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XCMS / Find peaks Orbitrap
LCMS data recoded on Orbitrap Elite with MS1 recorded in FTMS and then Top10 MS2 in the ITMS
I convert my Raw file to mzxml with msconvert
I then import into XCMS as follows
xrmsn <- xcmsRaw(filename="myfile.mzXML", includeMSn=TRUE)
xr <- msn2xcmsRaw(xrmsn)
I then try to find peaks with centwave
p <-findPeaks.centWave(xr, ppm=25, peakwidth=c(2,70), snthresh=10, prefilter=c(3,1000), mzCenterFun="wMean", integrate=1, mzdiff=-0.001, fitgauss=FALSE, scanrange= numeric(), sleep=0, verbose.columns=FALSE, ROI.list=list())
And I get the following
Detecting mass traces at 25 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
0 m/z ROI's.
No ROIs found !
If i increase the eror to 500ppm
Detecting mass traces at 500 ppm ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
2801 m/z ROI's.
Detecting chromatographic peaks ...
% finished: 0 10 20 30 40 50 60 70 80 90 100
624 Peaks.
But the raw data itself is fine and certainly not drifting around by 500ppm!
If I pull up one of the peaks it looks like ....
p[1,]
mz mzmin mzmax rt rtmin rtmax
133.0115 132.9754 133.0240 14.1267 12.7792 14.7760
into intb maxo sn
9091.3612 8931.8760 13151.5371 35.0000
which is ridiculous as my MS1 is acquired over 160-2000 - i.e. I don't even start at 133Da
So i presume it is trying to do peak finding on the MS2 data?
How do I extract features from the MS1?
ta
Chris