Formalin-fixed, paraffin-embedded (FFPE) tissue archives and their associated 
diagnostic records represent an invaluable source of proteomic information on 
diseases where the patient outcomes are already known. Over the last few years, 
advances in methodology have made it possible to recover peptides from FFPE 
tissues that yield a reasonable representation of the proteins recovered from 
identical fresh or frozen specimens. These new methods, based largely upon 
heat-induced antigen retrieval techniques borrowed from immunohistochemistry, 
have developed sufficiently to allow at least a qualitative analysis of the 
proteome of FFPE archival tissues. This chapter describes the approaches for 
performing proteomic analysis on FFPE tissues by liquid chromatography and mass 
spectrometry.