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.