molecular_formula_library_search

This function attempts to match candidate molecular formulas against a library of molecular formulas using a set of ionization pathways.

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_library_search function

<dl> <dt>MolecularFormulaAnnotationTable</dt>
<dd>A molecular formula annotation table from the 'molecular_formula_annotator' module.</dd> <dt>MFlibrary</dt>
<dd>A library of molecular formulas generated using the 'molecular_formula_library_generator' module.</dd> <dt>IonPathways</dt>
<dd>A vector of ionization pathways. Pathways should be like [Coeff*M+ADD1-DED1+...] where "Coeff" should be an integer between 1-9 and ADD1 and DED1 may be ionization pathways. ex: 'IonPathways &lt;- c("[M]+", "[M+H]+", "[2M-Cl]-", "[3M+CO2-H2O+Na-KO2+HCl-NH4]-")'</dd> <dt>number_processing_threads</dt>
<dd>Number of processing threads for multi-threaded processing</dd></dl>

Arguments

Molecular Formula Library Search — molecular_formula_library_search

<dl>

 <dt>MolecularFormulaAnnotationTable</dt>
<dd>A molecular formula annotation table from the 'molecular_formula_annotator' module.</dd>

 <dt>MFlibrary</dt>
<dd>A library of molecular formulas generated using the 'molecular_formula_library_generator' module.</dd>

 <dt>IonPathways</dt>
<dd>A vector of ionization pathways. Pathways should be like [Coeff*M+ADD1-DED1+...] where "Coeff" should be an integer between 1-9 and ADD1 and DED1 may be ionization pathways. ex: 'IonPathways &lt;- c("[M]+", "[M+H]+", "[2M-Cl]-", "[3M+CO2-H2O+Na-KO2+HCl-NH4]-")'</dd>

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

</dl>

molecular_formula_library_search: Molecular Formula Library Search

Description

Usage

Arguments