4D-FastDIA-based quantitative proteomics reveals protein biomarkers linked to flavor traits between triploid and diploid oysters (Crassostrea angulata)

In this study, the 4D-FastDIA-based quantitative proteomics strategy was employed to identify protein biomarkers linked to flavor traits in triploid and diploid oysters ( Crassostrea angulata ). A comprehensive analysis identified a total of 61,947 peptides and 9703 protein groups across four sample groups, with 3679 common proteins shared among all groups. Differentially expressed proteins (DEPs) were found to be significantly associated with flavor-related traits, revealing notable differences in amino acids, lipids, and nucleotides between triploid and diploid oysters. Enrichment analysis further elucidated significant pathways involved in metabolic processes, biosynthesis, and immune responses. Among the DEPs, 864 were correlated with flavor quality traits, highlighting key proteins such as S-adenosylmethionine synthase and pyruvate kinase as potential biomarkers for flavor traits. These findings provide valuable insights into the molecular mechanisms underlying flavor differences in oysters and offer potential biomarkers for evaluating and enhancing oyster quality. • 4D-FastDIA-based proteomics reveals key protein biomarkers in triploid and diploid oysters. • Significant differences in amino acids, lipids, and nucleotides enhance oyster flavor traits. • 864 differentially expressed proteins correlate with flavor quality traits in oysters. • Proteomic analysis identifies metabolic pathways crucial for oyster flavor profiles. • Potential biomarkers like S-adenosylmethionine synthase improve flavor assessment.