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Extracellular vesicles (EVs) are reminiscent of their cell of origin and thus represent a
valuable source of biomarkers. However, for EVs to be used as biomarkers in clinical practice, simple,
comparable, and reproducible analytical methods must be applied. Although progress is being
made in EV separation methods for human biofluids, the implementation of EV assays for clinical
diagnosis and common guidelines are still lacking. We conducted a comprehensive analysis of
established EV separation techniques from human serum and plasma, including ultracentrifugation
and size exclusion chromatography (SEC), followed by concentration using (a) ultracentrifugation,
(b) ultrafiltration, or (c) precipitation, and immunoaffinity isolation. We analyzed the size, number,
protein, and miRNA content of the obtained EVs and assessed the functional delivery of EV cargo.
Our results demonstrate that all methods led to an adequate yield of small EVs. While no significant
difference in miRNA content was observed for the different separation methods, ultracentrifugation
was best for subsequent flow cytometry analysis. Immunoaffinity isolation is not suitable for
subsequent protein analyses. SEC + ultracentrifugation showed the best functional delivery of
EV cargo. In summary, combining SEC with ultracentrifugation gives the highest yield of pure
and functional EVs and allows reliable analysis of both protein and miRNA contents. We propose
this combination as the preferred EV isolation method for biomarker studies from human serum
or plasma.