findNeutralLoss: Find pseudospectra that contains a specific neutral loss

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

Find pseudospectra that contains a specific neutral loss

Description

The method searches in every pseudospectra for a distance between two ions matching a provided mass difference. It returns a xcmsSet object containing the matching peaks.

Usage

  findNeutralLoss(object, mzdiff=NULL, mzabs=0, mzppm=10)

Arguments

object	xsAnnotate object
mzdiff	neutral loss in Dalton
mzabs	absolut allowed mass difference
mzppm	relative allowed mass difference

Details

The function needs a xsAnnotate object after groupCorr or groupFWHM. The resulting object is a artificial xcmsSet, where the peaks with the specific neutral loss are stored in xcmsSet@peaks.

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)
  #Searches for Peaks with water loss
  xs.pseudo <- findNeutralLoss(an,mzdiff=18.01,mzabs=0.01) 
  xs.pseudo@peaks #show Hits

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