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This study evaluates the immortalized human brain capillary endothelial cell lines hCMEC\/D3 and hBMEC for their use as a brain endothelial cells to investigate the OATP2B1 transporter following adenoviral infection. We assessed the impact of adenoviral-mediated OATP2B1 expression on BBB marker proteins and transporters using targeted and untargeted mass spectrometry-based proteomics. Targeted proteomics identified measurable levels of endothelial markers PECAM1 and CDH5 in hCMEC\/D3, whereas these markers were undetectable in hBMEC. Both cell lines exhibited similar Pgp levels, while BCRP was absent in hCMEC\/D3. The expression of uptake transporters was also evaluated, revealing comparable levels of GLUT1, ENT1, MCT1 and OAT7 in hCMEC\/D3 and hBMEC. Although OATP2B1 levels did not significantly increase post-infection in targeted proteomics, untargeted proteomics confirmed enhanced OATP2B1 expression. Other BBB markers and transporters remained unaffected in both cell lines. Notably, hCMEC\/D3 demonstrated a stronger BBB phenotype, indicated by higher expression of BBB markers and transporters, while adenoviral infection was more effective in hBMEC. The differences between targeted and untargeted proteomics underscore the need for diverse methods to verify protein expression levels. This comparative analysis provides insights into the strengths and limitations of hCMEC\/D3 and hBMEC for BBB research, particularly regarding drug transport mechanisms.<\/jats:p>","DOI":"10.1007\/s12035-025-04807-7","type":"journal-article","created":{"date-parts":[[2025,3,14]],"date-time":"2025-03-14T08:22:06Z","timestamp":1741940526000},"page":"9074-9088","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Targeted and Untargeted Proteomics-based Comparison of Adenoviral Infected hCMEC\/D3 and hBMEC as a Human Brain Endothelial Cells to Study the OATP2B1 Transporter"],"prefix":"10.1007","volume":"62","author":[{"given":"Valerio","family":"Taggi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anima M.","family":"Sch\u00e4fer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonny","family":"Kinzi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Danilo","family":"Ritz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isabell","family":"Seibert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Oswald","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Henriette E. 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