IDSL.CSA_referenceMSPgenerator

This function creates reference standard .msp files.

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

IDSL.CSA_referenceMSPgenerator function

<dl> <dt>REF_peaklist</dt>
<dd>A dataframe peaklist of co-detected peaks</dd> <dt>refTable</dt>
<dd>reference CSA table</dd> <dt>selectedIPApeaks_IDref</dt>
<dd>selectedIPApeaks_IDref</dd> <dt>msLevel</dt>
<dd>MS level = c(1, 2)</dd> <dt>spectral_search_mode</dt>
<dd>Type of analysis. spectral_search_mode = c("dda", "dia", "csa")</dd> <dt>spectral_search_mode_option</dt>
<dd>Secondary type of analysis. spectral_search_mode_option = c(NA, "rawddaspectra", "alignedtable")</dd></dl>

Arguments

IDSL.CSA Reference MSP Generator — IDSL.CSA_referenceMSPgenerator

<dl>

 <dt>REF_peaklist</dt>
<dd>A dataframe peaklist of co-detected peaks</dd>

 <dt>refTable</dt>
<dd>reference CSA table</dd>

 <dt>selectedIPApeaks_IDref</dt>
<dd>selectedIPApeaks_IDref</dd>

 <dt>msLevel</dt>
<dd>MS level = c(1, 2)</dd>

 <dt>spectral_search_mode</dt>
<dd>Type of analysis. spectral_search_mode = c("dda", "dia", "csa")</dd>

 <dt>spectral_search_mode_option</dt>
<dd>Secondary type of analysis. spectral_search_mode_option = c(NA, "rawddaspectra", "alignedtable")</dd>

</dl>

IDSL.CSA_referenceMSPgenerator: IDSL.CSA Reference MSP Generator

Description

Usage

Value

Arguments