Our study unveils four unique dynamic phosphoproteome profiles of thrombin signaling regulated by p38 and the identification of multiple enriched biological functions associated with microtubules, focal adhesions, stress fiber, endocytosis, Rho, small GTPases, and cell–cell adherens junctions, which function as key modulators of endothelial dysfunction. This evidence concerns the gene MAPK1 and endothelial dysfunction.