spectra_ion_filter

This function can detect m/z peaks that are related to each other across selected spectra lists.

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

spectra_ion_filter function

<dl> <dt>spectraList</dt>
<dd>a list of matrices of m/z and intensity values for each chromatogram scan</dd> <dt>indexSpectraList</dt>
<dd>a vector of spectra indices for the analysis. This vector should have at least 3 elements to run this function.</dd> <dt>massError</dt>
<dd>required mass error for m/z values</dd> <dt>rsdCutoff</dt>
<dd>Relative standard deviations (in percent) to remove constant peaks (usually noisy peaks)</dd> <dt>minPercentageDetectedScans</dt>
<dd>Minimum percentage of detected scans for an m/z peak</dd> <dt>pearsonRHOthreshold</dt>
<dd>A threshold for pairwise Pearson's correlation coefficient across the selected spectra lists. This feature is recommended to find co-occurring peaks within a chromatographic peak. This feature may be used to eliminate instrument noises from MS2 data channels within an MS1 chromatographic peak for DDA analysis.</dd></dl>

Arguments

Spectra Ion Filter — spectra_ion_filter

<dl>

 <dt>spectraList</dt>
<dd>a list of matrices of m/z and intensity values for each chromatogram scan</dd>

 <dt>indexSpectraList</dt>
<dd>a vector of spectra indices for the analysis. This vector should have at least 3 elements to run this function.</dd>

 <dt>massError</dt>
<dd>required mass error for m/z values</dd>

 <dt>rsdCutoff</dt>
<dd>Relative standard deviations (in percent) to remove constant peaks (usually noisy peaks)</dd>

 <dt>minPercentageDetectedScans</dt>
<dd>Minimum percentage of detected scans for an m/z peak</dd>

 <dt>pearsonRHOthreshold</dt>
<dd>A threshold for pairwise Pearson's correlation coefficient across the selected spectra lists. This feature is recommended to find co-occurring peaks within a chromatographic peak. This feature may be used to eliminate instrument noises from MS2 data channels within an MS1 chromatographic peak for DDA analysis.</dd>

</dl>

spectra_ion_filter: Spectra Ion Filter

Description

Usage

Value

Arguments