pspec2metfrag: Export the putative fragments as MetFrag query files

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

Export the putative fragments as MetFrag query files

Description

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.

Usage

  pspec2metfrag(object, pspecidx=NULL, filedir=NULL) 
  pspec2metfusion(object, pspecidx=NULL, filedir=NULL) 

Arguments

object	an xsAnnotate object
pspecidx	Index of pspectra to export, if NULL then all are exported.
filedir	Directory for placement of batch query files

Details

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.

Value

Returns a list

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 step
an          <- findAdducts(an, polarity="positive")

pspec2metfrag(an, pspecidx=c(1))

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