Figure 2

Quantitative analysis of nuclear proteome during tomato fruit ripening. Nuclear proteins were extracted from tomato fruits at mature green (MG), breaker (Br), orange (Or), and red ripe (RR) ripening stages, and subjected to isobaric tags for relative and absolute quantification (iTRAQ) labeling coupled with NanoLC-MS/MS. The 136 differentially expressed proteins were classified into seven functional categories and the expression patterns within each were hierarchically clustered. Expression ratios were calculated using the earlier ripening stage, that is, MG, as denominator, and plotted in a heat map on a log₂ scale. Each row in the color heat map indicates a single protein, and the gene identifiers (Solyc numbers) and functional annotations are shown. The green and red colors indicate down- and upregulation, respectively, in an indicated ripening stage relative to the MG stage. Black represents no significant expression change. Data from biologically repeated samples are averaged and the detailed information on proteins is listed in Additional file 2.