Defining the reference proteomes for small extracellular vesicles and non-vesicular components

Extracellular vesicles (EVs) are key mediators of intercellular communication and promising biomarkers. However, their molecular characterization remains challenging due to the heterogeneity of EV subtypes and co-isolated non-vesicular components. Here we leverage protein correlation profiling along density gradients to systematically analyse over 9,000 proteins in human cancer cell lines and biofluids, providing a rigorous reassessment of virtually all protein constituents associated with small EVs (sEVs) and non-vesicular entities. We show that sEVs primarily incorporate plasma membrane proteins via selective cargo-loading mechanisms, with low inclusion of intraluminal soluble proteins. By contrast, the abundant cytosolic proteins frequently detected in sEV preparations are not encapsulated within vesicles but are externally associated, probably originating from copurifying cellular debris and aggregates. Our work provides a reference resource for understanding the biogenesis, molecular determinants of cargo selection and functional roles of sEVs. Morales-Sanfrutos, Etxeberria-Ugartemendia, Barroso-Gomila and colleagues map the elution profiles of small extracellular vesicles along density gradients from human biofluids and cell lines, distinguishing extracellular vesicle content from co-isolation components.