findAdducts-methods {CAMERA}R Documentation

Calculate Adducts and Annotate LC/ESI-MS Spectra

Description

Annotate adducts (and fragments) for a xsAnnotate object. Returns a xsAnnotate object with annotated pseudospectra.

Usage

 findAdducts(object,ppm=5,mzabs=0.015,multiplier=3,polarity=NULL)

Arguments

object the xsAnnotate object
ppm ppm error for the search
mzabs allowed variance for the search
multiplier highest number(n) of allowed clusterion [nM+ion]
polarity Which polarity mode was used for measuring of the ms sample

Details

Adducts (and fragments) are annotated for a xsAnnotate object. For every pseudospectra group, generated bei groupFWHM and groupCorr, all possible Adducts are calculated and mapped to the peaks. If at least two adducts match, a possible molecule-mass for the group can be calculated. After the annotation every masshypothese is checked against the charge of the calculated isotopes. It is recommend to call findIsotopes() before the annotation step.

Author(s)

Carsten Kuhl <ckuhl@ipb-halle.de>

Examples

 library(CAMERA)
 file <- system.file('mzdata/MM14.mzdata', package = "CAMERA")
 xs   <- xcmsSet(file, method="centWave", ppm=30, peakwidth=c(5,10))
 an   <- xsAnnotate(xs)
 an   <- groupFWHM(an)
# an <- groupCorr(an,xs) # optional but very recommended step

 an <- findIsotopes(an)  # optional but recommended.
 an <- findAdducts(an,polarity="positive")
 peaklist <- getPeaklist(an) # get the annotated peak list

[Package CAMERA version 1.0.0 Index]