Extracellular vesicle proteomics and metabolomics: analytical frameworks and translational insights

In recent years, the study of extracellular vesicles (EVs) has gained increasing attention due to their pivotal role in intercellular communication and their potential as noninvasive biomarkers and innovative therapeutic tools. Their molecular cargo, shaped by the source cell and its microenvironment, offers an accurate mirror of cellular states and pathophysiological dynamics. Characterizing this content provides critical insights into disease mechanisms, while paving the way for novel diagnostic, prognostic and therapeutic strategies. Among their components, proteins and metabolites stand out for their functional relevance and biomarker potential. In this context, proteomics and metabolomics have emerged as key approaches to unravel the molecular complexity of EVs and clarify their biological functions, thereby advancing their translation into clinical applications. This review highlights the contributions of these disciplines, outlines associated analytical workflows, and discusses major technical challenges. A systematic literature search was conducted in PubMed, Web of Science, Scopus, and Google Scholar for studies published between 2012 and 2025, focusing on proteomic and metabolomic analyses of EVs. Emphasis is placed on the need for methodological consensus to standardize protocols, improve inter-laboratory reproducibility, and support the successful clinical application of EV-based strategies.