molecular_formula_annotator

This module annotates candidate molecular formulas in the peaklists from the IDSL.IPA pipeline using isotopic profiles.

A pipeline to annotate chromatography peaks from the 'IDSL.IPA' workflow <doi:10.1021/acs.jproteome.2c00120> with molecular formulas of a prioritized chemical space using an isotopic profile matching approach. The 'IDSL.UFA' workflow only requires mass spectrometry level 1 (MS1) data for formula annotation. The 'IDSL.UFA' methods was described in <doi:10.1021/acs.analchem.2c00563> .

Dinesh Barupal

IDSL.UFA

United Formula Annotation (UFA) for HRMS Data Processing

Sadjad Fakouri-Baygi

molecular_formula_annotator function

<dl> <dt>IPDB</dt>
<dd>An isotopic profile database produced by the IDSL.UFA functions.</dd> <dt>spectraList</dt>
<dd>a list of mass spectra in each chromatogram scan.</dd> <dt>peaklist</dt>
<dd>Peaklist from the IDSL.IPA pipeline</dd> <dt>selectedIPApeaks</dt>
<dd>selected IPA peaklist</dd> <dt>massAccuracy</dt>
<dd>Mass accuracy in Da</dd> <dt>maxNEME</dt>
<dd>Maximum value for Normalized Euclidean Mass Error (NEME) in mDa</dd> <dt>minPCS</dt>
<dd>Minimum value for Profile Cosine Similarity (PCS)</dd> <dt>minNDCS</dt>
<dd>Minimum value for Number of Detected Chromatogram Scans (NDCS)</dd> <dt>minRCS</dt>
<dd>Minimum value for Ratio of Chromatogram Scans (RCS) in percentage</dd> <dt>scoreCoefficients</dt>
<dd>A vector of five numbers representing coefficients of the identification score</dd> <dt>RTtolerance</dt>
<dd>Retention time tolerance (min)</dd> <dt>correctedRTpeaklist</dt>
<dd>corrected retention time peaklist</dd> <dt>exportSpectraParameters</dt>
<dd>Parameters for export MS/MS match figures</dd> <dt>number_processing_threads</dt>
<dd>Number of processing threads for multi-threaded processing</dd></dl>

Arguments

Molecular Formula Annotator — molecular_formula_annotator

<dl>

 <dt>IPDB</dt>
<dd>An isotopic profile database produced by the IDSL.UFA functions.</dd>

 <dt>spectraList</dt>
<dd>a list of mass spectra in each chromatogram scan.</dd>

 <dt>peaklist</dt>
<dd>Peaklist from the IDSL.IPA pipeline</dd>

 <dt>selectedIPApeaks</dt>
<dd>selected IPA peaklist</dd>

 <dt>massAccuracy</dt>
<dd>Mass accuracy in Da</dd>

 <dt>maxNEME</dt>
<dd>Maximum value for Normalized Euclidean Mass Error (NEME) in mDa</dd>

 <dt>minPCS</dt>
<dd>Minimum value for Profile Cosine Similarity (PCS)</dd>

 <dt>minNDCS</dt>
<dd>Minimum value for Number of Detected Chromatogram Scans (NDCS)</dd>

 <dt>minRCS</dt>
<dd>Minimum value for Ratio of Chromatogram Scans (RCS) in percentage</dd>

 <dt>scoreCoefficients</dt>
<dd>A vector of five numbers representing coefficients of the identification score</dd>

 <dt>RTtolerance</dt>
<dd>Retention time tolerance (min)</dd>

 <dt>correctedRTpeaklist</dt>
<dd>corrected retention time peaklist</dd>

 <dt>exportSpectraParameters</dt>
<dd>Parameters for export MS/MS match figures</dd>

 <dt>number_processing_threads</dt>
<dd>Number of processing threads for multi-threaded processing</dd>

</dl>

molecular_formula_annotator: Molecular Formula Annotator

Description

Usage

Value

Arguments