Integrating mass spectrometry-based multi-omic signatures of extracellular vesicles: from discovery to clinical translation.

Extracellular vesicles (EVs) are increasingly recognised as key mediators of intercellular communication and disease progression. Their capacity to carry bioactive molecules, namely proteins, lipids and metabolites, reflects the physiological and pathological states of their cells of origin, making them surrogates for diagnostic, prognostic and therapeutic endpoints. Recent advances in mass spectrometry have enabled comprehensive, high-resolution profiling of EVs across multiple omics layers. Proteomics has uncovered both conserved and disease-specific protein markers; lipidomics has revealed structurally distinct membrane compositions influencing EV stability and function; and metabolomics has captured dynamic snapshots of cellular metabolism. However, significant challenges persist for standardisation and interpretation of EVs, which include variation in EV isolation purity, scalability, EV heterogeneity and cross-study comparability. This perspective critically synthesises findings from recent EV multi-omics studies and proposes a conceptual framework for integrating these omics layers to better define EV identity and functionality. We highlight emerging clinical applications and outline future directions involving single-vesicle omics and the rational engineering of therapeutic EVs. The integration of multi-omics approaches with translational aims holds promise for advancing EVs from experimental tools to new pillars of precision medicine.