Extended Data Fig. 2: Reproducibility assessment of the decryptE workflow.

a) Left panel: number of quantified protein groups from DMSO control samples that were analyzed along the entire time frame of the proteomic screen plotted as a function of the consecutive order in which the samples were analyzed. Right panel: Cumulative density plot summarizing the precision with which proteins were quantified across DMSO control samples. Dotted lines indicate the respective fraction of proteins (50% and 90%) that were quantified with the given coefficient of variation (CoV). b) Volcano plot analysis for n = 4694 protein groups from 48 DMSO control samples from the proteomic screen which were randomly assigned to two groups. Analysis of significance was done using a two-sided Welch’s t-test without multiple testing correction. c) Cumulative density plot showing the reproducibility of pEC50 estimations from replicate dose-response analysis (n = 4) of palbociclib, panobinostat, and colchicine. 69.5 % of all pEC50 estimates were reproducible within ½ log10 step of drug concentration. Blue and pink dots indicate the SD for example curves of panel d) and e) respectively. d) Replicate dose-response curves of ATAD2 regulated by palbocicblib along with the SD for the pEC50. e) Same as panel d) but for AURKA regulated by colchicine. f) Upper panel: Violine plots showing the distribution of CoV of all proteins which were not regulated by drug treatment for each of the 144 drugs. Median values are given above each violine for each drug. Lower panel: same as upper panel but for all proteins that showed drug induced expression changes.