FSA_msp_annotator

This function arranges the parameters for the annotation process

The 'IDSL.FSA' package was designed to annotate standard .msp (mass spectra format) and .mgf (Mascot generic format) files using mass spectral entropy similarity, dot product (cosine) similarity, and normalized Euclidean mass error (NEME) followed by intelligent pre-filtering steps for rapid spectra searches. 'IDSL.FSA' also provides a number of modules to convert and manipulate .msp and .mgf files. The 'IDSL.FSA' workflow was integrated in the 'IDSL.CSA' and 'IDSL.NPA' packages introduced in <doi:10.1021/acs.analchem.3c00376>.

Dinesh Barupal

IDSL.FSA

Fragmentation Spectra Analysis (FSA)

Sadjad Fakouri-Baygi

FSA_msp_annotator function

<dl> <dt>PARAM_SPEC</dt>
<dd>a parameter driven from the `FSA_SpectraSimilarity_xlsxAnalyzer` module.</dd> <dt>libFSdb</dt>
<dd>a converted .msp library reference files (FSDB) using the `msp2FSdb` module</dd> <dt>address_input_msp</dt>
<dd>address of the .msp files</dd> <dt>output_path</dt>
<dd>output path</dd> <dt>allowedVerbose</dt>
<dd>c(TRUE, FALSE). A `TRUE` allowedVerbose provides messages about the flow of the function.</dd></dl>

Arguments

FSA msp annotator — FSA_msp_annotator

<dl>

 <dt>PARAM_SPEC</dt>
<dd>a parameter driven from the `FSA_SpectraSimilarity_xlsxAnalyzer` module.</dd>

 <dt>libFSdb</dt>
<dd>a converted .msp library reference files (FSDB) using the `msp2FSdb` module</dd>

 <dt>address_input_msp</dt>
<dd>address of the .msp files</dd>

 <dt>output_path</dt>
<dd>output path</dd>

 <dt>allowedVerbose</dt>
<dd>c(TRUE, FALSE). A `TRUE` allowedVerbose provides messages about the flow of the function.</dd>

</dl>

FSA_msp_annotator: FSA msp annotator

Description

Usage

Value

Arguments