Fig. 3.

Ground-truth protein quantification results from MaxQuant and IonQuant from a mixture of three different proteomes. MaxQuant results are as published by Prianichnikov et al. 2020. “MBR+” and “MBR−” indicate that the analysis was performed with and without match-between-runs (MBR), respectively. S. cerevisiae proteins are shown in orange, H. sapiens in green, and E. coli in purple. The known ratios of condition A over condition B are 2:1 (S. cerevisiae), 1:1 (H. sapiens), and 1:4 (E. coli). The horizontal colored dashed lines (orange, green, and purple) indicate the true ratios. The black dashed lines are fitted curves from observed ratios. Box plots of the intensities are shown to the right of each scatter plot panel.