Figure 1
Kinase inhibitor proteome impact analysis (KOPI) workflow and outputs. (A) The cell line is treated with kinase inhibitor/s at different concentrations under normal (37 °C) temperature and a heat challenge (52 °C). (B) The soluble fraction is harvested for tryptic digestion and multiplexed for quantitative mass spectrometry. (C) The fold changes relative to the untreated are fitted with a smoothing curve. (D) The average slope per curve is calculated to indicate the proteins’ response to drug treatment. The same analysis is performed on the enriched phospho-peptides to quantify the phosphoproteome’s response. (E) Each phosphosite was sorted into 4 possible responses based on the trend of their curves. The results are represented as the (F) ProteomeImpact and the (G) Phospho-Response. (F) ProteomeImpact: the average slope of each protein’s dose–response at 37 °C and 52 °C. Proteins with the average slope value on either axis larger than 0.5 are annotated, with kinases in beige. Stars represent common hits between this publication and Savitski et al. (G) PhosphoResponse: phosphopeptides are plotted against their number of continuous upward intervals (x-axis) and average slope under 37 °C (y-axis). Response categories: hypo-(blue), hyper-phosphorylation (red), biphasic (yellow) and non-responsive (grey). The pie chart indicates global proportions.
