A novel fixed paraffin-embedded tissue processing for proteomic analysis

Human tissues are an important biological material for the discovery of biomarkers and identification of novel therapeutic targets. Formalin fixed and paraffin embedded (FFPE) tissue represents the most abundant supply of archival material for clinical and molecular analyses. Although FFPE preserves the cellular and architectural morphologic details in tissue sections, formalin facilitates the formation of protein-protein crosslinks rendering FFPE tissues refractory to many protein studies. The aim of this study was to assess the feasibility of proteomic investigations of a new non-toxic fixative using a comprehensive panel of proteomic methods. Tissues were processed for quality and quantity of protein conservation, as compared to frozen and FFPE tissues using complementary proteomic analysis approaches. Similar protein patterns were observed between our tissue fixative protocol and frozen tissues using mono and bidimensional electrophoresis and protein identification by mass spectrometry was not affected. Several proteins were successfully detected using western blot and immunohistochemistry showed comparable results between both tissue storage methods. We demonstrate that our new fixative protocol represents an easy-to-use alternative to FFPE compatible with both current diagnostic pathology practice and tissue proteomic investigations.