Annotated formalin-fixed, paraffin-embedded (FFPE) tissue archives constitute a 
valuable resource for retrospective biomarker discovery. However, proteomic 
exploration of archival tissue is impeded by extensive formalin-induced covalent 
cross-linking. Robust methodology enabling proteomic profiling of archival 
resources is urgently needed. Recent work is beginning to support the 
feasibility of biomarker discovery in archival tissues, but further developments 
in extraction methods which are compatible with quantitative approaches are 
urgently needed. We report a cost-effective extraction methodology permitting 
quantitative proteomic analyses of small amounts of FFPE tissue for biomarker 
investigation. This surfactant/heat-based approach results in effective and 
reproducible protein extraction in FFPE tissue blocks. In combination with a 
liquid chromatography-mass spectrometry-based label-free quantitative proteomics 
methodology, the protocol enables the robust representative and quantitative 
analyses of the archival proteome. Preliminary validation studies in renal 
cancer tissues have identified typically 250-300 proteins per 500 ng of tissue 
with 1D LC-MS/MS with comparable extraction in FFPE and fresh frozen tissue 
blocks and preservation of tumor/normal differential expression patterns (205 
proteins, r = 0.682; p < 10(-15)). The initial methodology presented here 
provides a quantitative approach for assessing the potential suitability of the 
vast FFPE tissue archives as an alternate resource for biomarker discovery and 
will allow exploration of methods to increase depth of coverage and investigate 
the impact of preanalytical factors.