getMRMChromatograms

Extract full chromatograms for each mass transition

Read raw and processed data from acoustic ejection mass
spectrometry (AEMS) files produced by the Sciex EchoMS instrument. Includes
functions to create interactive reader objects, extract raw intensity
measurements, mass spectra, and fully-processed mass-transition intensity
areas. Methods for data processing and analysis are described in Rimmer et
al. (2025) <doi:10.1021/acs.analchem.5c03730>. Supports both multiple
reaction monitoring (MRM) and full-scan (neutral loss and precursor ion)
data formats.

Nathaniel Twarog

rtmsEcho

Extract and Analyze EchoMS Data from Sciex Wiff Files

Mary Ashley Rimmer

Lei Yang

getMRMChromatograms function

<dl><dt>scanfile</dt>
<dd>A file path to a Sciex raw scan file (extension .wiff.scan)
containing the raw data referenced by the .wiff file from which the other
parameters were extracted</dd>
<dt>tic</dt>
<dd>A total ion chromatogram data.frame as extracted by <code>getTIC()</code> or
<code>getAllTIC()</code></dd>
<dt>sample</dt>
<dd>A "sample" object representing a run in a .wiff file, from the
<code>samples</code> field of an <code>rtmsWiffReader</code> object, containing information about
the mass transitions measured in that run</dd></dl>

Arguments

Extract full chromatograms for each mass transition — getMRMChromatograms

<dl>

<dt>scanfile</dt>
<dd>A file path to a Sciex raw scan file (extension .wiff.scan)
containing the raw data referenced by the .wiff file from which the other
parameters were extracted</dd>


<dt>tic</dt>
<dd>A total ion chromatogram data.frame as extracted by <code>getTIC()</code> or
<code>getAllTIC()</code></dd>


<dt>sample</dt>
<dd>A "sample" object representing a run in a .wiff file, from the
<code>samples</code> field of an <code>rtmsWiffReader</code> object, containing information about
the mass transitions measured in that run</dd>

</dl>

getMRMChromatograms: Extract full chromatograms for each mass transition

Description

Usage

Value

Arguments