Use of foodomics, mostly proteomic and genomic based methods, for study of allergens in food is presented. Immunological methods and nucleic acid- based methods are still most frequently used for diagnosis of allergies and for qualitative and quantitative determination of food allergens. They are sensitive, and can be used for the determination of allergens in trace concentrations. However, lack of specificity and cross-reaction of some antibodies can still be a relevant source of bias. The epitopes of protein allergens with posttranslational modifications and their changes originated during food processing cannot be traced by use of nucleic acid-based strategies. Recent developments of both antibody and nucleic acid-based biosensors, their miniaturization and increasing application of nanotechnology, significantly supported further use of both strategies. Regarding accuracy, reliability and sensitivity, mass spectrometry-based methods bring important advantage over both above presented strategies. Furthermore, the increasing use of mass spectrometry (MS) is discussed. Combined with proper sample preparation, liquid chromatography (LC) and/or different electrophoretic methods, targeted approach in mass spectrometry-based allergen analysis brings an additional strategic advance. However, MS is still rarely used for high-throughput analyses and detection and quantification of allergens for the reasons of price and relatively long time necessary for analysis. Recent developments of new high-resolution instruments are encouraging and enable development in the direction of a high-throughput strategy. Consequently, fast, very sensitive, reliable and accurate detection and quantification of allergens in highly complex samples such as food matrices, and the use of MS in routine determination of allergens can be reached in near future.