CAMERA (version 1.28.0)

findIsotopes: Deconvolute/Annotate LC/ESI-MS data

Description

Annotate isotope peaks for a xsAnnotate object. Returns a xsAnnotate object with annotated isotopes.

Usage

findIsotopes(object, maxcharge=3, maxiso=4, ppm=5, mzabs=0.01, intval=c("maxo","into","intb"), minfrac=0.5, isotopeMatrix = NULL,filter = TRUE)

Arguments

object

the xsAnnotate object

maxcharge

max. number of the isotope charge

maxiso

max. number of the isotope peaks

ppm

ppm error for the search

mzabs

allowed variance for the search

intval

choose intensity values for C12/C13 check. Allowed values are into, maxo, intb

minfrac

in case of multiple samples, percentaged value of samples, which have to contain the correct C12/C13 ratio and are not NA

isotopeMatrix

four column m/z-diff and ratio Matrix, for matching isotopic peaks.

filter

Should C12/C13 filter be applied

Details

Isotope peaks are annotated for a xsAnnotate object according to given rules (maxcharge, maxiso). The algorithm benefits from a earlier grouping of the data, with groupFWHM. Generates a list of all possible isotopes, which is stored in object@isotopes. Those isotope information will be used in the groupCorr funtion. The itensity of the C13 isotope peak is checked against the C12 of proper ratio. In the case of mulitiple sample, all samples will be tested. Minfrac describe the minimal percentaged of samples, which must passed the test. If peaks are NA, then this sample is skipped and the ratio is (found correct C12/C13 ratio) / (samples containing C12 and C13 peak).

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   <- findIsotopes(an)