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XCMS / Optimize peak-picking
I´m looking for advice to optime perfomance of peak-picking for my MS data.
I am having some trouble to get all peaks of a chromatogram. I have tried to optimize the parameters to get most of them but i still loss one of the most intense peaks. In contrast, if I change the parameters to get that peak, I loss some of the less intense. I show the commands I am using above and i leave a link to get a file with the chromatograms and the peaks I am finding at the moment and the mzXML file. If it is possible i'd like to get all of the peaks.
https://github.com/maialba3/peak-picking-doubts
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library(xcms)
file <- "acq1.mzXML"
xs <- xcmsSet(file, method="centWave", ppm=10, peakwidth=c(3,25),
snthresh=2, mzCenterFun="wMean", integrate=2, fitgauss=F,
scanrange=NULL, noise=0, sleep=0, verbose.columns=F)
########################
Thank you,
Maribel