Proteomic analyses of human tissues are sometimes conducted on autopsy samples. However, no comparative analysis between proteomic data derived from autopsy samples and fresh frozen samples has been undertaken, nor has there been an assessment of the post-mortem interval (PMI) influences on protein quantification.

In the current study, 94 human left anterior descending (LAD) coronary artery were collected from deceased patients. Proteins were analysed using nanoflow liquid chromatography-tandem mass spectrometry. Data were processed with Proteome Discoverer and Mascot. The correlations between the protein abundances and the PMI were calculated. DAVID software was used for pathway and GO annotation enrichment.

Among consistently quantified proteins, approximately 40% of the protein abundances exhibited significant correlations with PMI, most of which being inverse. Notably, smooth muscle cell markers displayed substantial reduction with prolonged PMI. Conversely, positive correlations with PMI were observed for immunoglobulins, coagulation factors, and complement factors, including coagulation factor XII, plasminogen, and lactotransferrin.

Comparative analyses of sex differences between autopsy LAD samples and fresh-frozen LAD samples (n=65) showed no concordance in protein quantification (Figure A). However, a robust correlation was observed within a sex comparison conducted between fresh-frozen carotid endarterectomies (CEA) from 2 different cohorts (n=104 and n=200) (Figure B).

This study represents the first large-scale proteomics investigation into the influence of PMI on the protein composition of human vasculature. We observed significant correlations with PMI for nearly 40% of the consistently 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.