getFullScanSpectrum

Extract a full mass spectrum for a given well

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

getFullScanSpectrum 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 of the format outputby <code>getTIC()</code> or
<code>getAllTIC()</code></dd>
<dt>sample</dt>
<dd>The particular object from the <code>samples</code> field of the
<code>rtmsWiffReader</code> object, which in this case contains binary offsets into the
.wiff.scan file</dd>
<dt>ejections</dt>
<dd>An ejection table listing the timing and boundaries of the
total ion chromatogram peaks for all shots in the run, as returned by
<code>measureEjections()</code></dd>
<dt>well</dt>
<dd>The well (a string) or well index (an integer) to be measured</dd></dl>

Arguments

Extract a full mass spectrum for a given well — getFullScanSpectrum

<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 of the format outputby <code>getTIC()</code> or
<code>getAllTIC()</code></dd>


<dt>sample</dt>
<dd>The particular object from the <code>samples</code> field of the
<code>rtmsWiffReader</code> object, which in this case contains binary offsets into the
.wiff.scan file</dd>


<dt>ejections</dt>
<dd>An ejection table listing the timing and boundaries of the
total ion chromatogram peaks for all shots in the run, as returned by
<code>measureEjections()</code></dd>


<dt>well</dt>
<dd>The well (a string) or well index (an integer) to be measured</dd>

</dl>

getFullScanSpectrum: Extract a full mass spectrum for a given well

Description

Usage

Value

Arguments