Table 2.
Experimental Reproducibility
| Ratio | MASCOT | X!Tandem/OpenMS | PPINGUIN | |
|---|---|---|---|---|
| NZO_SD/SJL_SD | 0.13 | 0.12 | 0.10 | |
| CV | NZO_HFD/SJL_SD | 0.17 | 0.16 | 0.14 |
| SJL_HFD/SJL_SD | 0.18 | 0.17 | 0.15 | |
| NZO_SD/SJL_SD | 0.19 | 0.17 | 0.14 | |
| StDev log2 | NZO_HFD/SJL_SD | 0.25 | 0.22 | 0.20 |
| SJL_HFD/SJL_SD | 0.24 | 0.24 | 0.21 | |
Experimental reproducibility using the analysis methods investigated (columns). For the 3 experimental ratios (NZO_SD/SJL_SD, NZO_HFD/SJL_SD and SJL_HFD/SJL_SD) the mean coefficient of variation (CV) and the mean standard deviation for log2 quantitation ratios (see Methods) of all proteins are stated.