Metabolite Analysis from Protein Deposits

Pseudoexfoliation syndrome (PEX) is an age-related ocular disorder marked by the formation of proteinaceous extracellular deposits on the anterior ocular structures and other organs. Although the exact pathogenic mechanism of PEX deposit formation remains unclear, these deposits can elevate intraocular pressure, potentially leading to optic nerve degeneration and pseudoexfoliation glaucoma (PEXG), a severe form of open-angle glaucoma. Essential proteins implicated in PEX include lysyl oxidase-like 1, clusterin, and fibulin-5. PEX also possesses a unique metabolome, making metabolite analysis crucial to understanding the biochemical changes and pathways involved in its pathogenesis. Recent theories suggest that aberrant vitamin-D-binding protein may act as a nucleation center for protein clumping, exacerbating PEX. Advanced techniques like liquid chromatography-mass spectrometry are vital for profiling the metabolomic, proteomic, and lipidomic composition of PEX and PEXG deposits, providing insights into disease mechanisms and potential treatments. We aim to review methods for metabolite and protein extraction in addition to metabolic and proteomic analysis utilized in distinguishing the compositional differences between PEX and PEXG deposits and to understand the transition between these conditions. Such metabolomic analyses may play a crucial role in identifying potential biomarkers and potential therapeutic targets. In this book chapter, we discuss the methods to characterize extraction of metabolite associated with protein deposits and their analysis.