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Nuts are one of the most common sources of allergies in individuals of all ages. In order for a particular protein to render an allergic reaction, it must resist proteolytic digestion by intestinal enzymes. In this study, three well-known allergenic nuts, almonds, cashew nuts, and peanuts, were used as samples, and enzyme digestion with Bacillus protease and porcine pepsin was tested. A proteomic approach using two-dimensional gel electrophoresis and an MS/MS analysis was applied to visualize and identify the proteins that were resistant to enzyme digestion. Among the 150 protein spots tested, 42 proteins were assigned functions. Due to the lack of genomic databases, 41% of the identified proteins were grouped as hypothetical. However, 12% of them were well-known allergens, including AraH. The remainder were grouped as storage, enzymes, and binding proteins.