Milk is one among the most common food allergens and the proteins representing caseins and whey fractions of milk have been characterized as the major triggers for allergic responses in susceptible individuals. Milk or milk-derived ingredients- varying in their casein and whey protein content and composition- are present as an ingredient in many foods. This project was designed to identify candidate target peptides for casein and whey fractions of milk which can be used for milk allergen detection from foods irrespective of the type of ingredients used in them.