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

Dylan M. Marchione | Zendy; Ilyana Ilieva | Zendy; Kyle M. Devins | Zendy; Danielle Sharpe | Zendy; Darryl Pappin | Zendy; Benjamin A. García | Zendy; John P. Wilson | Zendy; John Wojcik | Zendy

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

Author(s) -

Dylan M. Marchione,

Ilyana Ilieva,

Kyle M. Devins,

Danielle Sharpe,

Darryl Pappin,

Benjamin A. García,

John P. Wilson,

John Wojcik

Publication year - 2020

Publication title -

journal of proteome research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 1.644

H-Index - 161

eISSN - 1535-3907

pISSN - 1535-3893

DOI - 10.1021/acs.jproteome.9b00686

Subject(s) - proteomics , workflow , proteome , computer science , computational biology , biomarker discovery , sonication , database , biology , bioinformatics , chromatography , chemistry , biochemistry , gene

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.

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