D.

Photo of Dr. Hui Zhang, M.S., Ph.D.

Director, Mass Spectrometry Core Facility, Center for Biomarker Discovery and Translation, Johns Hopkins University

Associate Professor of Pathology

Research Interests: Protein function and disease progression; Proteome scale; Protein modification

Contact for Research Inquiries

400 N. Broadway
Smith Building, Room 4011
Baltimore, MD 21287 map


Dr. Hui Zhang is an associate professor of pathology at the Johns Hopkins University School of Medicine. She specializes in clinical chemistry, with particular emphasis on protein modification on the proteome scale and the effects of modification on protein function and disease progression.

Dr. Zhang received her B.S. in plant biochemistry and her M.S. in gene and protein engineering, both from Beijing University. She completed her Ph.D. in biochemistry at the University of Pennsylvania in 1999, and subsequently conducted postdoctoral research in protein chemistry at the Institute for Systems Biology. She joined the faculty of Johns Hopkins in 2006 as an assistant professor and became an associate professor in 2011.

Dr. Zhang has authored or co-authored more than 120 peer-reviewed publications and four book chapters, holds five patents, and has won numerous other awards of distinction for her work. She is a member of several professional organizations and sits on the Board of Directors of the United States Human Proteomic Organization. She is the Associate Editor of the journal Clinical Proteomics and sits on the editorial board of Clinical Proteomics. more


  • Director, Mass Spectrometry Core Facility, Center for Biomarker Discovery and Translation, Johns Hopkins University
  • Associate Professor of Pathology
  • Associate Professor of Oncology

Departments / Divisions



  • B.S., Beijing University (China) (1989)
  • M.S., Beijing University (China) (1992)
  • Ph.D., University of Pennsylvania (Pennsylvania) (1999)

Additional Training

Institute for Systems Biology, Seattle, WA, 2003, Protein Chemistry

Research & Publications

Research Summary

Dr. Zhang studies protein modification on the proteome scale and the effects of modification on protein function and disease progression. For the past few years, her research has focused on the development of high-throughput technologies to isolate and identify two of the most abundant protein modifications - phosphorylation and glycosylation.

One technology enables capturing and identification of modified peptides using affinity chromatography. To do so, she has developed a group of antibodies reactive against a variety of protein modification sites, such as phosphorylation, nitration, acetylation, and substrates of a specific modification enzyme, etc. Among those, phospho-specific antibodies have enabled isolation of a large number of phosphorylated peptides that can be subsequently identified by tandem mass spectrometry.

A second technology enables capturing glycopeptides using solid phase extraction, which has become a powerful tool to analyze glycoproteins on cell surface and in body fluids. Thus far, thousands of novel glycosylation sites have been identified from different tissues using this novel glycopeptide capture technology; this significantly expends the limited number of glycosylation sites experimentally identified prior to the new technology.

These methods are highly sensitive, holding a strong promise for discovering low abundance disease marker proteins in tissue, plasma or other body fluids.

Currently, Dr. Zhang is applying these proteomics technologies to determine protein modifications associated with cancer, which well help for early detection and improved monitoring of therapeutic effects. She is also developing novel methods to study protein modifications that will have major implications for a wide range of health issues.

Selected Publications

Hoofnagle AN, Whiteaker JR, Carr SA, Kuhn E, Liu T, Massoni SA with Zhang H et al., Recommendations for the Generation, Quantification, Storage, and Handling of Peptides Used for Mass Spectrometry–Based Assays. Clin Chem 2016; Accepted.

Yang S, Wang M, Chen L, Yin B, Song G, Turko IV,. Phinney KW, Betenbaugh MJ, Zhang H*, Li S*. QUANTITY: An Isobaric Tag for Quantitative Glycomics. Sci Rep. 2015; Accepted.

Kumar A, Baycin-Hizal D, Wolozny D, Ebdrup Pedersen L, Lewis NE, Heffner K, Chaerkady R, Cole RN, Shiloach J, Zhang H, Bowen MA, Betenbaugh MJ*. Elucidation of the CHO super-ome (CHO-SO) by proteoinformatics. J Proteome Res. 2015; Accepted.

