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 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.