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Merge pull request #330 from Bioinformatic-squad-DorresteinLab/master
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Updated GNPS and Sirius Export Documentation
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@tomas-pluskal
tomas-pluskal authored Jul 19, 2017
2 parents cb26c33 + aa5bb1d commit 2014c9a
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10 changes: 5 additions & 5 deletions src/main/java/net/sf/mzmine/modules/peaklistmethods/io/gnpsexport/GNPSExportParameters.java
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Expand Up @@ -44,11 +44,11 @@ public GNPSExportParameters() {
public ExitCode showSetupDialog(Window parent, boolean valueCheckRequired) {
String message = "<html>GNPS Module Disclaimer:" +
"<br> - If you use the GNPS export module for <a href=\"http://gnps.ucsd.edu/\">GNPS web-platform</a>, cite <a href=\"https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-395\">MZmine2 paper</a> and the following article:"+
"<br> <a href=\"https://www.nature.com/nbt/journal/v34/n8/full/nbt.3597.htm\">Wang et al., Nature Biotechnology 34.8 (2016): 828-837</a>." +
"<br> - <a href=\"https://bix-lab.ucsd.edu/display/Public/Mass+spectrometry+data+pre-processing+for+GNPS\">See the documentation</a> about MZmine2 data pre-processing for <a href=\"http://gnps.ucsd.edu/\">GNPS</a> molecular " +
"<br> networking and MS/MS spectral library search. <a href=\"\">https://bix-lab.ucsd.edu/display/Public/GNPS+data+analysis+workflow+2.0</a></html>";
"<br> <a href=\"https://www.nature.com/nbt/journal/v34/n8/full/nbt.3597.html\">Wang et al., Nature Biotechnology 34.8 (2016): 828-837</a>." +
"<br> - <a href=\"https://bix-lab.ucsd.edu/display/Public/GNPS+data+analysis+workflow+2.0\">See the documentation</a> about MZmine2 data pre-processing for <a href=\"http://gnps.ucsd.edu/\">GNPS</a> molecular " +
"<br> networking and MS/MS spectral library search. <a href=\"https://bix-lab.ucsd.edu/display/Public/GNPS+data+analysis+workflow+2.0\">https://bix-lab.ucsd.edu/display/Public/GNPS+data+analysis+workflow+2.0</a></html>";
ParameterSetupDialog dialog = new ParameterSetupDialog(parent, valueCheckRequired, this, message);
dialog.setVisible(true);
return dialog.getExitCode();
dialog.setVisible(true);
return dialog.getExitCode();
}
}
73 changes: 73 additions & 0 deletions src/main/java/net/sf/mzmine/modules/peaklistmethods/io/gnpsexport/help/help.html
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<html>
<head>
<title>Export - GNPS Export</title>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
<link rel="stylesheet" type="text/css" href="/net/sf/mzmine/desktop/impl/helpsystem/HelpStyles.css">
</head>
<body>

<h1>GNPS Export</h1>

<h2>Description</h2>
<p>
The module Export for GNPS exports a list of MS/MS spectra (one per row) for
a selected peaklist or an aligned peaklist as .MGF format.
</p>

<h2>Instructions</h2>
<p>
Before using the module, perform the following:
<ol>
<li> Filter out peak without associated MS/MS spectrum.
<br>- MZmine2 Menu: Peak list methods / Filtering / Peak list row filter / Keep only
peaks with MS2 scan (GNPS)
<li> Reset the peak number ID:
<br>- MZmine2 Menu : Peak list methods /
Filtering / Peak list row filter / Reset the peak number ID
<li> Perform mass detection on MS level 2.
<br>- MZmine2 Menu: Raw data methods / Mass detection
<br>[Make sure to use a noise threshold consistent with the MS level 2]
</ol>
</p>

