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Messages - maialba

1
XCMS / Re: Optimize peak-picking
Hi,
I still miss T338, T345, T370, T470, T500, T510, T580 and T620. Do you find them?

I've also tried to change the minimum peakwidth but I still miss some peaks... when I find peaks with overlapping I miss the less intense peaks.
2
XCMS / Optimize peak-picking
Hi,

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

########################
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