Extended Data Fig. 8. Protein turnover quality control and relationship between protein abundance and turnover.

a, Experimental design of dynamic SILAC turnover experiments. Aneuploid or euploid isolates (n = 60) were grown on minimal medium agar supplemented with unlabelled lysine (SM + Lys-0), pre-cultured for 16 h, and then diluted to a low OD. After reaching early mid-log phase (~OD 0.3), cells were transferred into minimal medium supplemented with heavy-isotope labelled lysine (SM + Lys-8) and samples were collected and prepared for proteomics after 90, 135, and 180 min. b, Box plots depicting the number of peptides per isolate (dots, n = 56) with valid SILAC ratios per time point after the switch from unlabelled to Lys-8-labelled SILAC medium. Box plot hinges mark the 25th and 75th percentiles and whiskers show all values that, at maximum, fall within 1.5 times the interquartile range. c, Distribution of the number of proteins per isolate (n = 55) for which turnover rates were determined. d, Pearson correlation between relative Age2 protein expression and isolate turnover rate across euploid isolates (top, light teal line) as well as aneuploid chromosomes of aneuploid isolates (bottom, dark teal line). The dotted grey line denotes 0. e, Pearson correlation coefficients (PCC) between relative protein abundances and the overall protein turnover rate across euploid isolates for genes annotated as structural components of the proteasome (KEGG, identified via gene set enrichment analysis of ranked PCCs, p = 0.0019/FDR: 0.16). PCC were calculated across all euploid isolates for which isolate-wise turnover rates could be determined (n = 8).