Zhu G, Liu Z, Epstein JI, Davis C, Christudass CS, Carter HB, Landis P, Zhang H, Chung J, Hewitt SM, Miller MC, Veltri RW*. A novel quantitative multiplex tissue immunoblotting for biomarkers predicts a prostate cancer aggressive phenotype. Cancer Epidem Biomar. 2015; Accepted.

DeLeon-Pennell KY, Tian Y, Zhang B, Cates CA, Padmanabhan Iyer R, Cannon P, Shah P, Aiyetan P, Halade GV, Ma Y, Flynn E, Zhang Z, Jin YF, Zhang H, Lindsey ML*. CD36 Is a Matrix Metalloproteinase-9 Substrate that Stimulates Neutrophil Apoptosis and Removal during Cardiac Remodeling Circ Cardiovasc Genet. 2015; Accepted.

Yang S, Rubin A, Toghi Eshghi S, Zhang H*. Chemoenzymatic method for glycomics: isolation, identification, and quantitation. Proteomics. 2015; Sep 21. doi: 10.1002/pmic.201500266.

Tian Y, Zhou Y, Elliott S, Aebersold R, and Zhang H. "Solid-phase extraction of N-linked glycopeptides." Nature Protocols (2007) 2: 334.

Zhang H, Liu AY, Loriaux P, Wollscheid B, Zhou Y, Watts JD, and Aebersold R. "Mass spectrometric detection of tissue-derived proteins in blood." Molecular & Cellular Proteomics (2007) 6: 64.

Zhang H, Loriaux P, Eng J, Campbell D, Keller A, Moss P, Bonneau R, Zhang N, Zhou Y, Wollscheid B, Cooke K, Yi EC, Lee H, Peskind ER, Zhang J, Smith RD, and Aebersold R. "UniPep, a database for human N-linked glycosites: A Resource for Biomarker Discovery." Genome Biology (2006) 7: R73.

Zhang H, Li XJ, Martin DB, and Aebersold R. "Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry." Nature Biotechnology (2003) 21:660.

Zhang H, Zha X, Tan Y, Hornbeck PV, Mastrangelo AJ, Alessi DR, Polakiewicz RD, and Comb MJ. "Phosphoprotein analysis using antibodies broadly reactive against phosphorylated motifs." Journal of Biological Chemistry (2002) 277:39379.


Production of Motif-Specific and Context-Independent Antibodies Using Peptide Libraries as Antigens
Patent # 7,259,022 | 11/13/2001

A method is provided for producing motif-specific, context-independent antibodies which recognize a plurality of peptides or proteins within a genome that contain the same motif. The method includes the step of immunizing a host with a degenerate peptide library antigen featuring (i) a fixed target motif containing one or more invariant amino acids including at least one modified amino acid, and (ii) a plurality of degenerate amino adds flanking the motif. Motif-specific, context-independent antibodies produced by the disclosed method are also provided. The method encompasses motifs consisting of a single modified amino acid, as well as short motifs comprising multiple invariant amino acids including one or more modified amino acids, such as all or part of kinase consensus substrate motifs, protein-protein binding motifs, or other cell signaling motifs. Methods of using the antibodies, e.g. for genome-wide profiling, are also provided.

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Immunoaffinity Isolation of Modified Peptides From Complex Mixtures
Patent # 7,198,896 | 06/19/2002

The invention provides methods for isolating a modified peptide from a complex mixture of peptides, the method comprising the steps of: (a) obtaining a proteinaceous preparation from an organism, wherein the preparation comprises modified peptides from two or more different proteins; (b) contacting the preparation with at least one immobilized modification-specific antibody; and (c) isolating at least one modified peptide specifically bound by the immobilized modification-specific antibody in step (b). The method may further comprise the step of (d) characterizing the modified peptide isolated in step (c) by mass spectrometry (MS), tandem mass spectrometry (MS--MS), and/or MS.sup.3 analysis, or the step of (e) utilizing a search program to substantially match the spectra obtained for the modified peptide during the characterization of step (d) with the spectra for a known peptide sequence, thereby identifying the parent protein(s) of the modified peptide. Also provided are an immunoaffinity isolation device comprising a modification-specific antibody, and antibodies against novel UFD1 and PTN6 phosphorylation sites.

