Abstract

The ultimate goals of this proposal are to develop broadly applicable tools to analyze glycopeptides in complex matrices and to apply those tools for the analysis of human milk and aggressive breast cancer cells. This work would be accomplished by completing three specific aims: (1) Complete our fully automated glycopeptide analysis tool package, which we started during the first period of this grant's funding (2) Develop the usage of massive inclusion lists to increase the number of glycopeptide ions characterized by MS/MS. (3) Tackle two challenges in glycopeptide analyses that are beyond the reach of today's technology: Project 1) Identify glycopeptide-based biomarkers that are only present in aggressive breast cancer. Project 2) Provide a complete profiling of N- and O-linked glycopeptides in human milk. The bulk of the work would be completed by combining expertise in software design, biological sample handling, HPLC, and mass spectrometry to develop the necessary tools. The utility of the tools would be demonstrated by applying them to complete projects relevant women's health: Specifically, we would provide a more detailed insight into the unique properties of human milk than has ever before been provided, and we would characterize the glycosylation on 10-50 known glycopeptide markers of aggressive breast cancer. In addition to the contributions we make to women's health, this work would drive the field of glycoproteomics forward: The methods for glycoprotein analysis are enabling bioanalytical technologies that can be used in a variety of venues, from protein structure/function analyses to pharmaceutical development, to biomarker discovery and development.

Public Health Relevance

We aim to develop tools for the rapid analysis of glycopeptides and to characterize glycopeptides in human milk and aggressive breast cancer cells. The tools we would develop are broadly applicable to biomarker discovery and biochemical studies. The glycopeptides we characterize may be useful for identifying aggressive breast cancer.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM103547-08
Application #
9302462
Study Section
Enabling Bioanalytical and Imaging Technologies Study Section (EBIT)
Program Officer
Smith, Ward
Project Start
2009-09-15
Project End
2019-06-30
Budget Start
2017-07-01
Budget End
2019-06-30
Support Year
8
Fiscal Year
2017
Total Cost
Indirect Cost

  Institution

Name
University of Kansas Lawrence
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
076248616
City
Lawrence
State
KS
Country
United States
Zip Code
66045

  Publications

Lakbub, Jude C; Su, Xiaomeng; Hua, David et al. (2018) Dissecting the Dissociation Patterns of Fucosylated Glycopeptides Undergoing CID: A Case Study in Improving Automated Glycopeptide Analysis Scoring Algorithms. Anal Methods 10:256-262
Lakbub, Jude C; Su, Xiaomeng; Zhu, Zhikai et al. (2017) Two New Tools for Glycopeptide Analysis Researchers: A Glycopeptide Decoy Generator and a Large Data Set of Assigned CID Spectra of Glycopeptides. J Proteome Res 16:3002-3008
Go, Eden P; Ding, Haitao; Zhang, Shijian et al. (2017) Glycosylation Benchmark Profile for HIV-1 Envelope Glycoprotein Production Based on Eleven Env Trimers. J Virol 91:
Hu, Wenting; Su, Xiaomeng; Zhu, Zhikai et al. (2017) GlycoPep MassList: software to generate massive inclusion lists for glycopeptide analyses. Anal Bioanal Chem 409:561-570
Lakbub, Jude C; Clark, Daniel F; Shah, Ishan S et al. (2016) Disulfide Bond Characterization of Endogenous IgG3 Monoclonal Antibodies Using LC-MS: An Investigation of IgG3 Disulfide-mediated Isoforms. Anal Methods 8:6046-6055
Go, Eden P; Cupo, Albert; Ringe, Rajesh et al. (2016) Native Conformation and Canonical Disulfide Bond Formation Are Interlinked Properties of HIV-1 Env Glycoproteins. J Virol 90:2884-94
Imaduwage, Kasun P; Go, Eden P; Zhu, Zhikai et al. (2016) HAMS: High-Affinity Mass Spectrometry Screening. A High-Throughput Screening Method for Identifying the Tightest-Binding Lead Compounds for Target Proteins with No False Positive Identifications. J Am Soc Mass Spectrom 27:1870-1877
Go, Eden P; Herschhorn, Alon; Gu, Christopher et al. (2015) Comparative Analysis of the Glycosylation Profiles of Membrane-Anchored HIV-1 Envelope Glycoprotein Trimers and Soluble gp140. J Virol 89:8245-57
Zhu, Zhikai; Su, Xiaomeng; Go, Eden P et al. (2014) New glycoproteomics software, GlycoPep Evaluator, generates decoy glycopeptides de novo and enables accurate false discovery rate analysis for small data sets. Anal Chem 86:9212-9
Go, Eden P; Hua, David; Desaire, Heather (2014) Glycosylation and disulfide bond analysis of transiently and stably expressed clade C HIV-1 gp140 trimers in 293T cells identifies disulfide heterogeneity present in both proteins and differences in O-linked glycosylation. J Proteome Res 13:4012-27

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