It is important to develop tools that can be used to understand the effects of processing on allergenic foods in order to achieve personalized food labeling. To evaluate the effect of heating on the allergy-relevant structural properties of tropomyosin (TM), arginine kinase (AK), myosin light chain (MLC) and sarcoplasmic calcium-binding protein (SCP) shrimp allergens, trypsin digests of raw, fried and baked shrimp extracts were analyzed by peptidomics and epitope correlations. Processing altered the number of peptides released from the distinct allergens, and each treatment generated a specific epitope-matched peptide allergen fingerprint. Among the four allergens, TM led to a number of released peptides and epitope changes being detected, and AK provided the epitope-matched 331MGLTEFQAVK340 sequence as a common differentiating peptide for heat processing. These results provide new views on the structural effects of processing on major shrimp allergens and peptide candidates as processing biomarkers.