Methods for Quantitative Proteome Analysis of Glycoproteins
Patent # 7183118B2 | 06/03/2003

The invention provides a method for identifying and quantifying polyglycopeptides in a sample. The method can include the steps of immobilizing glycopolypeptides to a solid support; cleaving the immobilized glycopolypeptides, thereby releasing non-glycosylated peptides and retaining immobilized glycopeptides; releasing the glycopeptides from the solid support; and analyzing the released glycopeptides. The method can further include the step of identifying one or more glycopeptides, for example, using mass spectrometry.

Affinity Capture Of Peptides By Microarray And Related Methods
Patent # 7,794,947 | 07/10/2003

The invention provides methods of detecting polypeptides in a sample. The method can include the steps of cleaving polypeptides in a test sample to generate peptides; adding a predetermined amount of isotopically labeled peptide standards to the cleaved test sample, wherein the peptide standards correspond to peptides cleaved with the same reagent used to cleave the test sample; contacting the cleaved test sample containing peptide standards with an array of immobilized binding agents specific for the peptide standards; washing the array to remove unbound peptides, thereby retaining affinity captured sample peptides and standard peptides; analyzing the affinity captured peptides using mass spectrometry; and determining the presence of bound test peptides and standard peptides. The method can further include the step of quantifying the amount of the test peptides by comparing the ratio of test peptide to corresponding standard peptide.

Biomarkers for Prostate Cancer.
Patent # 8,603,734 | 06/04/2007

The instant invention provides methods and compositions for the detection of prostate cancer is a subject. In one embodiment, a method of detecting prostate cancer in a subject comprises the steps of (a) detecting the presence of at least one biomarker listed in Table 1 in a serum sample, wherein the presence of the biomarker in the serum sample is indicative of prostate cancer.

Academic Affiliations & Courses

Courses and Syllabi

  • Techniques in Glycobiology (ME340.710)
    Classroom Instruction and Laboratory Instruction
    Johns Hopkins University School of Medicine
  • Fundamentals of Glycobiology (ME340.709)
    Classroom Instruction
    Johns Hopkins University School of Medicine
  • Mass Spectrometry, lecturer for course “Pharmacology Tutorials" organized by Dr. Heng Zhu et al.
    Classroom Instruction

Activities & Honors


  • Pre-doctoral Fellowship, American Heart Association, 1997
  • Technology Development Award, Cell Signaling Technology, 2003
  • Young Scientist Award, Human Proteome Organization (HUPO), 2004
  • Selected to Board of Director, United States Human Proteomic Organization, 2012
  • Elected as a Council Member, World Human Proteomic Organization (HUPO), 2015


  • American Chemical Society (ACS)
  • American Society for Biochemistry and Molecular Biology (ASBMB)
  • American Society for Mass Spectrometry (ASMS)
  • Society for Glycobiology
  • United States Human Proteomic Organization (US HUPO)
  • Chinese American Society for Mass Spectrometry (CASMS), 2015
  • American Association for Cancer Research (AACR), 2015
  • World Human Proteomic Organization (HUPO), 2010

Professional Activities

  • Member, Editorial Board of Clinical Proteomics, 2011
  • Associate Editor, Journal of Intergrated-omics, 2010
  • Guest editor of two special issues, Clinical Proteomics on Glycoproteomics, 2008
  • Associate Editor, Clinical Proteomics, 2011
  • Guest Editor, Special Issue of Clinical Proteomics on Glycoproteomics and Glycomics, 2013 - 2013
  • Member, Editorial Board of Journal of Bioinformatics, 2014
  • Member, Search Committee on Endowed Chairs of Bloomberg Distinguished Professorships, 2015
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