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

Overview

Journal J Proteome Res

Publisher American Chemical Society

Specialty Biochemistry

Date 2020 Jan 15

PMID 31935107

Citations 23

Authors

Dylan M Marchione

Ilyana Ilieva

Kyle Devins

Danielle Sharpe

Darryl J Pappin

Benjamin A Garcia

John P Wilson

John B Wojcik

Affiliations

Soon will be listed here.

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 = 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.

Citing Articles

Overlap of Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Matched Tissues for Proteomics and Phosphoproteomics.

Humphries E, Hains P, Robinson P ACS Omega. 2025; 10(7):6891-6900.

PMID: 40028131 PMC: 11865994. DOI: 10.1021/acsomega.4c09289.

Proteomics-Based Analysis of Laser-Capture Micro-dissected, Formalin-Fixed Paraffin-Embedded Tissue Samples.

Mendes Maia T, Van Haver D, Dufour S, Van der Linden M, Dendooven A, Impens F Methods Mol Biol. 2024; 2884:333-354.

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Proteogenomic characterization of pancreatic neuroendocrine tumors uncovers hypoxia and immune signatures in clinically aggressive subtypes.

Tanaka A, Ogawa M, Zhou Y, Otani Y, Hendrickson R, Miele M iScience. 2024; 27(8):110544.

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