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index-proteomics.html
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<!DOCTYPE html>
<html lang="en">
<head>
<title>Galaxy Europe</title>
<meta property="og:title" content="" />
<meta property="og:description" content="" />
<meta property="og:image" content="/assets/media/galaxy-eu-logo.512.png" />
<meta name="description" content="The European Galaxy Instance">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<link rel="stylesheet" href="/assets/css/bootstrap.min.css">
<link rel="stylesheet" href="/assets/css/main.css">
<link rel="canonical" href="https://galaxyproject.eu/index-proteomics.html">
<link rel="shortcut icon" href="/assets/media/galaxy-eu-logo.64.png" type="image/x-icon" />
<link rel="alternate" type="application/rss+xml" title="Galaxy Europe" href="/feed.xml">
<link href="/assets/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-wvfXpqpZZVQGK6TAh5PVlGOfQNHSoD2xbE+QkPxCAFlNEevoEH3Sl0sibVcOQVnN" crossorigin="anonymous">
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</head>
<body>
<div id="wrap">
<div id="main">
<div class="container" id="maincontainer">
<div class="home">
<p><br /></p>
<h1 class="no_toc" id="welcome-to-galaxy-proteomics">Welcome to <strong>Galaxy Proteomics</strong></h1>
<table class="table">
<thead>
<tr>
<th> </th>
<th> </th>
</tr>
</thead>
<tbody>
<tr>
<td><a href="http://galaxyp.org" target="_blank"><img src="/assets/media/galaxyp_banner.png" width="350px" alt="GalaxyP logo" /></a><br /><br /><em>This European Galaxy branches off from the main<br /><a href="https://usegalaxy.eu" target="_blank">usegalaxy.eu</a> server and focuses on one specific<br />domain: Proteomics.</em><br /><br /><strong>Galaxy Proteomics</strong> is a multiple-‘omics’ data-analysis<br />platform with particular emphasis on mass<br />spectrometry-based proteomics. It is hosted by<br />GalaxyEU and maintained by the <a href="http://galaxyp.org/people/" target="_blank">GalaxyP team</a> from<br />the University of Minnesota, USA.<br /><br /><strong>GalaxyP Resources:</strong><br /><a href="http://galaxyp.org/about/" target="_blank">About Us</a><br /><a href="http://galaxyp.org/publications/" target="_blank">Publications</a><br /><a href="http://galaxyp.org/conference-presentations/" target="_blank">Conference presentations</a><br /><a href="http://galaxyp.org/workshops/" target="_blank">Workshops</a></td>
<td><a class="twitter-timeline" data-width="350px" data-height="420px" href="https://twitter.com/usegalaxyp?ref_src=twsrc%5Etfw">Tweets by usegalaxyp</a> <script async="" src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>*</td>
</tr>
</tbody>
</table>
<hr />
<h1 class="no_toc" id="content">Content</h1>
<ol id="markdown-toc">
<li><a href="#tutorials" id="markdown-toc-tutorials">Tutorials</a></li>
<li><a href="#gateways" id="markdown-toc-gateways">Gateways</a></li>
<li><a href="#research-projects" id="markdown-toc-research-projects">Research Projects</a></li>
<li><a href="#news-and-events" id="markdown-toc-news-and-events">News and Events</a></li>
<li><a href="#contributors" id="markdown-toc-contributors">Contributors</a></li>
</ol>
<hr />
<h1 id="tutorials">Tutorials</h1>
<p>Are you new to Galaxy, or returning after a long time, and looking for help to get started? Take <a href="https://proteomics.usegalaxy.eu/tours/core.galaxy_ui" target="_blank">a guided tour</a> through Galaxy’s user interface.</p>
<p><strong>Want to learn more about proteomics? Check out the following lesson tutorials from the <a href="https://galaxyproject.github.io/training-material/topics/proteomics/" target="_blank">Galaxy Training Network</a>:</strong></p>
<table class="table table-striped">
<thead>
<tr>
<th>Lesson</th>
<th>Hands-on</th>
<th>Input dataset</th>
<th>Workflows</th>
<th>Galaxy tour</th>
</tr>
</thead>
<tbody>
<tr>
<td>Detection and quantitation of N-termini degradomics via N-TAILS</td>
