CAMERA (version 1.28.0)

pspec2metfrag: 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

Value

Returns a list

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.

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

pspec2metfrag(an, pspecidx=c(1))