DDA_rawSpectraDeconvolution

This function stacks all DDA scans.

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_rawSpectraDeconvolution 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>rawDDAspectraVar</dt>
<dd>c(NULL, list(precursorMZvec, precursorRTvec, massError, RTtolerance)). When NULL, all scans with precursor values are used for DDA peaklist generation. When the list is provided, it filters the scans with respect to predefined `precursorMZvec` and `precursorRTvec` values.</dd> <dt>number_processing_threads</dt>
<dd>Number of processing threads for multi-threaded processing</dd></dl>

Arguments

DDA Raw Spectra Deconvolution — DDA_rawSpectraDeconvolution

<dl>

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

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

 <dt>rawDDAspectraVar</dt>
<dd>c(NULL, list(precursorMZvec, precursorRTvec, massError, RTtolerance)). When NULL, all scans with precursor values are used for DDA peaklist generation. When the list is provided, it filters the scans with respect to predefined `precursorMZvec` and `precursorRTvec` values.</dd>

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

</dl>

DDA_rawSpectraDeconvolution: DDA Raw Spectra Deconvolution

Description

Usage

Value

Arguments