Add a workflow example to the help file
</p>
<p>
- For details, see Jiang, W.; Qiu, Y.; Ni, Y.; Su, M.; Jia, W.; Du, X.: <b>An automated data analysis pipeline for GC-TOF-MS
+ For details, see Jiang, W.; Qiu, Y.; Ni, Y.; Su, M.; Jia, W.; Du, X.: <b>An automated data analysis pipeline for
+ GC-TOF-MS
metabonomics studies.</b> <i>Journal of proteome research</i> 2010, 9 (11), 5974-81
</p>
<h2>Requirements</h2>
<p>
- <strong>ADAP Aligner</strong> requires mass spectra to
- be constructed prior to the alignment (e.g. using Spectral Deconvolution or CAMERA).
+ <strong>ADAP Aligner</strong> requires mass spectra to be constructed prior to the alignment (e.g. using Spectral
+ Deconvolution or CAMERA). A typical workflow where this alignment is used can be as following:
</p>
+<ol>
+ <li><b>Raw data methods / Raw data import</b> imports raw data files</li>
+ <li><b>Raw datamethods / Peak detection / Mass detection</b> detects masses in the raw data</li>
+ <li><b>Raw datamethods / Peak detection / ADAP Chromatogram builder</b> builds extracted-ion chromatograms</li>
+ <li><b>Peak list methods / Peak deteciton / Chromatogram deconvoltion</b> detects peaks (features) in each
+ chromatogram
+ </li>
+ <li><b>Peak list methods / Spectral deconvolution / Multivariate Curve Resolution</b> combines the detected
+ peaks (features) into analytes and builds pure fragmentation mass spectra for each analyte
+ </li>
+ <li><b>Peak list methods / Alignment / ADAP Aligner (GC)</b> aligns the analytes produced by the previous step</li>
+ <li><b>Peak list methods / Export/Import / Export to MSP file</b> exports fragmentation mass spectra into
+ MSP format
+ </li>
+</ol>
<h2>Description</h2>
Similarity between two features f<sub>1</sub> and f<sub>2</sub> is calculated by the following score:
</p>
<div align="center" style="margin: 10pt">
- S(f<sub>1</sub>, f<sub>2</sub>) = w S<sub>time</sub>(f<sub>1</sub>, f<sub>2</sub>) + (1 - w) S<sub>spec</sub>(f<sub>1</sub>, f<sub>2</sub>)
+ S(f<sub>1</sub>, f<sub>2</sub>) = w S<sub>time</sub>(f<sub>1</sub>, f<sub>2</sub>) + (1 - w) S<sub>spec</sub>(f<sub>1</sub>,
+ f<sub>2</sub>)
</div>
<p>
where S<sub>time</sub>(f<sub>1</sub>, f<sub>2</sub>) is the relative retention time difference between two features
</li>
<li><b>Retention time range</b> (minutes) is the maximum allowed retention time difference between aligned features
- from different samples.</li>
+ from different samples.
+ </li>
<li><b>M/z tolerance</b> is the maximum m/z difference, when two peaks from different mass spectra are considered
- equal.</li>
+ equal.
+ </li>
<li><b>Score threshold</b> (number between 0 and 1) is the minimum value of the similarity function
S(f<sub>1</sub>, f<sub>2</sub>) required for features to be aligned together. The default value is 0.75.
