The present disclosure relates to nutritional compositions including a protein equivalent source including a peptide component comprising selected peptides from Tables 1 and 2 disclosed herein. The protein equivalent source may further include intact protein, hydrolyzed protein, including partially hydrolyzed protein, or combinations thereof. The disclosure further relates to methods of reducing the incidence of autoimmune disease and/or diabetes mellitus by providing said nutritional compositions to a target subject, which includes a pediatric subject.