FSA_spectra_marker_generator

This function generates spectra markers

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_spectra_marker_generator function

<dl> <dt>FSdb</dt>
<dd>FSdb object from the 'msp2FSdb' module</dd> <dt>ratio2basePeak4nSpectraMarkers</dt>
<dd>Ratio of peaks in fragmentation spectra to the basepeak to calculate minimum qualified number of matched abundant peaks</dd> <dt>aggregationLevel</dt>
<dd>c(NA, 0, 1, 2, 3). When `NA`, this function returns a matrix for the spectra markers. When integer numbers are used, the ion marker masses are grouped by a rounding digit equal to this number.</dd></dl>

Arguments

FSA Spectra Marker Generator — FSA_spectra_marker_generator

<dl>

 <dt>FSdb</dt>
<dd>FSdb object from the 'msp2FSdb' module</dd>

 <dt>ratio2basePeak4nSpectraMarkers</dt>
<dd>Ratio of peaks in fragmentation spectra to the basepeak to calculate minimum qualified number of matched abundant peaks</dd>

 <dt>aggregationLevel</dt>
<dd>c(NA, 0, 1, 2, 3). When `NA`, this function returns a matrix for the spectra markers. When integer numbers are used, the ion marker masses are grouped by a rounding digit equal to this number.</dd>

</dl>

FSA_spectra_marker_generator: FSA Spectra Marker Generator

Description

Usage

Value

Arguments