When we compared the estimated log-fold change and the obtained log-fold change for each tool, all Pearson correlations were higher than 0.85 (Supplementary Figure ), which means that the adjusted p-values are consistent within a tool but not comparable across different tools. It is important to notice for Perseus users, that the direct alternatives to the tool (ProVision, Eatomics and LFQ-Analyst) will produce values between 0.7 and 0.8 Pearson correlation compared to Perseus.