Table 2 Alignment parameters
From: Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements
Tool | Parameter | Metabolomics Data | Metabolomics Data | ||
|---|---|---|---|---|---|
| Â | Â | Data Set P1 | Data Set P2 | Data Set M1 | Data Set M2 |
msInspect | massWindow | 1.5 | 1.5 | 0.1 | 0.05 |
| Â | scanWindow | 250 | 300 | 250 | 300 |
MZmine | m/z tolerance size | 1.5 | 1.5 | 0.03 | 0.025 |
| Â | RT tolerance size (absolute) | 150 | 300 | 50 | 30 |
OpenMS | m/z bucket | 0.5 | 0.5 | 0.1 | 0.01 |
| Â | precision m/z | 2 | 2 | 0.1 | 0.1 |
| Â | precision RT | 150 | 300 | 100 | 100 |
SpecArray | (hard coded parameters) | - | - | - | - |
XAlign | m/z variation | 2 | 2 | 0.04 | 0.03 |
| Â | retention time variation | 3 | 3 | 0.5 | 0.5 |
XCMS | mzwid | 2.5 | 2.5 | 0.15 | 0.05 |
| Â | bw | 40 | 80 | 30 | 30 |
| Â | retcor method | loess | linear | loess | loess |
| Â | span | 0.75 | - | 0.75 | 0.75 |