pspec2metfrag {CAMERA} | R Documentation |
MetFrag is an in-silico metabolite identification system, which aims to putatively identify compounds from fragmentation MS data, expecially from tandem-MS, but also in-source fragments might give additional hints on top of the accurate mass of the precursor alone.
pspec2metfrag(object, pspecidx=NULL, filedir=NULL) pspec2metfusion(object, pspecidx=NULL, filedir=NULL)
object |
an xsAnnotate object |
pspecidx |
Index of pspectra to export, if NULL then all are exported. |
filedir |
Directory for placement of batch query files |
For each spectrum in pspecidx (or all in the xsAnnotate object), for each [M] mass hypothesis, remove all non-fragment peaks (isotopes, clusters, adducts) and pass them to MetFrag and MetFusion batch query files.
Returns a list
Carsten Kuhl <ckuhl@ipb-halle.de>
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 step an <- findAdducts(an, polarity="positive") pspec2metfrag(an, pspecidx=c(1))