findneutral {xcms} | R Documentation |
This is a method to find a neutral loss with a ppm window in a xcmsFragment object
findneutral(object, find, ppmE=25, print=TRUE)
object |
xcmsFragment object type |
find |
The neutral loss to be found |
ppmE |
the ppm error window for searching |
print |
If we should print a nice little report |
The method searches for a given neutral loss in an xcmsFragment object type given a certain ppm error window. The neutral losses are generated between neighbouring ions. The resulting data frame shows the whole scan in which the neutral loss was found.
A data frame with the following columns:
PrecursorMz |
The precursor m/z of the neutral losses |
MSnParentPeakID |
An index ID of the location of the precursor peak in the xcmsFragment object |
msLevel |
The level of the found fragment ion |
rt |
the Retention time of the found ion |
mz |
the actual m/z of the found fragment ion |
intensity |
The intensity of the fragment ion |
sample |
Which sample the fragment ion came from |
GroupPeakMSn |
an ID if the peaks were grouped by an xcmsSet grouping |
CollisionEnergy |
The collision energy of the precursor scan |
H. Paul Benton, hpbenton@scripps.edu
H. Paul Benton, D.M. Wong, S.A.Strauger, G. Siuzdak "XCMS^2" Analytical Chemistry 2008
## Not run: library(msdata) mzdatapath <- system.file("iontrap", package = "msdata") mzdatafiles<-list.files(mzdatapath, pattern = "extracted.mzData", recursive = TRUE, full.names = TRUE) xs <- xcmsSet(mzdatafiles, method = "MS1") ##takes only one file from the file set xfrag <- xcmsFragments(xs) found<-findneutral(xfrag, 58.1455, 50) ## End(Not run)