We compare the proteome of the brain endothelial cells obtained with the newly optimized protocol (iCE-BECs) to the primary human brain microvascular endothelial cells (HBMVECs) and the widely used immortalized brain endothelial cell line HCMECD3. The goal is to investigate the applicability of iCE-BECs for transport assays, measuring the expression of transporters and receptors with whole cell proteomics.