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

Dylan M. Marchione
Dylan M. Marchione
Epigenetics Institute, Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
More by Dylan M. Marchione
http://orcid.org/0000-0001-6941-0604
,
Ilyana Ilieva
Ilyana Ilieva
Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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,
Kyle Devins
Kyle Devins
Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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,
Danielle Sharpe
Danielle Sharpe
Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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,
Darryl J. Pappin
Darryl J. Pappin
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, United States
ProtiFi, LLC, Huntington, New York 11743, United States
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,
Benjamin A. Garcia
Benjamin A. Garcia
Epigenetics Institute, Department of Biochemistry & Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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http://orcid.org/0000-0002-2306-1207
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John P. Wilson*
John P. Wilson
ProtiFi, LLC, Huntington, New York 11743, United States
*Email: [email protected]
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John B. Wojcik*
John B. Wojcik
Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
*Email: [email protected]
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http://orcid.org/0000-0001-5403-3631

Cite this: J. Proteome Res. 2020, 19, 2, 973–983

Publication Date (Web):January 14, 2020

https://doi.org/10.1021/acs.jproteome.9b00686

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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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The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jproteome.9b00686.

Figure S1: Direct solubilization combined with ultrasonication efficiently solubilizes FFPE samples of various human tissue types; Figure S2: Peptides from FFPE samples contain missed cleavages and modifications (PDF)
Table S1: Experiment 1 Peptide Report (TXT)
Table S2: Experiment 1 Protein Report (TXT)
Table S3: Experiment 1 Unique Peptides and Protein Modifications (XLSX)
Table S4: Experiment 1 Gene Ontology Terms (XLSX)
Table S5: Experiment 2 Peptide Report (XLS)
Table S6: Experiment 2 Protein Report (XLS)
Table S7: Experiment 2 Protein Correlation Matrix (TXT)
Table S8: Experiment 2 Volcano Plots (XLSX)
Table S9: Archival FFPE Tumor Specimen Protein Report (XLSX)
Table S10: Archival FFPE Tumor Specimen Age and Number of Protein IDs (XLSX)
Table S11: Raw File Names and Conditions (XLSX)

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