We developed a novel asymmetric depth filtration (DF) approach to isolate extracellular vesicles (EVs) from biological fluids that outperforms ultracentrifugation and size‐exclusion chromatography in purity and yield of isolated EVs. By these metrics, a single‐step DF matches or exceeds the performance of multistep protocols with dedicated purification procedures in the isolation of plasma EVs. We demonstrate the selective transit and capture of biological nanoparticles in asymmetric pores by size and elasticity, low surface binding to the filtration medium, and the ability to cleanse EVs held by the filter before their recovery with the reversed flow all contribute to the achieved purity and yield of preparations. We further demonstrate the method's versatility by applying it to isolate EVs from different biofluids (plasma, urine, and cell culture growth medium). The DF workflow is simple, fast, and inexpensive. Only standard laboratory equipment is required for its implementation, making DF suitable for low‐resource and point‐of‐use locations. The method may be used for EV isolation from small biological samples in diagnostic and treatment guidance applications. It can also be scaled up to harvest therapeutic EVs from large volumes of cell culture medium.

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A novel asymmetric depth filtration (DF) approach for isolation of extracellular vesicles (EVs) from biological fluids is presented, and its performance is compared with established methods. The developed workflow is simple, inexpensive, and relatively fast. Compared with ultracentrifugation and size-exclusion chromatography, the developed method isolates EVs with higher purity and yield. Only standard laboratory equipment is needed for its implementation, which makes it suitable for low-resource locations. The described implementation of the method is suitable for EV isolation from small biological samples in diagnostic and treatment guidance applications. Following the scale-up routes adopted in the biomanufacturing of therapeutics, which routinely rely on DF as one of the product purification steps, the developed method may be scaled up to harvesting therapeutic EVs from large volumes of growth medium.

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The development of a sensitive and reliable method for the isolation and detection of pathologically relevant small extracellular vesicles (sEVs) remains a challenge. Herein we present a method for characterization of sEVs that is based on the isolation of sEVs by anti-CD63 aptamer conjugated magnetic beads and detecting the presence of the membrane proteins on their surface using anti-EpCAM and anti-HER2 designed ankyrin repeat proteins (DARPins). We perform a comparative study for identification of EpCAM and HER2 surface proteins in sEVs derived from MCF7, SKOV3, MDA-MB-231 and CHO cell lines and blood plasma of a healthy donor. Both DRAPins show high specificity to EpCAM and HER2 receptors with a limit of detection about 10 4 vesicles for MCF7 and Plasma sEVs and 10 5 vesicles for SKOV3 sEVs. Combination of magnetic capture with highly reactive DARPin probes made it possibly to reduce total assay time to 1 h. This method provides a basis for isolating and quantifying various sEV subpopulations that contain disease specific surface-markers.