Figure 2.

Correlation between the 2 technical replicates and determination of the cutoff value for significant fold changes. (a) Plots of iTRAQ ratios for two technical replicates. Forty-four proteins were commonly observed from technical replicate 1 (labeled 115/114), and 26 proteins were commonly observed from technical replicate 2 (labeled 117/116). These differentially excreted proteins (P value < 0.05, more than two unique peptides: >95%) were plotted in the linear dynamic range. The technical variations yielded a correlation coefficient of r ² = 0.9527 and r ² = 0.9178 between iTRAQ experiments 1 and 2, respectively. (b) The % variations for the common proteins from the two technical replicates. The 44 and 26 common proteins from the 2 technical replicates were used as inputs to calculate % variations. The vertical axis represents the number of proteins, and the horizontal axis denotes % variation. Ninety percent of the proteins fell within 25% of the respective experimental variation. Thus, we considered a fold-change of >1.25 or <0.80, a meaningful cutoff that represented actual differences in the iTRAQ experiments.