The quantitative TMT experiment to determine RNase- and puromycin-dependent RAPs.
A, Overview of the quantitative-MS experiment approach. Three biological replicates (BR) are used for each control, RNase, and puromycin-treatment. Pearson correlation coefficients for each BR within a treatment are calculated using normalized log2 TMT intensities.
B, Scatter plot of normalized log2 RNase/control ratios versus P-values. FDR and negative predictive values (NPV) are estimated by mixture modeling of test statistics (Efron, 2004). 14% of the interactions are estimated to be RNase-dependent (Figure S4). At 99% NPV, 438 interactions are estimated to be RNase-independent. Representative examples of RNase-dependent ribosome-interactions are highlighted. See Table S3.
C, Scatter plot with normalized log2 puromycin/control ratios versus P-values. Representative examples of puromycin dependent interactions are highlighted.