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. 2014 Dec 8;14(2):1147–1160. doi: 10.1021/pr5010983

Figure 7.

Figure 7

With noncalibrated scores, Käll’s method is more conservative than TDC. The ratio of the number of Käll discoveries to TDC discoveries at FDR ≤ 0.1 when using the raw score. The median ratio (with respect to 1000 independently drawn decoys) in solid line is flanked by the 0.95 and 0.05 quantiles of the ratios. Results are for raw scores, but keep in mind that MS-GF+ E-value is partially calibrated even in its raw form, so the ratio of Käll to TDC discoveries fluctuates above and below 1.