DDA_fragmentationPeakDetection

This function detects fragmentation peaks for the Data-Dependent Acquisition (DDA) analysis.

A fragmentation spectra detection pipeline for high-throughput LC/HRMS data processing using peaklists generated by the 'IDSL.IPA' workflow <doi:10.1021/acs.jproteome.2c00120>. The 'IDSL.CSA' package can deconvolute fragmentation spectra from Composite Spectra Analysis (CSA), Data Dependent Acquisition (DDA) analysis, and various Data-Independent Acquisition (DIA) methods such as MS^E, All-Ion Fragmentation (AIF) and SWATH-MS analysis. The 'IDSL.CSA' package was introduced in <doi:10.1021/acs.analchem.3c00376>.

Dinesh Barupal

IDSL.CSA

Composite Spectra Analysis (CSA) for High-Resolution Mass
Spectrometry Analyses

Sadjad Fakouri-Baygi

DDA_fragmentationPeakDetection function

<dl> <dt>DDA_hrms_address</dt>
<dd>path to the HRMS file</dd> <dt>DDA_hrms_file</dt>
<dd>DDA HRMS file</dd> <dt>peaklist</dt>
<dd>IDSL.IPA peaklist</dd> <dt>selectedIPApeaks</dt>
<dd>A vector of selected IDSL.IPA peaks only when a number of IDSL.IPA peaks from one peaklist is processed.</dd> <dt>massErrorPrecursor</dt>
<dd>Mass accuracy (Da) to find precursor m/z in IDSL.IPA peaklists</dd> <dt>DDAprocessingMode</dt>
<dd>c('MostIntenseDDAspectra', c('DDAspectraIntegration', massErrorIntegration), c('IonFiltering', massErrorIonFiltering, minPercentageDetectedScans, rsdCutoff, pearsonRHOthreshold)). Required variables for each DDA processing mode should be provided in this vector.</dd> <dt>outputDDAspectra</dt>
<dd>When `NULL` DDA spectra are not plotted. `outputDDAspectra` represents an address to save DDA spectra figures.</dd> <dt>number_processing_threads</dt>
<dd>Number of processing threads for multi-threaded processing</dd></dl>

Arguments

DDA Fragmentation Peaks Detection — DDA_fragmentationPeakDetection

<dl>

 <dt>DDA_hrms_address</dt>
<dd>path to the HRMS file</dd>

 <dt>DDA_hrms_file</dt>
<dd>DDA HRMS file</dd>

 <dt>peaklist</dt>
<dd>IDSL.IPA peaklist</dd>

 <dt>selectedIPApeaks</dt>
<dd>A vector of selected IDSL.IPA peaks only when a number of IDSL.IPA peaks from one peaklist is processed.</dd>

 <dt>massErrorPrecursor</dt>
<dd>Mass accuracy (Da) to find precursor m/z in IDSL.IPA peaklists</dd>

 <dt>DDAprocessingMode</dt>
<dd>c('MostIntenseDDAspectra', c('DDAspectraIntegration', massErrorIntegration), c('IonFiltering', massErrorIonFiltering, minPercentageDetectedScans, rsdCutoff, pearsonRHOthreshold)). Required variables for each DDA processing mode should be provided in this vector.</dd>

 <dt>outputDDAspectra</dt>
<dd>When `NULL` DDA spectra are not plotted. `outputDDAspectra` represents an address to save DDA spectra figures.</dd>

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

</dl>

DDA_fragmentationPeakDetection: DDA Fragmentation Peaks Detection

Description

Usage

Value

Arguments