High-resolution mass spectrometry-based selection of peanut peptide biomarkers considering food processing and market type variation

•Strategy for peptide biomarker selection for allergen detection and quantification.•Empirical identification of 16 potential peptide biomarkers for peanut with HRMS.•Analysis of processed peanut matrices produced in semi-industrial conditions.•Protein variation due to peanut market type.•Consideration of multiple allergen isoforms. To protect allergic patients and guarantee correct food labeling, robust, specific and sensitive detection methods are urgently needed. Mass spectrometry (MS)-based methods could overcome the limitations of current detection techniques. The first step in the development of an MS-based method is the identification of biomarkers, which are, in the case of food allergens, peptides. Here, we implemented a strategy to identify the most salient peptide biomarkers in peanuts. Processed peanut matrices were prepared and analyzed using an untargeted approach via high-resolution MS. More than 300 identified peptides were further filtered using selection criteria to strengthen the analytical performance of a future, routine quantitative method. The resulting 16 peptides are robust to food processing, specific to peanuts, and satisfy sequence-based criteria. The aspect of multiple protein isoforms is also considered in the selection tree, an aspect that is essential for a quantitative method’s robustness but seldom, if ever, considered.