Allergen analysis is central to implementing and monitoring food allergen risk assessment and management processes by the food industry, but current methods for the determination of allergens in foods give highly variable results. The European Union-funded "Integrated Approaches to Food Allergen and Allergy Risk Management" (iFAAM) project has been working to address gaps in knowledge regarding food allergen management and analysis, including the development of novel MS and immuno-based allergen determination methods. Common allergenic food ingredients (peanut, hazelnut, walnut, cow's milk [Bos domesticus], and hen's egg [Gallus domesticus]) and common food matrixes (chocolate dessert and cookie) have been used for both clinical studies and analytical method development to ensure that the new methods are clinically relevant. Allergen molecules have been used as analytical targets and allergenic ingredients incurred into matrixes at levels close to reference doses that may trigger the use of precautionary allergen labeling. An interlaboratory method comparison has been undertaken for the determination of peanut in chocolate dessert using MS and immuno-based methods. The iFAAM approach has highlighted the need for methods to report test results in allergenic protein. This will allow food business operators to use them in risk assessments that are founded on clinical study data in which protein has been used as a measure of allergenic potency.