export2MSP

Export spectra to MSP format for comparison with the NIST library.

Automated compound deconvolution, alignment across samples, and identification of metabolites by spectral library matching in Gas Chromatography - Mass spectrometry (GC-MS) untargeted metabolomics. Outputs a table with compound names, matching scores and the integrated area of the compound for each sample. Package implementation is described in Domingo-Almenara et al. (2016) <doi:10.1021/acs.analchem.6b02927>.

Xavier Domingo-Almenara

erah

Automated Spectral Deconvolution, Alignment, and Metabolite
Identification in GC/MS-Based Untargeted Metabolomics

export2MSP function

<dl><dt>Experiment</dt>
<dd>A 'MetaboSet' S4 object containing the experiment.</dd>
<dt>export.id</dt>
<dd>If NULL, all the spectra in the experiment will be exported. Otherwise, only the AlignID in export.id will be exported</dd>
<dt>id.database</dt>
<dd>The mass-spectra library used in the experiment.</dd>
<dt>store.path</dt>
<dd>The path where the converted files are to be exported.</dd>
<dt>alg.version</dt>
<dd>Different algorithm implementations. Users have to chose what version works with their NIST MSearch or other software version. By default, alg.version is set to 1. If it not works, try setting alg.version to 2 ;).</dd></dl>

Arguments

Export spectra to MSP — export2MSP

<dl>

<dt>Experiment</dt>
<dd>A 'MetaboSet' S4 object containing the experiment.</dd>


<dt>export.id</dt>
<dd>If NULL, all the spectra in the experiment will be exported. Otherwise, only the AlignID in export.id will be exported</dd>


<dt>id.database</dt>
<dd>The mass-spectra library used in the experiment.</dd>


<dt>store.path</dt>
<dd>The path where the converted files are to be exported.</dd>


<dt>alg.version</dt>
<dd>Different algorithm implementations. Users have to chose what version works with their NIST MSearch or other software version. By default, alg.version is set to 1. If it not works, try setting alg.version to 2 ;).</dd>

</dl>

export2MSP: Export spectra to MSP

Description

Usage

Arguments