An overview is presented of the use of foodomics in the study of food allergies. Immunological, as well as DNA-based and mass spectrometry-based methods are the most frequently used techniques for determination of food allergens. Some immunological and DNA-based methods are suitable because of their high-throughput detection and characterization. However, these methods also bring the risk of biases. Allergen detection and quantification using mass spectrometry based foodomic techniques brings an important advantage over antibody and nucleic acid based techniques, especially regarding method reliability and reproducibility. Reliable and reproducible high-throughput detection and quantitative determination of allergens shall be implemented in food industry and control laboratories as a part of quality assurance and quality control during production and distribution.