Find neutral losses in xcmsFragment objects
findneutral.Rd
This is a method to find a neutral loss with a ppm window in a xcmsFragment object
Arguments
- object
xcmsFragment object type
- find
The neutral loss to be found
- ppmE
the ppm error window for searching
If we should print a nice little report
Details
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.
Value
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
References
H. Paul Benton, D.M. Wong, S.A.Strauger, G. Siuzdak "XC\(MS^2\)" Analytical Chemistry 2008
Author
H. Paul Benton, hpbenton@scripps.edu
Examples
if (FALSE) {
library(msdata)
mzMLpath <- system.file("iontrap", package = "msdata")
mzMLfiles<-list.files(mzMLpath, pattern = "extracted.mzML",
recursive = TRUE, full.names = TRUE)
xs <- xcmsSet(mzMLfiles, method = "MS1")
##takes only one file from the file set
xfrag <- xcmsFragments(xs)
found<-findneutral(xfrag, 58.1455, 50)
}