findMZ: Find fragment ions in xcmsFragment objects

In xiaodfeng/DynamicXCMS: LC-MS and GC-MS Data Analysis

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

Details

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

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

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

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)

xiaodfeng/DynamicXCMS documentation built on Aug. 6, 2023, 3:02 p.m.