Proteomic analyses of human tissues are often conducted on autopsy samples. However, no detailed comparative analysis between proteomic changes derived from autopsy samples and fresh-frozen samples has been undertaken. In this study, human left anterior descending (LAD) coronary artery samples (n = 94) from deceased patients were analyzed using nanoflow LC-MS/MS. Among consistently quantified proteins, 37% of the protein abundances exhibited significant correlations with the post-mortem interval (PMI), most of which are inverse. Notably, smooth muscle cell markers displayed substantial reduction with prolonged PMI. Conversely, positive correlations were observed for immunoglobulins, coagulation factors, and complement factors, including coagulation factor XII, plasminogen, and lactotransferrin. Comparative analyses of sex-specific protein changes in autopsy LAD samples versus fresh-frozen LAD samples (n = 65) showed no concordance. However, a robust correlation was observed between 2 different cohorts of fresh-frozen carotid endarterectomies (n = 120 and n = 200). This study represents the first large-scale proteomics investigation into the influence of PMI on the protein composition of the human vasculature, showing significant correlations with PMI for 37% of the quantified proteins. Our findings underscore potential discrepancies in the quantitative accuracy of proteomics data derived from autopsy samples. Consequently, results obtained from post-mortem specimens may not be reproducible in fresh-frozen samples.