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. 2023 Apr 5;22(5):1466–1482. doi: 10.1021/acs.jproteome.2c00834

Figure 6.

Figure 6

Controlled data sets 1, 2, and 3: Statistical analyses by MSstats v2.0 and v4.0. The true positives (TP) and false positives (FP) reported by each version. The FP are shown on the top, and the TP are shown at the bottom of each bar, with the black line showing 0. In all data sets, the TP numbers were similar between versions, while the FP were much lower when using v4.0. (a) Data set 1: Controlled Mixture–DDA–MaxQuant. (b) Data set 2: Controlled Mixture–DIA–Spectronaut. (c) Data set 3: Controlled Mixture–DDA–Skyline.