findneutral {xcms} | R Documentation

## 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, hpbenton@scripps.edu

### 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)
        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)

[Package xcms version 3.16.1 Index]