Integrated Multiomics Enabled by Sequential Extraction for Comprehensive Molecular Profiling of Small Extracellular Vesicles

Small extracellular vesicles (sEVs) are membrane-bound particles whose protein, lipid, and metabolite cargo reflects the molecular state of their cells of origin, making them attractive targets for biomarker discovery and therapeutic development. However, comprehensive characterization of sEVs remains challenging due to the extremely limited material available. Here, we present an integrated mass spectrometry-based multiomics platform for simultaneous characterization of lipids, metabolites, and proteins from a single sEV sample enabled by sequential extraction, maximizing sample utilization. To enhance molecular coverage and analytical depth, the platform combines iterative tandem mass spectrometry for improved small-molecule fragmentation and nanoflow proteomics with data-independent acquisition. We achieved deep and reproducible multiomic characterization of proteins, lipids, and metabolites using 10 million sEVs. We further demonstrated the compatibility of our multiomics platform with sEVs isolated from plasma by ultracentrifugation, size exclusion chromatography with ultrafiltration, and polymer precipitation, revealing purification-dependent differences in molecular profiles associated with trade-offs in yield and purity of sEVs. By enabling integrated multiomics from the same sample, this strategy addresses a key challenge in low-input sEV analysis and establishes a robust analytical foundation for synergistic biomarker discovery and therapeutic applications.