Pressure-Assisted Protein Extraction: A Novel Method for Recovering Proteins from Archival Tissue for Proteomic Analysis

Formaldehyde-fixed, paraffin-embedded (FFPE) tissue repositories represent a valuable resource for the retrospective study of disease progression and response to therapy. However, the proteomic analysis of FFPE tissues has been hampered by formaldehyde-induced protein modifications, which reduce pro...

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Bibliographic Details
Published in:Journal of proteome research 2012-04, Vol.11 (4), p.2602-2608
Main Authors: Fowler, Carol B, Waybright, Timothy J, Veenstra, Timothy D, O’Leary, Timothy J, Mason, Jeffrey T
Format: Article
Language:English
Subjects:
Animals
Formaldehyde
Hot Temperature
Hydrostatic Pressure
Liver - chemistry
Mice
Paraffin Embedding
Proteins - analysis
Proteins - chemistry
Proteins - isolation & purification
Proteome - analysis
Proteome - chemistry
Proteome - isolation & purification
Proteomics - methods
Technical Note
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Summary:Formaldehyde-fixed, paraffin-embedded (FFPE) tissue repositories represent a valuable resource for the retrospective study of disease progression and response to therapy. However, the proteomic analysis of FFPE tissues has been hampered by formaldehyde-induced protein modifications, which reduce protein extraction efficiency and may lead to protein misidentification. Here, we demonstrate the use of heat augmented with high hydrostatic pressure (40,000 psi) as a novel method for the recovery of intact proteins from FFPE mouse liver. When FFPE mouse liver was extracted using heat and elevated pressure, there was a 4-fold increase in protein extraction efficiency, a 3-fold increase in the extraction of intact proteins, and up to a 30-fold increase in the number of nonredundant proteins identified by mass spectrometry, compared to matched tissue extracted with heat alone. More importantly, the number of nonredundant proteins identified in the FFPE tissue was nearly identical to that of matched fresh-frozen tissue.
ISSN:1535-3893
1535-3907
DOI:10.1021/pr201005t