In PXD007145, we know the true positive rate and could plot ROC curves based on adjusted p-values for each case to assess performance (Figure ). We see that MSstats has higher accuracy, with area under the curve (AUC) values of 0.93 and 0.87 at 4-fold and 10-fold change, respectively. Although both tools had similar AUCs after normalization, MSstats obtained a more concentrated fold change distribution. MSstats also returns more proteins at a fixed FDR level than Proteus (Supplementary Figure ). For a 4-fold change, MSstats returns 357 DE proteins at 1% FDR, Proteus returns 332. For a 10-fold change, MSstats returns 426 DE proteins at 1% FDR, Proteus returns 407.