Method T1D vs. NGT T1D vs. NGT+T2D T1D vs. T2D M-test (original study) 103 79 27 T-test 39 23 0 SAM 19 10 11 LIMMA 0 1 0 Wilcoxon rank sum test 0 1 0 Rank Product 736 885 548 ROTS 15 5 6

Table 2: Number of differentially expressed proteins detected with the different tools (FDR<0.05). The data contains measurements from 16 T1D patients, 16 T2D patients, and 27 healthy controls with normal glucose tolerance (NGT).