Fig. 4.

Quantification of MRM/QTRAP and IDA/QSTAR data. (a) Linear regression comparing quantification results obtained by MRM and IDA methods. Each data point represents the level of phosphorylation for a given phosphorylated peptide at a given time point, relative to 4-min stimulation for that same peptide, quantified by either MRM or IDA. Regression parameters show a strong correlation R² = 0.94. The slope is 1 and offset is 0, indicating that the MRM method does not introduce bias and MRM-based quantification is equivalent to IDA-based quantification. (b) Distribution of the MRM/IDA quantification ratio. The data follow a Laplace distribution with location parameter of 1.01 and scaling parameter of 0.09. (c) Phosphorylation time courses for six phosphorylation sites (Cbl pY552, EGFR pY1173, ERK2 pT184/pY186, PLC-γ pY1253, N-WASP pY256, and STAT3-1 pY705) measured by using MRM (blue) and IDA (red), respectively. Error bars are from two biological replicates.