Figure 3. Between-experiment data evaluation. (A) Principal component analysis of 177 normalized and scaled iTRAQ ratios identified in three experiments. Plot displays component 1 against component 2 for the individual iTRAQ experiments. (B) Cluster analysis of the normalized and scaled iTRAQ ratios for 177 proteins that were detected in all three experiments. Experiment 3 is divided into 3A and 3B because they were separated into two iTRAQ labelling and MS procedures. Labels are the cell name and experiment number. Note: Values were imputed for 15 and 25 missing proteins in experiment 3A and 3B, respectively.