Fig. 2.

Measuring acetylation stoichiometry. A, The column graph shows the number of acetylated peptides, and acetylated peptides with SILAC ratios, that were identified at the indicated mixing ratios of 100% acetylated (Ac) peptides and native peptides. The fraction (%) of peptides with SILAC ratios is indicated. B, The column graph shows the quantification error for acetylated peptides that were identified at the indicated mixing ratios of 100% acetylated (Ac) peptides and native peptides. C, The category scatterplot shows the distributions of acetylated peptide stoichiometry or the degree of partial chemical acetylation (Degree PCA, experiment 3) for the indicated experiments. CCA = complete chemical acetylation, PCA = partial chemical acetylation, (L) = SILAC light labeled, (H) = SILAC heavy labeled, WT = wild type, EP = exponential phase, SP = stationary phase, NAM = nicotinamide, knock out (Δ) strains are as indicated. The median of the distributions are indicated by the red lines. D, The column graph shows the percent quantification error (% error) for the indicated experiments. The median stoichiometry of native acetylation for each experiment is indicated by the red lines. E, The scatterplot shows the correlation between differences in acetylation stoichiometry between SP and EP cells (stoichiometry ratio SP/EP) and independent SILAC quantification of those same differences (SILAC ratio SP/EP). The number of acetylated peptides analyzed (n), Pearson's correlation (r), and p value (P) of correlation is shown. F, The scatterplot shows the correlation between differences in acetylation stoichiometry between cobBΔ and WT cells (stoichiometry ratio cobBΔ/WT) and previous SILAC quantification (12) of the same acetylated peptides (SILAC ratio cobBΔ/WT). G, The scatterplot shows the correlation between differences in acetylation stoichiometry between ackAΔ and ptaΔ cells (stoichiometry ratio ackAΔ/ptaΔ) and previous SILAC quantification (12) of the same acetylated peptides (SILAC ratio ackAΔ/ptaΔ).