processAllFullScanAreas

A convenient wrapper function to extract all full scan areas from a file
without storing the intermediate reader and ejection data structures.

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

processAllFullScanAreas function

<dl><dt>wiffFile</dt>
<dd>A valid file path to the Sciex data file (extension .wiff)
containing the metadata for one or more EchoMS runs</dd>
<dt>wiffScanFile</dt>
<dd>An file path the the Sciex scan file (extension
.wiff.scan) containing the full raw EchoMS data</dd>
<dt>peaks</dt>
<dd>A named list of peak objects of class <code>rtmsPeak</code>, often
generated by <code>rtmsPeakList()</code></dd>
<dt>...</dt>
<dd>Additional arguments passed to <code>measureEjections()</code></dd></dl>

Arguments

Fully process a Full Scan Wiff and scan File — processAllFullScanAreas

<dl>

<dt>wiffFile</dt>
<dd>A valid file path to the Sciex data file (extension .wiff)
containing the metadata for one or more EchoMS runs</dd>


<dt>wiffScanFile</dt>
<dd>An file path the the Sciex scan file (extension
.wiff.scan) containing the full raw EchoMS data</dd>


<dt>peaks</dt>
<dd>A named list of peak objects of class <code>rtmsPeak</code>, often
generated by <code>rtmsPeakList()</code></dd>


<dt>...</dt>
<dd>Additional arguments passed to <code>measureEjections()</code></dd>

</dl>

processAllFullScanAreas: Fully process a Full Scan Wiff and scan File

Description

Usage

Value

Arguments