Fig. 3.

Reproducibility of protein turnover rate determination by pulsed SILAC-TMT labeling. A, Turnover rates were determined for between 5528 and 6367 protein groups per cell culture replicate (R1-R4). B, In total, rates were obtained for 7203 proteins, and for 83% of these turnover information was available from both label increase and decrease. C, Correlation matrix depicts color-coded Pearson's correlation coefficients for log transformed protein turnover rates determined from synthesis and degradation curves for cell culture (R1-R4) and MS injection (R2 and R2′) replicates. The boxplots (10th–90th percentile) show the coefficients of variation of turnover rates across replicate MS injections, synthesis and degradation curve pairs within a sample and cell culture replicates. D, Examples of the reproducibility of turnover determination across cell culture replicates are displayed for the high turnover protein G2/mitotic-specific cyclin-B1 (CCNB1) and the stable 60S ribosomal protein L32 (RPL32).