findneutral: Find neutral losses in xcmsFragment objects
In xcms: LC-MS and GC-MS Data Analysis

Description Usage Arguments Details Value Author(s) References See Also Examples

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

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

`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

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.

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

H. Paul Benton, hpbenton@scripps.edu

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

findMZ,

## 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)