Defense Date
2026
Document Type
Dissertation
Degree Name
Doctor of Philosophy
Department
Pharmaceutical Sciences
First Advisor
Dr. Adam Hawkridge
Abstract
Glycosylation is one of the most structurally diverse and biologically important post-translational modifications, influencing protein stability, molecular recognition, and cell–cell communication. Despite its importance, comprehensive characterization of glycans and glycoproteins remains analytically challenging due to their structural heterogeneity and complexity. Liquid chromatography–tandem mass spectrometry (LC-MS/MS) has emerged as a powerful platform for glycomic and glycoproteomic analysis. However, continued methodological advances are required to improve sensitivity, quantitative accuracy, and analytical robustness. The overarching goal of this dissertation was to develop and apply LC-MS/MS-based analytical workflows for the characterization of glycans and glycoproteins in both methodological and biological contexts.
The first part of this work focused on improving compositional analysis of glycosaminoglycan (GAG) disaccharides through optimization of a reducing-end chemical derivatization strategy for LC-UV-MS/MS analysis. Reaction conditions were systematically evaluated with respect to derivatization efficiency, chromatographic performance, and electrospray ionization efficiency, establishing optimized conditions for robust comparative GAG compositional profiling.
The second part of the dissertation established a quantitative glycoproteomic workflow for the characterization of the platelet glycoproteome. A tandem mass tag (TMT)-based strategy was optimized for glycopeptide analysis using complementary high-energy collision dissociation (HCD) and electron transfer/high-energy collision dissociation (EThcD) fragmentation methods in combination with zwitterionic hydrophilic interaction liquid chromatography (ZIC-cHILIC) glycopeptide enrichment and integrated proteomic–glycoproteomic data analysis.
Building on this analytical framework, the optimized glycoproteomic workflow was applied to investigate glycoproteomic alterations in platelets from patients with myelodysplastic syndrome (MDS). Label-free proteomics together with ZIC-cHILIC enrichment strategies revealed proteomic and glycoproteomic differences between MDS and healthy control platelets, identifying candidate glycoproteins and glycosylation changes associated with disease-related platelet dysfunction.
Together, this work advances analytical methodologies for both GAG glycomics and quantitative glycoproteomics while demonstrating the utility of LC-MS/MS-based glycoanalytical platforms for investigating clinically relevant biological systems.
Rights
© Nidhi Naik
Is Part Of
VCU University Archives
Is Part Of
VCU Theses and Dissertations
Date of Submission
5-8-2026