Plasma-Derived Extracellular Vesicle Proteomics

Extracellular vesicles (EVs) are nanometer-scale lipid bilayer-enclosed particles released by cells under physiological and pathological conditions. Their molecular cargos, including proteins, can reflect the chemical composition and physiological state of the parent cells, carrying signatures of health and disease. As such, EVs are valuable tools for biomarker discovery and mechanistic studies. Among them, plasma-derived EVs (pEVs) are particularly promising, as sampling plasma allows capture of EVs from virtually all of the tissues and organs. The minimally invasive nature of plasma collection further enhances the diagnostic and therapeutic potential of the pEVs. Proteomic profiling of pEVs enables the identification of disease-specific EV-biomarkers. However, the complexity of plasma, with high levels of abundant proteins and large EV heterogeneity, presents challenges for pEV proteomics. Mass spectrometry (MS) has emerged as the preferred state-of-the-art analytical tool for pEV studies due to its nonbiased ability to characterize thousands of proteins in an experiment and its ability to identify low-abundance EV proteins. Here, a comprehensive overview of the advancements in MS-based pEV proteomics in the recent 5 years is presented with a focus on three key areas: sample preparation methodologies, MS-based approaches for protein identification and quantification, and description of pEV studies for basic and disease research. Technical advancements enable greater proteomic details from pEVs, enhancing biomarker discovery, elucidating disease mechanisms, and advancing an understanding of EVs’ biological roles.