The aim of this study was to investigate the effect of different storage temperatures (4 °C, 25 °C and 45 °C, denoted as T-4, T-25 and T-45, respectively) on the physical stability and protein-lipid co-oxidation of whey protein functional emulsions during the storage period at storage times of 1, 2, 3 and 6 months. At the 6th month of storage, samples stored at 45 °C were less physically stable than samples stored at 4 °C, as evidenced by an increase in particle size (5.50%), a decrease in zeta potential (7.93%), and a decrease in adsorbed protein concentration (36.8%). The most severe protein-lipid co-oxidation was induced in whey protein functional emulsions under 45 °C temperature conditions with increasing storage time. Protein oxidation products (carbonyls, N′-formyl-L-kynurenine, and sulfhydryl groups) and lipid oxidation products (lipid hydroperoxides, thiobarbituric acid reactive substances) were at their highest levels, and significant molecular changes were observed in the molecules of adsorbed protein or unadsorbed proteins. As the storage temperature rises it exposes the active sites such as internal sulfhydryl and hydrophobic groups in the protein, promoting cross-linking and aggregation. Cluster and correlation analyses showed that protein-lipid co-oxidation of emulsions inevitably occurs during storage, but low-temperature storage can delay this process. This study is of guiding significance for the quality maintenance of functional nutritional emulsions and the selection of storage conditions. In addition, this study may provide clearer solutions to the problems of whey protein denaturation and formation of lipid oxides caused by protein-lipid co-oxidation in the food industry, as well as to the problem of increasing the shelf life of products by choosing the appropriate storage, packaging, and transportation temperatures.
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