Table 2 Tools and Parameter used for pre-processing the LCMS raw data.
From: LC-MS based plant metabolic profiles of thirteen grassland species grown in diverse neighbourhoods
Tool name | Description | Version | Parameter | Value |
|---|---|---|---|---|
MSnbase readMSData | Import mass-spectrometry data files | 2.8.2.1 | ||
findChromPeaks | feature detection | 3.4.4.1 | extraction method | 40 |
peak width (s) | 5, 20 | |||
signal to noise ratio | 5 | |||
prefilter | 3, 100 | |||
noise filter | 100 | |||
xcms findChromPeaks Merger | merging xcms findChromPeaks | 3.4.4.0 | ||
xcms groupChromPeaks (group) | grouping of chromatographic peaks | 3.4.4.0 | method | PeakDensity |
bandwidth | 6 | |||
minimum fraction | 0.75 | |||
minimum number | 1 | |||
width of m/z slices | 0.005 | |||
xcms adjustRtime (retcor) | retention time correction | 3.4.4.1 | method | PeakGroups |
minimum fraction | 0.75 | |||
maximum number | 1 | |||
smooth method | Loess – non-linear alignment | |||
degree smoothing | 0.2 | |||
family | gaussian | |||
xcms groupChromPeaks (group) | grouping of chromatographic peaks | 3.4.4.0 | method | PeakDensity |
bandwidth | 6 | |||
minimum fraction | 0.75 | |||
minimum number | 1 | |||
width of m/z slices | 0.005 | |||
CAMERA.annotate | Annotation of putative compounds | 2.2.4 | multiplier of sd | 6 |
general ppm error | 5 | |||
general abs error | 0.005 | |||
maximum ion charge | 3 | |||
maximum number | 4 | |||
isotope annotation | 0.5 | |||
correlation threshold | 0.75 | |||
grouping into pseudospectra | hcs | |||
correlation threshold | 0.05 | |||
Check Format | Checking/formatting the sample and variable names | 3.0.0 | ||
Generic_Filter | Deleting samples and/or variables | 2017.06 | remove in “…” values upper | “rt”, 840 (s) |
remove in”…” values lower | “rt”, 80 (s) |
