The present invention concerns the methods and compositions involving endopeptidase enzymes, especially PepO2 and PepO3 from L. helveticus, and their use in reducing bitterness by cleaving bitter peptides. In particular embodiments of the invention, these methods and compositions apply to the cheesemaking process. The invention also concerns the use of PepO2 and/or PepO3 polypeptides in the treatment or prevention of celiac sprue or as a food additive.