findAdducts-methods: Calculate Adducts and Annotate LC/ESI-MS Spectra

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

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, rules=NULL, max_peaks=100, psg_list=NULL, intval="maxo")

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
rules	personal ruleset or with NULL standard ruleset will be calculated
max_peaks	If run in parralel mode, this number defines how much peaks will be calculated in every thread
psg_list	Vector of pseudospectra indices. The correlation analysis will be only done for those groups
intval	choose intensity values. Allowed values are into, maxo, intb

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

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