Food allergies are caused by severe hypersensitivity to specific food allergens such as the egg protein ovalbumin. It is therefore important to test food products for the presence of allergens to protect allergic people from accidental ingestion. For egg detection, ELISA is the only reasonable commercially available test format, although the recognition of target allergens can be affected by food processing, which may lead to false negative results. Current mass spectrometry-based detection methods may overcome this issue, but these approaches are often less sensitive. Here we combined the advantages of antibody-based and MS-based methods by developing an immunoaffinity LC-MS/MS technique to detect the common egg allergen Gal d 2. We investigated the principal functionality of this method with incurred cookie material containing whole egg powder. We found that the new method matched easily the sensitivity of egg specific ELISA tests. Further western blot experiments indicated that this strategy may be unaffected by food processing, providing an important alternative strategy for the detection and quantification of allergens in food.