Advancing LC-MS/MS Bioanalytical Techniques to Investigate Glycomic, Glycoproteomic, and Proteomic Alterations in Complex Biological Systems and Diseases

Liquid Chromatography Mass Spectrometry (LC-MS) is a powerful analytical tool for both the quantitative and qualitative investigation of biologically complex systems. One of the most common and functionally significant post-translational modifications of proteins is glycosylation, which influences a wide range of biological functions, including protein stability, function, cell-cell signaling, immune response, and cell-cell adhesion. Alterations in glycosylation patterns have been implicated in various diseases and disorders, underscoring the need for advanced analytical approaches to characterize these modifications. This dissertation applies state-of-the-art LC-MS/MS techniques to explore glycomic, glycoproteomic, and proteomic alterations first in Sertoli cells (SC) and followed by Alzheimer’s disease. SC are immune-privileged and play a crucial role in xenotransplantation research. By characterizing the biological landscapes of SC, this work provides insights into their resilience against the human complement system, addressing critical challenges in organ transplantation, including immune rejection and organ shortages. The Alzheimer’s disease work analyzing brain tissue, cerebrospinal fluid (CSF), and plasma samples to identify shared molecular signatures and potential blood-based biomarkers with diagnostic utility. Additionally, this research includes the development of an R-based computational framework to ensure robust, reproducible, and well-documented data processing, statistical analysis, and visualization. The integration of advanced bioinformatics tools enhances the accuracy and efficiency of large-scale LC-MS/MS data interpretation, paving the way for more precise biomolecular discoveries in biomedical research. This work contributes to the broader understanding of disease pathophysiology, immune evasion mechanisms, and translational applications of glycomics and proteomics, reinforcing the role of LC-MS/MS in modern biomedical science.