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Small extracellular vesicles (sEVs) are nanoscale, membrane-bound particles secreted by all cell types, carrying protein, lipid, and metabolite cargoes that reflect their cell of origin. Because they circulate in biofluids and carry disease-relevant molecular information, they are increasingly attractive targets for liquid biopsy and biomarker discovery, particularly in cancer. However, comprehensive multi-omics characterisation of sEVs has remained technically difficult due to the extremely limited material available, and most existing workflows require separate samples for each omics layer, introducing variability and wasting precious sample.

To address this, Perciaccante et al. developed an integrated LC-MS multi-omics platform enabling simultaneous proteomic, lipidomic, and metabolomic profiling from a single sEV sample via sequential extraction. For proteomics, peptides were separated using a nanoElute 2 with an Aurora® Ultimate™ 25×75 CSI C18 UHPLC column coupled to a timsTOF Pro, and analysed by diaPASEF.

From 10 million sEVs, the platform identified an average of 5,623 protein groups. Applied to plasma-derived sEVs isolated by ultracentrifugation (UC), size exclusion chromatography with ultrafiltration (SECUF), and polymer precipitation (PPT), the platform revealed distinct molecular signatures for each isolation method.

This platform offers a practical, sample-efficient foundation for sEV-based biomarker discovery using limited clinical material.

Publication
bioRxiv

Authors

Andrew J. Perciaccante, Holden T. Rogers, Yanlong Zhu, Aditi Barnwal, David Inman, Man-Di Wang, Song Jin, Suzanne M. Ponik, & Ying Ge;

Title

Integrated multi-omics enabled by sequential extraction for comprehensive molecular profiling of small extracellular vesicles