<h2>Documentation</h2>
<p>
Please refer to the following documentation for detailed tutorial:
<ul>
<li> If you use the GNPS export module for
<a href="http://gnps.ucsd.edu/">GNPS web-platform<a/>, cite
<a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-395">MZmine2
paper</a> and the following article: <a href="https://www.nature.com/nbt/journal/v34/n8/full/nbt.3597.html">Wang et al., Nature
Biotechnology 34.8 (2016): 828-837</a>.
<li> <a href="https://bix-lab.ucsd.edu/display/Public/GNPS+data+analysis+workflow+2.0">See the documentation</a> about
MZmine2 data pre-processing for <a href="http://gnps.ucsd.edu/">GNPS</a>
molecular networking and MS/MS spectral library search.
</ul>
</p>
<!--
<h2>Parameters</h2>
<dl>
<dt>FEATURE_ID</dt>
<dd>Row number in the peak list</dd>
<dt>PEPMASS</dt>
<dd>Mass of the peak. If each row in the peak list contains several peaks (e.g. after performing alignment), the
mass of the highest peak is chosen
</dd>
<dt>RTINSECONDS</dt>
<dd>Retention time of the peak. If each row in the peak list contains several peaks, the average retention time
is chosen</dd>
<dt>SCANS</dt>
<dd>The same as FEATURE_ID</dd>
<dt>CHARGE</dt>
<dd>The charge for the specified row</dd>
<dt>MSLEVEL</dt>
<dd>Always equals 2</dd>
</dl>
-->
</body>
</html>
78 changes: 78 additions & 0 deletions src/main/java/net/sf/mzmine/modules/peaklistmethods/io/siriusexport/help/help.html
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@@ -0,0 +1,78 @@
<html>
<head>
<title>Export - Sirius Export</title>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
<link rel="stylesheet" type="text/css" href="/net/sf/mzmine/desktop/impl/helpsystem/HelpStyles.css">
</head>
<body>

<h1>Sirius Export</h1>

<h2>Description</h2>
<p>
The module Export for Sirius exports spectral features for a selected peaklist or an aligned peaklist as .MGF format.
This .MGF file can be directly processed with Sirius (version 3.4 minimum).
Sirius uses both the deconvoluted isotopic pattern for each peak and the corresponding MS2 spectrum to rank molecular formula candidates.
Spectral features exported consist of a pair of MS1 and MS2 spectrum for each row.
Note that the MS1 spectrum can contain the deconvoluted isotopic peaks.
A masslist with mass detection performs on MS level 2 has to be generated first and selected.
</p>

<h2>Instructions</h2>
<p>
Before using the module, perform the following:
<ol>
<li> Deconvolute isotopic peaks:
<br>- MZmine2 Menu: Peak list methods / Isotopes / Isotopic peaks grouper
<li> Filter out peak without MS/MS spectrum associated.
<br>- MZmine2 Menu: Peak list methods / Filtering / Peak list row filter / Keep only peaks with MS2 scan (GNPS)
<li> Reset the peak number ID.
<br>- MZmine2 Menu: Peak list methods / Filtering / Peak list row filter / Reset the peak number ID
<li> Perform mass detection on MS level 2 and select.
<br>- MZmine2 Menu: Raw data methods / Mass detection
<br>[Make sure to use a noise threshold consistent with the MS level 2]
</ol>
</p>

<h2>Documentation</h2>
<p>
This module can be used in combination with the Export for GNPS module and imported back into GNPS molecular networks.
Please refer to the following documentation for a detailed tutorial:
<br>

<ul>
<li> Information about <a href="../../gnpsexport/help/help.html" target="_blank">GNPS export</a>
<li> If you use the SIRIUS export module, cite <a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-395">MZmine2 paper</a>
and the following articles: <a href="http://www.pnas.org/content/112/41/12580.abstract">Dührkop et al., Proc Natl Acad Sci USA 112(41):12580-12585</a> and
<a href="https://jcheminf.springeropen.com/articles/10.1186/s13321-016-0116-8">Boecker et al., Journal of Cheminformatics (2016) 8:5</a>
<li> Sirius can be downloaded at the following address: <a href="https://bio.informatik.uni-jena.de/software/sirius/">https://bio.informatik.uni-jena.de/software/sirius/</a>
<li> Sirius results can be mapped into <a href="http://gnps.ucsd.edu/">GNPS</a> molecular networks. <a href="https://bix-lab.ucsd.edu/display/Public/Mass+spectrometry+data+pre-processing+for+GNPS">See the documentation</a> here.
</ul>
</p>
<!--
<h2>Parameters</h2>
<dl>
<dt>FEATURE_ID</dt>
<dd>Row number in the peak list</dd>
<dt>PEPMASS</dt>
<dd>Mass of the peak. If each row in the peak list contains several peaks (e.g. after performing alignment), the
mass of the highest peak is chosen
</dd>
<dt>RTINSECONDS</dt>
<dd>Retention time of the peak. If each row in the peak list contains several peaks, the average retention time
is chosen</dd>
<dt>SCANS</dt>
<dd>The same as FEATURE_ID</dd>
<dt>CHARGE</dt>
<dd>The charge for the specified row</dd>
<dt>MSLEVEL</dt>
<dd>Either equals 1 (MS) or 2 (MS/MS)</dd>
</dl>
-->
</body>
</html>

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