The objective of this study was to analyse allergenic proteins by identifying their molecular biomarkers for detection in food using bioinformatics tools. The protein and epitope sequences were from BIOPEP database, proteolysis was simulated using BIOPEP program and UniProt database screening via BLAST and FASTA programs. The biomarkers of food proteins were proposed: for example for whey proteins - TPEVDDEALEKFDKALKALPMHIR (β-Lg: fragment 141-164), chicken egg - AAVSVDCSEYPKPDCTAEDRPL (ovomucoid: 156-177), wheat - KCNGTVEQVESIVNTLNAGQIASTDVVEVVVSPPY (triose phosphate isomerase: 12-46) and peanuts - QARQLKNNNPFKFFVPPFQQSPRAVA (arachin: 505-530). The results are annotated in the BIOPEP database of allergenic proteins and epitopes, available at http://www.uwm.edu.pl/biochemia. The epitope-receptor interactions are attributed to the epitope's sequence and suggest that in silico proteolysis products showing the highest degree of sequence identity with an epitope or its part are characteristic of a given protein or a group of cross-reactive homologs. The protein markers from basic food groups were proposed based on the above assumption.