Abstract: Polygonatum cyrtonema Hua (P. cyrtonema), a medicinal and edible, has a long-standing tradition of treating respiratory diseases, regulating immune function, and enhancing liver health. Although polysaccharides, saponins, and flavonoids have been identified as its major bioactive components, the presence and properties of bioactive peptides in P. cyrtonema are relatively understudied. This study utilized an alkali extraction-acid precipitation method to extract crude protein from P. cyrtonema. Subsequently, Nano-LC-Q Exactive MS was utilized to characte rize successfully the sequences and abundances of endogenous peptides from different sources. A total of 2571 M1(endogenous) peptides and 2122 M2(crude protein) peptides were identified using a combination of database searches and de novo strategies, with significantly higher confidence levels observed for M2 peptides identified through the database search approach. Further analysis of subsequent overall differences reveals that, based on the chemical properties and bioinformatics analyses of peptides from different sources, the M1 peptide primarily consists of 4–6 amino acids (62.1 %), while the M2 peptide is mainly composed of more than 8 amino acids (60.8 %). Molecular docking technology was then applied to verify the antioxidant prediction results and to evaluate the differences in antioxidant potential between M1 peptides and M2 peptides, with seven of the top ten ranked peptides in terms of docking energy being M1 peptides. These findings notably advance our understanding of endogenous peptides in P. cyrtonema and provide valuable reference information for identifying potential candidate bioactive compounds. This information will support future comprehensive validation of the biological activities of these peptides in P. cyrtonema and contribute to drug discovery research.
