pspec2metfrag {CAMERA} | R Documentation

## 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 <ckuhl@ipb-halle.de>

### 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))

[Package CAMERA version 1.42.0 Index]