Fig. 2.

a, equal aliquots of tryptic peptides derived from murine BaF3 cells were processed as two sets of technical replicates, iTRAQ labeled as indicated, and subjected to LC-MS/MS using a dual scan CAD-HCD method (Fig. 1a). b, a log-log plot of the reporter ion ratios as a function of their geometric mean spectral peak height for technical replicates yielded a best fit curve with constant variance at high signal intensity. c, 95% acceptance region after MACL-based fit to data normalized for linear trap ion injection time. d, precision of the data in c plotted as a function of measured signal-to-noise ratio (SNR) and number of data points, K, across an iTRAQ reporter ion spectral peak (33, 34). Precision based on MACL-derived variance function (Equation 1, black line) and previous theory (33, 34) (dashed orange line) is shown. Experimental data from previous studies are indicated as yellow (33) and purple (34) triangles, respectively. e, data from a biological replicate generated 3 months later and processed as a second set of technical replicates (red) were generated as described above and overlaid with the corrected data in c (green). f, Q-Q plot of the data in e after transformation to uniform variance confirmed the approximate normality of error in log intensities.