In addition, we compared the adjusted p-values obtained by the seven different tools (except for the ProStaR tool because its only calculates the p-value) with the best combination of parameters (Best PPV and NPV results) (Supplementary Figure ). High Pearson correlation is observed among the three tools: ProVision, Eatomics and LFQ-Analyst which can be related to the similar approaches to the three tools used for data normalization. However, MSstats, Proteus, and prolfqua adjusted p-values are weakly correlated with other tool results. The adjusted p-values from MSstats, for example, are more distributed close to 1, therefore, the consistency and Pearson correlations with other tools are not high. These results proved that is difficult to make comparisons between different tools for downstream analysis.