findneutral: Find neutral losses in xcmsFragment objects

In sneumann/xcms: LC-MS and GC-MS Data Analysis

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

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

Author(s)

H. Paul Benton, [e-mail]

References

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

See Also

findMZ,

Examples

## Not run: 
    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)

## End(Not run)

sneumann/xcms documentation built on Nov. 23, 2024, 6:53 p.m.