The proteomics of formalin-fixed wax-embedded tissue

Proteomics, which is the global analysis of protein expression in cells and tissues, has emerged over the last ten to fifteen years as a key set of technologies to improve our understanding of disease processes and to identify new diagnostic, prognostic and predictive disease biomarkers. Whilst most proteomic studies have been conducted on fresh frozen tissue, the continuous improvements in technical procedures for protein extraction and separation, coupled with increasingly powerful bioinformatics, have provided the opportunity for proteomic analysis to be conducted on formalin-fixed wax-embedded tissue. This potential advance should allow proteomic analysis to be performed on the extensive archives of clinically annotated formalin fixed wax embedded tissue blocks stored in pathology departments worldwide. In this review the main techniques and their limitations involved in proteomic analysis of formalin fixed wax embedded tissue will be outlined and examples of their successful application will be indicated.

► Formalin-fixed wax-embedded tissue (FFPE) can be used for proteomic analysis.
► Facilitated by advances in mass spectrometry and bioinformatics.
► Proteomic studies can provide information on disease mechanisms.
► Diagnostic, prognostic and predictive biomarkers can be identified.