1 Analysis of the formalin-fixed paraffin-embedded proteome: pitfalls, challenges and future prospectives Evelyne Maes 1,2,* , Valérie Broeckx 1 , Inge Mertens 2,3 , Xavier Sagaert 4 , Hans Prenen 5 , Bart Landuyt 1 and Liliane Schoofs 1 1 Research group of Functional Genomics and Proteomics, University of Leuven, Leuven, Belgium 2 Flemish Institute for Technological Research (VITO), Mol, Belgium 3 CFP-CeProMa, University of Antwerp, Antwerpen, Belgium 4 Centre For Translational Cell & Tissue research, Leuven, Belgium 5 Department of gastro-enterology, Digestive oncology unit, University hospital Gasthuisberg, Leuven, Belgium. * Corresponding author: evelyne.maes@bio.kuleuven.be Postal address: Research group of Functional Genomics and Proteomics, KU Leuven, Naamsestraat 59, Leuven, Belgium Phone: +32 16 323913 Fax: +32 16 323902