This study integrated metabolomics, gas chromatography–mass spectrometry, and molecular docking to investigate the fermentation potential and flavor formation mechanisms of Staphylococcus saprophyticus protease in Harbin dry sausage. Gel electrophoresis demonstrated that the S. saprophyticus protease induced a significant reduction in the band intensities of myosin heavy chain, phosphorylase, and glyceraldehyde dehydrogenase, while increasing the band intensity of myosin light chain. Fourier transform infrared spectroscopy revealed that the intensities of amide A, B, I, and II bands were reduced following protease supplementation. Correspondingly, secondary structure analysis indicated increased α-helix and random coil contents, alongside decreased β-sheet and β-turn structures (P < 0.05). A total of 325 differential metabolites and 9 key volatile compounds were identified in the sausage samples. Specifically, S. saprophyticus protease facilitated increased proportions of taste peptides, amino acids and their derivatives, as well as acids, ketones, and esters, while lipid oxidation was moderately inhibited. Protein digestion and absorption, aminoacyl-tRNA biosynthesis, and biosynthesis of amino acids were the three most significantly enriched metabolic pathways. Molecular docking results showed that hydrogen bonding was the predominant interaction between S. saprophyticus protease and its target proteins (myosin heavy chain and phosphorylase). Moreover, the pH, water activity, shear force, and sensory scores of the sausages were significantly improved (P < 0.05). Both the hydrolytic activity and product quality exhibited a concentration-dependent enhancement with increasing protease levels. The optimal product quality was achieved at a S. saprophyticus protease addition level of 1.6 g/kg, which outperformed direct inoculation of S. saprophyticus.
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