CAMERA (version 1.28.0)

findAdducts-methods: 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)

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

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.

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