Updated project metadata. Age-related decline in brain endothelial cell (BEC) function critically contributes to cerebrovascular and neurodegenerative disease. Comprehensive atlases of the BEC transcriptome have become available but results from proteomic profiling are lacking. To gain insights into endothelial pathways affected by aging, we developed a magnetic-activated cell sorting (MACS)-based mouse BEC enrichment protocol compatible with high-resolution mass-spectrometry based proteomics. In this experiment, we have compared MACS sorted BEC and full brain tissue a massive enrichment of endothelial markers including Nos3, Cdh5, and Pecam1 in BECs compared to FT.