Quantitative proteomics of FFPE-preserved cardiac specimens

Archival human heart tissue, preserved as formalin-fixed, paraffin-embedded (FFPE) samples in pathology collections worldwide, represents a largely untapped resource for cardiac proteomics. This study employs a comprehensive proteomic workflow optimized for human FFPE heart tissue and leverages paired FFPE and fresh frozen (FF) tissue from the same hearts to assess its performance. We evaluate the reproducibility and depth of protein quantification across preservation methods using TMT-multiplexed measurements and further evaluate the performance of diaPASEF for profiling cardiac FFPE tissue proteomes.