Updated publication reference for PubMed record(s): 28270225. Identification of protease targets is essential to understand the molecular mechanism by which a protease regulates the biological processes. In this study, we applied an iTRAQ-based quantitative proteomic approach to identify the potential targets of a vacuolar processing enzyme in the cellular context in tomato. Proteins were isolated from fruits of wild-type and RNAi tomato plants. More than 300 proteins were finally screened as significantly altered in the RNAi fruits. Based on Blast2go, a web-based bioinformatic tool that categorizes proteins according to their Gene Ontology (GO) annotations, the proteins experienced significant changes in abundance in the RNAi fruits were classified into fifteen functional categories.