Changes in nuclear proteome in rin mutant reveal the potential downstream targets of RIN. (a) Nuclear proteins were isolated from wild-type (WT) and rin mutant fruits at breaker (Br) and orange (Or) ripening stages, and subjected to isobaric tags for relative and absolute quantification (iTRAQ) labeling coupled with NanoLC-MS/MS. A total of 127 proteins showing differential expression in the rin mutant relative to the wild-type at Br or Or stage were identified and classified into seven functional categories. The expression patterns of the proteins within each functional category were hierarchically clustered based on the expression ratio as a log2 scale. Each row in the color heat map indicates a single protein. The gene identifiers (Solyc numbers) and the functional annotations are shown. The green and red colors indicate down- and upregulation, respectively, in the rin mutant relative to the wild-type. Black represents no significant expression change. Data from biologically repeated samples are averaged and the detailed information on proteins is listed in Additional file 4. (b) Venn diagram showing the overlap of proteins that changed abundance in the process of fruit ripening and those that changed abundance in the rin mutant at the same ripening stage (Br or Or).