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.
Technology Expertise Keywords
Proteomics; mass spectrometry; glycoproteimics; glycomics; phosphoproteomics
Selected Publications
Zhang H, Liu T, Zhang Z, Payne SH, Zhang B, McDermott JE, Zhou J, Petyuk VA, Chen L, Ray D, Sun S, Yang F, Chen L, Wang J, Shah P, Cha S-W, Aiyetan P, Woo S, Tian Y, Gritsenko MA, Choi C, Monroe ME, Thomas S, Moore RJ, ,Yu K-H, Tabb DL, Fenyö D, Bafna V, Wang Y, Rodriguez H, Boja ES, Hiltke T, Rivers RC, Sokoll L, Zhu H, Shih I-M, Pandey A, Zhang B, Snyder MP, Levine DA, Smith RD, Chan DW, Rodland KD, and the CPTAC investigators. Deep proteogenomic characterization of human ovarian cancer. Cell. 2016; 166: 755-765.
Sun S, Shah P, Toghi Eshghi S, Yang W, Trikannad N, Yang S, Chen L, Aiyetan P, Hoti NU, Zhang Z, Chan DW, Zhang H*. Comprehensive analysis of protein glycosylation by solid-phase extraction of N-linked glycans and glycosite-containing peptides. Nature Biotechnology. 2016; 34: 84-88.
Shah P, Wang X, Yang W, Toghi Eshghi S, Sun S, Hoti N, Pasay J, Rubin A, Zhang H*. Integrated proteomic and glycoproteomic analyses of prostate cancer cells reveals glycoprotein alteration in protein abundance and glycosylation. Molecular & Cellular Proteomics. 2015; 14: 2753-2763.
Toghi Eshghi S, Shah P, Yang W, Li X, Zhang H*. GPQuest: A Spectral Library Matching Algorithm for Site-Specific Assignment of Spectra from Tandem Mass Spectrometric Analysis of Intact Glycopeptides. Analytical Chemistry. 2015; 87: 5181-5188.
Zhang, H., Li, X. J., Martin, D. B., and Aebersold, R. Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nature Biotechnology (2003) 21:660.
Patents
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.
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.
