New workflow boosts sensitivity in extracellular vesicle proteomics without sample loss

Researchers at the Fondazione Pisana per la Scienza have developed an improved method for analyzing extracellular vesicles (EVs) — tiny particles released by cells that carry important molecular information. EVs are of growing interest in cancer research and diagnostics, but isolating them in a form suitable for protein analysis has traditionally been challenging.

The common technique, size exclusion chromatography (SEC), separates EVs from other molecules based on size but requires a concentration step before proteomics, which often leads to EV loss. The researchers created a novel workflow that avoids this step entirely by isolating EVs in just 80 microliters of solution — a volume that’s ready for direct protein analysis.

The researchers confirmed the presence of EVs using advanced tools like transmission electron microscopy, nanoparticle tracking, and Western blotting. They then compared their new method to a standard automated SEC platform and found that it identified more proteins and EV markers. Impressively, it captured 96 out of the 100 most common exosomal proteins listed in the ExoCarta database, compared to 91 using the standard approach.

When tested on pancreatic cancer cell lines, the new method proved even more effective by detecting a higher number of cancer-related EV markers, highlighting its potential for use in diagnostics and biomarker discovery.

By simplifying the process and improving sensitivity, this workflow marks an important step forward in EV research, making proteomic analysis more accessible and reliable — especially for applications like cancer detection.

Botto A, De Cesari C, Ndimurwanko N, Finamore F, Greco F, Cappello V, Casieri V, Immordino B, Lionetti V, Gemmi M, Tonazzini I, Giovannetti E, McDonnell LA. (2025) Novel PPT+SEC Workflow for High-Sensitivity Extracellular Vesicle Proteomics from Cell Media. J Proteome Res [Epub ahead of print]. [article]

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