Fig. 3

Comparison of contrast between spike-in levels in DIA Umpire and PeakView. These panels show part of the statistical interface in OmicLoupe, showing how the unadjusted p values for features relate to fold-changes in the statistical comparison between the two spike-in levels. a Features passing the significance threshold FDR < 0.05 and log2 fold > 0.5 in individual datasets, and in both. Green points (“contra” in the legend) are passing the significance threshold in both datasets, but with reversed log2 fold direction. b Coloring based on the spike-in source. c The outcome of interactively highlighting a set of six features only significant in PeakView and one significant in both. This reveals their distribution in DIA Umpire, showing that the features upregulated in both are true positives, while one of the two found in lower abundance in DIA Umpire is a false hit