Journal
JOURNAL OF PROTEOME RESEARCH
Volume 11, Issue 4, Pages 2602-2608Publisher
AMER CHEMICAL SOC
DOI: 10.1021/pr201005t
Keywords
FFPE; formalin-fixed paraffin-embedded; high-pressure protein extraction; mouse liver; mass spectrometry; heat and pressure; proteomics
Categories
Funding
- National Cancer Institute, National Institutes of Health [1R21 CA134359, NO1-CO-12400]
- Veterans Health Administration
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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.
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