The quality issues of ultra-high-temperature (UHT) milk, such as protein hydrolysis and aging gels throughout shelf life, are caused by proteases from psychrophilic bacteria. However, existing enzyme activity detection techniques have low sensitivity and cannot accomplish the detection of product deterioration caused by low enzyme activity. In this study, an attempt was made to analyze the relationship between enzymatically cleaved peptides and product quality using peptidomics techniques. The impact of psychrophilic bacteria proteases on the quality of UHT milk was investigated based on peptidomics by exogenously adding proteases. The results indicated that the protease activity and protein hydrolysis increased significantly in UHT milk over the storage period. Through peptidomic analysis, 2479 peptides were identified, in which 32 proteins linked to the identified peptides. 17 potential marker peptides, including αS1-casein143–156, β-lactoglobulin99–108, and β-casein39–66, were screened. The correlation of all identified peptides with protease activity and protein hydrolysis was explored by the weighted gene co-expression network analysis (WGCNA) method. The peptidomics technology helps to study the release or degradation of peptides in UHT milk during storage, which can be applied to monitor the shelf life of UHT milk and predict spoilage.
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