HYPERsol: High-Quality Data from Archival FFPE Tissue for Clinical Proteomics
Dylan M. Marchione, Ilyana Ilieva, Kyle M. Devins, Danielle Sharpe, Darryl Pappin, Benjamin A. García, John P. Wilson, John Wojcik
Abstract
Massive formalin-fixed, paraffin-embedded (FFPE) tissue archives exist worldwide, representing an invaluable resource for clinical proteomics research. However, current protocols for FFPE proteomics lack standardization, efficiency, reproducibility, and scalability. Here we present high-yield protein extraction and recovery by direct solubilization (HYPERsol), an optimized workflow using ultrasonication and S-Trap sample processing that enables proteome coverage and quantification from FFPE samples comparable to that achieved from flash-frozen tissue (average R = 0.936). When applied to archival samples, HYPERsol resulted in high-quality data from FFPE specimens in storage for up to 17 years, and may enable the discovery of new immunohistochemical markers.