Preliminary Results on the Peptidomic Characterization of Traditional Greek PDO Cheeses from the Thessaly Region

This study presents the first preliminary biopeptide profiling of three Thessalian PDO cheeses (Kaseri, Manouri, and Batzos) using HPLC-ESI-MS coupled with in silico bioactivity prediction. The three cheeses were chosen as representative Thessalian PDO cheeses made from sheep and/or goat milk, reflecting the traditional dairy practices and regional identity of this area. A total of 212 peptide masses were putatively identified (86 in Kaseri, 85 in Batzos, 41 in Manouri), mainly originating from β-casein (45%) and αs1-casein (30%), indicating region-specific proteolysis driven by processing technologies and microbial ecology. Kaseri exhibited the greatest peptidomic diversity (31 bioactive peptides), whereas Manouri exhibited the greatest frequency of bioactive peptides (34/41; 83%), dominated by DPP-IV-inhibitory peptides (44%). Batzos displayed a balanced ACE and DPP-IV-inhibitory profile typical of brine-ripened cheeses. Screening with MBPDB, BIOPEP-UWM, and PeptideRanker identified 80 known bioactive peptides and 98 uncharacterized sequences, nine common across all cheeses. Peptide length distribution showed consistent proportions of tri- and tetrapeptides (16–19% and 5–7%), with Kaseri enriched in longer sequences (≥6 aa; 60.5%). Batzos peptides, not found in databases, with high PeptideRanker scores (>0.75) suggest potential authentication markers. These preliminary findings provide a basis for further investigation of the peptide profiles and potential bioactivities of Thessalian PDO cheeses.