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

Dylan M. Marchione; Ilyana Ilieva; Kyle Devins; Danielle Sharpe; Darryl J. Pappin; Benjamin A. Garcia; John P. Wilson; John B. Wojcik

doi:10.1021/acs.jproteome.9b00686

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

Dylan M. Marchione, Ilyana Ilieva, Kyle Devins, Danielle Sharpe, Darryl J. Pappin, Benjamin A. Garcia, John P. Wilson, John B. Wojcik

Research output: Contribution to journal › Article › peer-review

39 Scopus citations

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.

Original language	English
Pages (from-to)	973-983
Number of pages	11
Journal	Journal of Proteome Research
Volume	19
Issue number	2
DOIs	https://doi.org/10.1021/acs.jproteome.9b00686
State	Published - Feb 7 2020

Keywords

FFPE
S-Trap
clinical proteomics
immunohistochemistry
sample preparation
tissue

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10.1021/acs.jproteome.9b00686

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title = "HYPERsol: High-Quality Data from Archival FFPE Tissue for Clinical Proteomics",

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.",

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AU - Marchione, Dylan M.

AU - Ilieva, Ilyana

AU - Devins, Kyle

AU - Sharpe, Danielle

AU - Pappin, Darryl J.

AU - Garcia, Benjamin A.

AU - Wilson, John P.

AU - Wojcik, John B.

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

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