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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

Run this code
	## 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)

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