Ubiquitinated peptide identification in tomato

In this study, we identified ubiquitinated peptides that changed abundance in the mutant of an E3 ubiquitin ligase gene by coupling a K-(GG) peptide immunoprecipitation with quantitative proteomic analysis. Two independent replicates identified 265 and 236 ubiquitinated peptides, respectively. Seventy-four ubiquitinated peptides were overlapped in both biological replicates. Quantitative analysis revealed that 27 of these ubiquitinated peptides changed abundance significantly (P < 0.05) in the mutant.