Hi, I would use CAMERA to deconvolute EI-GC-MS chromatograms, i.e.separate co-eluting peaks. So my idea is to extract all the ion traces with xcms and group it together using CAMERA-groupFWHM(). The problem is that I obtain only a low number of preudospectra with more than six ions. This is not possible for EI ionization technique.
## xcms ##
xset <- xcmsSet(files = files, 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,)
## number of pseudospectra with more than 6 ions
data <- getPeaklist(xsC)
data$pcgroup <- as.numeric(data$pcgroup)
(a <- which(table(data$pcgroup) >= 6))
length(a)
I tried to play with the perfwhm parameter but I have't obtained significative changes.
Have you some suggestion?
Topic: Deconvolution of EI-GC-MS spectra