Food allergen has become a very important issue in food safe. It is very important to develop rapid and reliable detection methods for food allergen. The usual detection methods for food allergen are PCR and ELISA.With the development of mass spectrometry, it became a new method to study food allergen. MS methods have the advantage of accurate, fast and sensitive. The application in hazelnut, peanut and milk allergen detection has been reviewed in this paper.