This dataset comprises proteomic profiles of 87 human carotid atherosclerotic plaques from patients undergoing carotid endarterectomy (CEA). The study employed an integrated approach using Data Independent Acquisition (DIA) proteomics. A total of 87 human carotid plaques were analyzed to identify and quantify protein expression. The proteomic analysis of the 87 carotid plaques revealed 6143 proteins, highlighting diverse expression profiles across different plaque stages.