Fig. 2.
Statistical and comparative analyses of quantitative MS data. Quantified phosphopeptides were binned according to their log2 values of the ratio of their HB-EGF (A) or LPA (B) versus control ratios obtained in biological replicates. Gaussian regression analysis was applied to calculate the mean and S.D. for the log2-transformed ratios of ratios. C, correlation of phosphorylation site ratios upon HB-EGF or LPA treatment shown in a scatter plot comparison of biological replicates. Consistently up- and down-regulated sites enclosed by either of the two rectangles were considered for further analysis. D, regulated phosphosite ratios determined from kinase-enriched fractions were similar with or without normalization for protein abundance as visualized by a scatter plot.