findIsotopes-methods: Deconvolute/Annotate LC/ESI-MS data

In sneumann/CAMERA: Collection of annotation related methods for mass spectrometry data

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).

Author(s)

Carsten Kuhl <[e-mail]>

Examples

 library(CAMERA)
 file <- system.file('mzML/MM14.mzML', package = "CAMERA")
 xs   <- xcmsSet(file, method="centWave", ppm=30, peakwidth=c(5,10))
 an   <- xsAnnotate(xs)
 an   <- groupFWHM(an)
 an   <- findIsotopes(an)

sneumann/CAMERA documentation built on April 5, 2024, 2:33 a.m.