xcms (version 1.48.0)

findneutral: Find neutral losses in xcmsFragment objects

Description

This is a method to find a neutral loss with a ppm window in a xcmsFragment object

Usage

findneutral(object, find, ppmE=25, print=TRUE)

Arguments

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

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

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.

References

H. Paul Benton, D.M. Wong, S.A.Strauger, G. Siuzdak "XC$MS^2$" Analytical Chemistry 2008

See Also

findMZ,

Examples

	## 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)