Hi Steffen,
Thank you very much for having a look at the data I sent. The figure for the precursor distribution was very useful, thank you.
It is also interesting to hear that there may be some debugging required when using Orbitrap data. I was wondering though if you would know the reason I would get the following results:
Using the centWave method and the xcmsFragments method, a parent peak of rtmed 25 sec, rtmax 11 sec and rtmax 57 sec has been assigned to fragmentation data with retention times all greater than 1206 sec. To me it looks like MS2 precursor m/z is matching the feature m/z but the retention time is not being taken into account correctly.
See below code:
Standard xcms stuff
# xcms feature detetection and fragmentation methods
file <- "/path/2/file/example.mzML"
xs <- xcmsSet(file, method="centWave",ppm=10)
xfrag <- xcmsFragments(xs,snthresh=1)
xfragpeaks <- data.frame(xfrag@peaks)
Looking at parent peak 1
# Get all the fragmentation peaks witht the parent peak 1
sub <- xfragpeaks[xfragpeaks$MSnParentPeakID==1,]
# Plot the extracted ion chromatogram of the parent scan ion charge for the whole run
xeic <- getEIC(xs, rtrange= matrix(c(1,1800),nrow=1), mzrange= matrix(c(376.87,376.88),nrow=1))
plot(xeic)
# Draw a line where the fragmentation occurs
abline(v = sub$rt, col = "red")
# Draw a line where the rtmedian of the feature is
p1 <- data.frame(xs@peaks[1,])
abline(v = xs@peaks[1,][1], col = "blue")
Any further help would be really appreciated.
Kind regards,
Tom