Proteomics analysis reveals differences in fresh and processed fruit juice: A case of not from concentrate orange juice

Comparative proteomics of fresh versus processed orange juice was analyzed using tandem mass tag pro-labeled nano-UHPLC-Orbitrap Fusion MS, achieving comprehensive annotation of 4793 proteins. Quantitative analysis identified 90 and 37 differentially abundant proteins (DAPs) in pasteurized and high-pressure-processed juice, compared to the fresh juice. Gene ontology enrichment revealed that DAPs with higher abundance in processed juice were predominantly associated with cellular component of organelles, indicating cell disruption during processing. Greater disturbances in cell structure were observed in pasteurized juice, which may contribute to enhanced protein release. Notably, the 12 proteins that decreased in processed juice were primarily enzymes, with fructose-bisphosphate aldolase exhibiting significant variation and selected as processing marker. Molecular dynamics simulations revealed that processing led to structural change of the marker, manifesting as α-helix reduction and random coil elevation, probably resulting in conformational destabilization prone to degradation. This study firstly differentiates the fresh and processed orange juices using proteomics.