xcms (version 1.48.0)

findMZ: Find fragment ions in xcmsFragment objects

Description

This is a method to find a fragment mass with a ppm window in a xcmsFragment object

Usage

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

Arguments

object

xcmsFragment object type

find

The fragment ion 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 fragment

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 simply searches for a given fragment ion in an xcmsFragment object type given a certain ppm error window

References

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

See Also

findneutral,

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<-findMZ(xfrag, 657.3433, 50)
# 	## End(Not run)