Vallejo, Milene C.Sarkar, SoumyadeepElliott, Emily C.Henry, Hayden R.Powell, Samantha M.Diaz Ludovico, IvoYou, YoungkiHuang, FeiPayne, Samuel H.Ramanadham, SasankaSims, Emily K.Metz, Thomas O.Mirmira, Raghavendra G.Nakayasu, Ernesto S.2024-04-102024-04-102023-11-28Vallejo MC, Sarkar S, Elliott EC, et al. A proteomic meta-analysis refinement of plasma extracellular vesicles. Sci Data. 2023;10(1):837. Published 2023 Nov 28. doi:10.1038/s41597-023-02748-1https://hdl.handle.net/1805/39879Extracellular vesicles play major roles in cell-to-cell communication and are excellent biomarker candidates. However, studying plasma extracellular vesicles is challenging due to contaminants. Here, we performed a proteomics meta-analysis of public data to refine the plasma EV composition by separating EV proteins and contaminants into different clusters. We obtained two clusters with a total of 1717 proteins that were depleted of known contaminants and enriched in EV markers with independently validated 71% true-positive. These clusters had 133 clusters of differentiation (CD) antigens and were enriched with proteins from cell-to-cell communication and signaling. We compared our data with the proteins deposited in PeptideAtlas, making our refined EV protein list a resource for mechanistic and biomarker studies. As a use case example for this resource, we validated the type 1 diabetes biomarker proplatelet basic protein in EVs and showed that it regulates apoptosis of β cells and macrophages, two key players in the disease development. Our approach provides a refinement of the EV composition and a resource for the scientific community.en-USAttribution 4.0 InternationalProteomicsMembrane traffickingBiomarkersArticle