Small extracellular vesicles originating from human mesenchymal stem cells (MSC-sEVs) exhibit notable immunomodulatory and tissue-regenerative properties. Nonetheless, the absence of well-defined specific markers for these vesicles remains a critical barrier to their effective clinical deployment. In the present work, proteomic profiles of MSC-sEVs generated from three different cellular origins were examined in parallel. Candidate surface antigens commonly expressed by MSCs were identified based on their prominent representation within the MSC-sEV proteome. MSC-sEVs isolated from adipose tissue, umbilical cord, and induced pluripotent stem cells were subsequently labeled using fluorescein-conjugated antibodies and subjected to high-resolution analysis by NanoFCM at the individual vesicle level. The surface markers CD13, CD29, and CD90 displayed positive detection rates exceeding 60% across sEVs from all three MSC sources, in contrast to the generally lower rates observed for other tested candidates. These strong expression levels were further corroborated in MSC-sEVs obtained through alternative isolation procedures. Complementary validation by high-resolution microscopy confirmed the substantial presence of these markers on MSC-sEVs. Importantly, non-MSC-derived sEVs failed to show concurrent positivity for CD13, CD29, and CD90 above 40%, supporting the utility of this three-marker panel—applied with a minimum 50% positivity threshold for each marker—as a selective discriminator between MSC-sEVs and vesicles from other sources. In addition, the performance of this marker combination was monitored in sEVs released by MSCs over increasing culture passages. A progressive reduction in CD29 and CD90 positivity was observed with higher passage numbers, coinciding with diminished proliferative activity of the corresponding sEVs. Overall, this study establishes a reliable, quantifiable marker panel suitable for standardized characterization of MSC-sEVs, thereby aiding the development of robust quality control assays and supporting accelerated clinical advancement of MSC-sEV-based therapies.
