Fig 3.

Analysis of EGF-induced signaling dynamics in the presence of a PV-treated protein carrier.A, schematic of PV-boost versus no-boost experimental layout and pTyr peptide enrichment. B, isobaric labeling scheme and treatment conditions. C, reporter ion intensities for PV-boost (left) and no-boost (right) analyses. Boxes outline the interquartile range, and whiskers the 10 and 90th percentiles. D, number of unique pTyr peptides quantified in each sample. Venn diagram shows overlap in total pTyr peptides between analyses. E, Venn diagram of the number of unique pTyr peptides quantified across all samples in each analysis (no missing values). F, coefficients of variation of PV-boost (gray) and no-boost (purple) analyses. Boxes outline the interquartile range, and whiskers the 10 and 90th percentiles. PV-boost median CV: 14 to 78%, no-boost: 11 to 12%. G, hierarchical clustering (Euclidean) of Log₂(fold change) values of pTyr sites identified in both analyses. PV-boost∗ values represent the original values from the PV-boost analysis renormalized to the mean 0s intensity with the 0s-2 excluded. Source data can be found in supplemental Table S4. H and I, Log₂(fold change) values of peptides in clusters H and I (Fig. 3G). Significance values: two-tailed t test of 30s versus 2m time point. ∗p < 0.05, ∗∗p < 0.01, ∗∗∗p < 0.001. Error bars represent ± standard deviation.