Figure 2

Quantitative evaluation of LC/MS profile alignment using apLCMS. Top row shows Pearson correlation within sample duplicates in both datasets; bottom row shows the median PID of feature intensities within sample duplicates. The effect of re-aligning profiles after removing poor quality samples (correlation coefficient, R² < 0.7) on the quantitative reproducibility of features is shown in the bottom right panel. A noticeable difference in median PID can be seen between alignment using all samples and alignment using only high quality samples for both columns of Sample Set 2.