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. Author manuscript; available in PMC: 2022 Aug 6.
Published in final edited form as: J Proteome Res. 2021 Jul 8;20(8):4153–4164. doi: 10.1021/acs.jproteome.1c00483

Figure 5: Comparison of SNS and group-FDR.

Figure 5:

This plot compares the relative performance of SNS against group-FDR for the ricin (A and D), UPS1/yeast (B and E), and human dataset (C and F). For each mass spectrometry run, we determine the difference in the number of PSMs (A–C) detected between SNS and group-FDR at various q-value thresholds. In addition, we calculate the corresponding proportional increase (D–F). For F, we assigned a value of 0.5 when SNS detects any number of PSMs while group-FDR detects 0 PSMs and −0.5 when group FDR-detects any number of PSMs while SNS detects 0 PSMs. The vertical dashed line is at the conventional 1% FDR threshold. Note the plotted values in D–F are undefined for some q-values near 0, where neither SNS nor group-FDR detects any PSMs. For the human data (C and F), we only plot the median lines, where each line represents a different relevant protein.