Paul,
I found very interesting the discussion you suggest me, but I haven't found any suggestion about the extraction of the area of the grouped spectra. I would like to group the ions in the time domain, using their retention time, and extract them so to re-construct the EI mass spectra such to separate co-eluting peaks.
How can I use the information in the xcmsSet object?
In the xcmsSet object I have:
Time range: 153.8-3039 seconds (2.6-50.6 minutes)
Mass range: 31.1-348.7638 m/z
Peaks: 25337 (about 4223 per sample)
Peak Groups: 2004
Sample classes: crtz_VOCs
Does 'Peak Groups' contains the ions grouped according with their retention time?
Riccardo
-- EDIT --
I played with the xcms parameter and I noticed better results using the matchedFilter approach instead of centWave. This because I obtain more 'realistic' EI mass spectra with more fragment. So this are the new settings I'm using:
## xcms ##
xset <- xcmsSet(files = files[1:3], nSlaves = slaves, method = 'matchedFilter',## sleep = 3,
snthr = 1, fwhm = 10, step = .5, steps = 2, mzdiff = 0, max = 500)
xset <- group(xset, method = 'density', bw = 30, mzwid = 1, minfrac = 1, ## sleep = 3,
max = 500)
xsetRT <- retcor(xset, method = 'loess', family = 'gaussian')
plotrt(xsetRT, leg = FALSE, densplit = TRUE)
xsetRT <- group(xsetRT, method = 'density', bw = 10, mzwid = 1, minfrac = 1, ## sleep=5,
max = 500)
xsetFP <- fillPeaks(xsetRT)
## camera ##
xsA <- annotate(xsetFP, nSlaves = slaves, sigma = 3, perfwhm = .06, calcCaS = TRUE, mzabs = 1,
ppm = 100, sample = c(1:3), quick = TRUE, intval = 'maxo', max_peaks = 500,)