Fig. 4

Quantitative proteome analysis reveals the potential targets of SlVPE3. a Workflow of the quantitative proteome analysis. Proteins were isolated from wild-type (WT) and SlVPE3 RNAi fruit at 41 or 44 days post-anthesis (dpa), and subjected to isobaric tags for relative and absolute quantification (iTRAQ) labeling coupled with nanoLC–MS/MS. b A total of 314 proteins showing differential expression in the SlVPE3 RNAi fruit compared to the WT were identified. The expression patterns of the proteins were hierarchically clustered based on the expression ratio as a log₂ scale. Each row in the color heat map represents a single protein. The green and red colors indicate down- and up-regulation, respectively, in the SlVPE3 RNAi fruit relative to the WT. Black represents no significant expression change. Values from biological replicates were averaged and the detailed information associated with the identified proteins is listed in Additional file 6: Table S5. c Functional categories of the proteins that changed abundance in the SlVPE3 RNAi fruit at 41 or 44 dpa compared with WT