Identification of a novel selenium peptide from Oryzain α hydrolysate: Selenium-specific database establishment, sequence confirmation, and molecular interaction analysis

To enable the precision production and identification of bioactive selenium peptides from selenium-biofortified rice proteins, this study developed an approach combining controlled enzymatic hydrolysis, ultrafiltration, and high-resolution mass spectrometry. Rice proteins were subjected to chymotrypsin/trypsin digestion, followed by ultrafiltration to enrich low-molecular-weight selenium peptides. A selenium-specific peptide database was constructed by systematically replacing methionine (Met) and cysteine (Cys) with selenized forms in UniProtKB Oryza sativa L. protein sequences (195,302 entries), generating 88,176 unique selenium peptide entries to overcome limitations in traditional database annotations. Ultra-performance liquid chromatography coupled with quadrupole-Orbitrap (UHPLC-Q-Orbitrap) and dynamic mass calibration enabled high-confidence screening of selenium peptides under EU 2002/657/EC guidelines, identifying 104 candidate selenium peptides. Among these, 14 high-confidence peptides (coverage score >5 %) were sequenced de novo using mMass 5.5.0. Parallel reaction monitoring (PRM) and multidimensional validation (fragment ion matching and modification site localization) confirmed the structure and bioactivity of key selenium peptides, such as Leu-{Se-Met}-Ala-Lys, which exhibited strong binding affinity to dipeptidyl peptidase IV (DPP-IV) active sites (binding energy: −64.54 kcal mol −1 ). Research findings demonstrate that selenium peptides can be precisely isolated from biofortified crops and characterized for their functional properties. The dynamic database and high-resolution analysis framework can be expanded to include selenium morphology analysis, bioactive peptide discovery and precise nutrition research, promoting the development of data-driven functional food.