Supplementary Figure 4: Correlation analyses between protein abundance changes and the deviation in their ubiquitination sites in response to proteasomal inhibition.

a, DIA analyses of the total proteomes of bortezomib- (Bort), b-AP15- and mock-treated (Ctrl) Jurkat and Hep2 cells. Scatterplots showing correlations among the five independent replicates for each condition and cell line. Minimum and maximum sample sizes for Jurkat cells were 6,021 and 6,433 proteins, respectively. Minimum and maximum sample sizes for Hep2 cells were 6,120 and 6,527 proteins, respectively. Numbers in each box show the corresponding Pearson correlation coefficients. b, Scatterplots displaying the change in protein abundance versus protein’s ubiquitination site with the biggest change in response to bortezomib (BOR) and b-AP15 (AP15) as compared to mock-treated cells (CTR). R refers to Pearson correlation. c, Scatterplot showing the change in protein abundance versus protein’s mean ubiquitination site in response to bortezomib (BOR) (data extracted from Mol. Cell 44, 325–340, 2011). R refers to Pearson correlation coefficient. d, Scatterplot displaying the change in protein abundance versus protein’s mean ubiquitination site in response to MG132 (data extracted from J. Proteome Res. 16, 2848–2862, 2017). R refers to Pearson correlation coefficient. e, Accumulation of high-molecular-weight protein–ubiquitin conjugates upon treatment of cells with proteasomal inhibitors detected by immunoblotting on the same cellular lysates that were used for the DIA measurements. Shown is a representative of three independent experiments.