This unit provides a robust, reliable, and easy-to-use kit-based method for 
extraction of intact, non-degraded proteins from formalin-fixed, 
paraffin-embedded (FFPE) tissue, and their subsequent use for analysis by liquid 
chromatography/mass spectrometry (LC/MS). After deparaffinization, proteins are 
extracted from unstained sections of FFPE rat liver tissue. After a simple 
cleanup step using organic extraction, the sample is transferred into a buffer 
optimized for trypsin digestion of the extracted proteins. Subsequently, LC/MS 
is used to identify the proteins that gave rise to the tryptic peptides. 
Comparing formalin-fixed and frozen tissues, good correlation is observed in the 
mass spectrometric pattern attributable to the tryptic peptides and number of 
identified proteins. Since FFPE tissues are generally available in clinical 
practice, this method can be used to analyze biomarkers in different 
pathological situations (e.g., healthy vs. diseased). The method can also be 
used for protein extraction from fresh-frozen tissue.