Identification of proteins differentially expressed in atherosclerotic human carotid arteries by label-free proteomics

We present a proteomics dataset that permits the comparison of protein levels in samples obtained from patients by carotid endarterectomies and classified to show complicated lesions and atheromatous plaques, as well in samples from a healthy vasculature. We searched the acquired nanoLC-MS/MS-based shotgun proteomics raw data against a composite human protein sequence database by using MaxQuant and employed label-free quantification. Protein identifications were validated using rigorous criteria, and our statistical analyses based on spectral counts revealed 176 differentially expressed proteins among the study groups. By bioinformatic analyses, many of these proteins implicated acute phase response signaling, liver X receptor/retionid X receptor (LXR/RXR) and farnesoid X receptor/retionid X receptor (FXR/RXR) activation, clathrin-mediated endocytosis and atherosclerosis signaling as top overrepresented canonical pathways. Quantified alteration of protein expressions in the atherosclerosis signaling cascade also confirmed the involvement of macrophages and foam cell formation in the progression towards complicated atheromatous lesions in the atherosclerosis signaling pathway.