The article is devoted to the study of the processes of epimerization of L-amino acid residues with the formation of D-enantiomers, which affect the onco-associated properties of food products. A method for the chromatographic separation of optically active D- and L-amino acids using a chiral column has been developed. Measurements of the quantitative content of analytes were carried out using a diode array detector, followed by mass spectrometric confirmation. Methodological approaches to sample preparation are presented. It was revealed that during acid hydrolysis, leucine racemization from D-form to L-form. A procedure has been developed for enzymatic hydrolysis of samples by a complex of proteolytic enzymes, followed by purification of the hydrolyzate by solid-phase extraction. The degree of extraction, matrix effects, and the quantitative detection limit of the technique were determined. The data on post-translational modifications in the structure of proteins and peptides under the influence of technological operations and enzymatic processes in the production of meat products are presented.