Cereals-based foods cause immune-mediated adverse reactions including coeliac disease and IgE-mediated allergies. Proteomic profiling of proteins carrying coeliac toxic motifs and allergens has been undertaken in wheat, barley, rye and oats in order to understand whether some cereal species, such as oats, maybe safe for allergic consumers. Total protein extracts were subject to chymotryptic digestion and analysed using data independent ion mobility mass spectrometry and analysed using a pipeline employing a curated gluten protein sequence database. Between 376-2769 proteins were identified and were dominated by proteins with a nutrient reservoir function. Relative quantitation of proteins containing coeliac toxic motifs showed they were present in wheat, barley and rye, but none were common to all three cereals, but were present in a limited number and much lower abundance in oats. The most abundant allergens were the seed storage prolamins, with allergens belonging to the α-amylase/trypsin inhibitor family associated with the inhalant allergy being of only moderate abundance. Wheat allergen homologues were identified in other cereal species but at a very low level in oats. These data suggest that the relative risk of oats in the context of both coeliac disease and IgE-mediated allergy is low.