Fig 4.

pTyr-boost with 9× EGF-boost protein carrier improves quantitative accuracy but still yields large number of missing values.A, experimental layout of EGF-boost experiment with 9× protein carrier. B, isobaric labeling scheme and treatment conditions. C, total number of unique pTyr peptides identified in each analysis. D, proportion of PSMs with missing values for each sample. E, total number of unique pTyr peptides quantified in each analysis and Venn diagram of peptides commonly identified between analyses (no MV’s). F, coefficients of variation between replicates in EGF-boost and no-boost analyses. Boxes outline the interquartile range, and whiskers the 10 and 90th percentiles. EGF-boost 250 ms median CV: 12 to 14%, 500 ms IT: 9 to 12%, no-boost: 10 to 11%. G, samples plotted by principal component 1 (PC1) and PC2 score, colored by EGF stimulation condition for 500 ms EGF boost and no-boost analyses. Percentages describe the variance explained by the plotted PC.