In this study, for all four datasets (Table 1), the DModX was normalized in units of standard deviation, with the significance level of 0.05. Inspecting the DModX plots (Figure 1C,D and Figure S1C,D) showed the existence of some moderate outliers. What is important to notice is that these moderate outliers were different in the four PC models (Figure 1C,D and Figure S1C,D), suggesting that varying of the two processing parameters (mass tolerance and intensity threshold) clearly altered the structure in the X-space (particularly in higher-order components), and this impacts the statistical description thereafter. The moderate outliers were further investigated by computing the contribution plots (Figure S3) and no sample/observation had variable(s) with critical deviation from the rest of the dataset.