To identify proteins that may specifically characterize colonic polyps we have investigated the abundance of numerous proteins in epithelial cells from 15 normal colon specimens and 13 colonic polyps, using two-dimensional gel analysis to detect possible differences in expression. Silver-stained digitized images of the gels were analyzed with Melanie II 2.1 software. We consistently detected more than 700 protein spots on each gel, and found that the intensity of 59 of them was significantly altered in polyp specimens (Wilcoxon test assuming P< or =0.05). Immunostaining, microsequencing and mass spectrometry (matrix-assisted laser desorption/ionization - time of flight; MALDI-TOF) techniques were used to identify these proteins and selected others that did not show differential regulation. The expression of numatrin (nucleophosphine/B23), hsp 70, and hsp60 was increased in polyps; levels of fatty acid binding protein (L-FABP), 14-3-3 sigma, citokeratin 20, cytochrome c oxidase polypeptide Va, Rho GDP-dissociation inhibitor (Rho GDI), and beta- and gamma-actins were decreased. Although the levels of expression of a given protein often varied among polyp specimens, it generally held true that the direction of variation (up or down) remained constant across the panel. We concluded that proteins showing constant differential regulation across all or most of the polyp specimens represent the most characteristic regulatory pathways in colon polyps, while more sporadic variations reflect characteristics of individual polyps.