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HYPERsol: High-Quality Data from Archival FFPE Tissue for Clinical Proteomics

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posted on 14.01.2020, 18:04 by Dylan M. Marchione, Ilyana Ilieva, Kyle Devins, Danielle Sharpe, Darryl J. Pappin, Benjamin A. Garcia, John P. Wilson, John B. Wojcik
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.