Proteomics and peptidomics for investigating metabolic and neurological disorders via liquid chromatography-mass spectrometry

Endogenous proteins and peptides play fundamental roles in cellular function, signaling, and disease pathogenesis. Their characterization provides critical insights into physiological processes and potential therapeutic targets. However, identifying and quantifying these biomolecules present significant analytical challenges due to their low abundance, complex biological matrices, and dynamic regulation. Mass spectrometry, particularly liquid chromatography-tandem mass spectrometry (LC-MS/MS), has emerged as a powerful tool for proteomic and peptidomic analysis, offering high sensitivity, selectivity, and structural characterization. Depending on the purpose of a project, either untargeted or targeted MS approaches have been developed to optimize biomolecular analysis. Untargeted proteomics and peptidomics enable the broad characterization of proteins and peptides within a system without prior knowledge of their sequences. These approaches are instrumental in discovery-driven research, providing insights into novel biomarkers and disease mechanisms. High-resolution instruments such as quadrupole time-of-flight and Orbitrap mass spectrometers facilitate these analyses by offering high mass accuracy and resolving power. Recent advancements, including trapped ion mobility spectrometry coupled with parallel accumulation-serial fragmentation, enhance spectral clarity, sensitivity, and throughput, making large-scale proteomic and peptidomic studies more feasible. Targeted proteomics and peptidomics, in contrast, focus on quantifying predefined biomolecules with high specificity and reproducibility. These methods are essential for hypothesis-driven studies and biomarker validation. Triple quadrupole and high-resolution parallel reaction monitoring platforms enable precise quantification of target proteins and peptides. By integrating these approaches, both discovery-based and hypothesis-driven studies can be effectively performed, ensuring comprehensive and reliable characterization of biological systems. This thesis includes my work in developing and optimizing high-sensitivity LC–MS/MS methods capable of femtogram-level quantification of endogenous proteins and peptides, significantly broadening our ability to detect critical biomarkers from minimal sample volumes. These advancements enable robust and precise analyses of trace-level biomolecules, including hemorphins in sickle cell disease models and glycated albumin in tear fluid, offering deeper insights into disease mechanisms, potential diagnostic tools, and therapeutic targets. Additionally, this research advances our understanding of exercise-derived extracellular vesicle proteomes as mediators of oxidative stress defense and vascular protection, providing a translational framework that extends to human health and broader clinical applications. Furthermore, this work includes the development of both label-free and isotopic labeling based approaches for opioid peptide measurement, enabling a more comprehensive investigation into quantitative peptidomics and providing deeper insights into peptide regulation. These methodological innovations contribute to the expanding toolkit of mass spectrometry-based proteomics and peptidomics, facilitating more sensitive and reproducible analyses across diverse biological and clinical applications.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Chemistry

Grantor

University of Illinois Urbana-Champaign

Year dc:date

2025

Author dc:creator

• Tan, Yanqi

Contributors dc:contributor

• Sweedler, Jonathan V.
• Sweedler, Jonathan
• Leckband, Deborah
• Yau, Peter
• Shen, Mei

• Proteomics
• Peptidomics
• Mass Spectrometry
• Neuropeptides

Statement dc:rights

• Copyright 2025 Yanqi Tan

Language dc:language

en, eng

Handle dc:identifier

https://hdl.handle.net/2142/130076

OAI record oai:identifier

https://www.ideals.illinois.edu/oai-pmh?verb=GetRecord&metadataPrefix=etdms&identifier=oai%3Awww.ideals.illinois.edu%3A2142%2F130076