Table 2. Reoptimization of Published XCMS Parametersa.
| XCMS parameter | published parameters | with optimized peak finding | with optimized retcor and group |
|---|---|---|---|
| ppm | 15 | 12 | 12 |
| peak width | 10, 120 | 15, 140 | 15, 140 |
| mzwid | 0.015 | 0.015 | 0.015 |
| bw | 5 | 5 | 10 |
| gapInit | 0.6 | ||
| total features | 32010 | 27260 | 27260 |
| credentialed features | 1475 | 1776 | 1817 |
a
Parameters used and the results of each step in the optimization process are shown. Published parameters were taken from a previously published method (ref (6)). The column labeled “with optimized peak finding” shows results for the optimization of findPeaks.centWave().