Endogenous protein and peptide analysis with LC-MS/(MS): A feasibility study for authentication of raw-milk farmer's cheese

When consumers buy Dutch ‘Boerenkaas’ (farmer's cheese), a cheese made from raw milk protected under the European traditional specialties guaranteed (TSG) label, they expect this product to be authentic. Because of the difference in production costs and risks, it is tempting to sell cheeses made from heat-treated milk as ‘Boerenkaas’. It is therefore essential that there are methods that can verify the heat-treatment status of the milk in cheese. Here, for the first time a proof of principle method for analysis of endogenous cheese proteins/peptides with liquid chromatography-mass spectrometry (LC-MS) in combination with multivariate analysis to detect discriminatory protein/peptide biomarkers between ‘Boerenkaas’ and heat-treated milk cheese is described. A top-down MS method was developed for biomarker identification. The identified biomarkers were confirmed with the well-established bottom-up approach. Overall, there was good agreement between the outcome of the developed methods based on the known thermal treatment of the used sample set.