<td><a href="https://galaxyproject.github.io/training-material/topics/proteomics/tutorials/ntails/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a></td>
<td> </td>
<td><a href="https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/ntails/workflows/" target="_blank"><i class="fa fa-share-alt" aria-hidden="true"></i></a></td>
<td><a href="https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/ntails/tours/" target="_blank"><i class="fa fa-magic" aria-hidden="true"></i></a></td>
</tr>
<tr>
<td>Label-free versus Labelled - How to Choose Your Quantitation Method</td>
<td><a href="https://galaxyproject.github.io/training-material/topics/proteomics/tutorials/labelfree-vs-labelled/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a></td>
<td> </td>
<td> </td>
<td><a href="https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/labelfree-vs-labelled/tours/" target="_blank"><i class="fa fa-magic" aria-hidden="true"></i></a></td>
</tr>
<tr>
<td>Mass spectrometry imaging 1: Loading and exploring MSI data</td>
<td><a href="https://galaxyproject.github.io/training-material/topics/proteomics/tutorials/mass-spectrometry-imaging-loading-exploring-data/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a></td>
<td><a href="https://doi.org/10.5281/zenodo.1560645" target="_blank"><i class="fa fa-files-o" aria-hidden="true"></i></a></td>
<td><a href="https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/mass-spectrometry-imaging-loading-exploring-data/workflows/" target="_blank"><i class="fa fa-share-alt" aria-hidden="true"></i></a></td>
<td> </td>
</tr>
<tr>
<td>Metaproteomics tutorial</td>
<td><a href="https://galaxyproject.github.io/training-material/topics/proteomics/tutorials/metaproteomics/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a></td>
<td><a href="https://doi.org/10.5281/zenodo.839701" target="_blank"><i class="fa fa-files-o" aria-hidden="true"></i></a></td>
<td><a href="https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/metaproteomics/workflows/" target="_blank"><i class="fa fa-share-alt" aria-hidden="true"></i></a></td>
<td> </td>
</tr>
<tr>
<td>Peptide and Protein ID using OpenMS tools</td>
<td><a href="https://galaxyproject.github.io/training-material/topics/proteomics/tutorials/protein-id-oms/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a></td>
<td><a href="https://zenodo.org/record/546301" target="_blank"><i class="fa fa-files-o" aria-hidden="true"></i></a></td>
<td><a href="https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/protein-id-oms/workflows/" target="_blank"><i class="fa fa-share-alt" aria-hidden="true"></i></a></td>
<td><a href="https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/protein-id-oms/tours/" target="_blank"><i class="fa fa-magic" aria-hidden="true"></i></a></td>
</tr>
<tr>
<td>Peptide and Protein ID using SearchGUI and PeptideShaker</td>
<td><a href="https://galaxyproject.github.io/training-material/topics/proteomics/tutorials/protein-id-sg-ps/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a></td>
<td><a href="https://zenodo.org/record/546301" target="_blank"><i class="fa fa-files-o" aria-hidden="true"></i></a></td>
<td><a href="https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/protein-id-sg-ps/workflows/" target="_blank"><i class="fa fa-share-alt" aria-hidden="true"></i></a></td>
<td><a href="https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/protein-id-sg-ps/tours/" target="_blank"><i class="fa fa-magic" aria-hidden="true"></i></a></td>
</tr>
<tr>
<td>Peptide and Protein Quantification via Stable Isotope Labelling (SIL)</td>
<td><a href="https://galaxyproject.github.io/training-material/topics/proteomics/tutorials/protein-quant-sil/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a></td>
<td><a href="https://zenodo.org/record/1051552" target="_blank"><i class="fa fa-files-o" aria-hidden="true"></i></a></td>
<td><a href="https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/protein-quant-sil/workflows/" target="_blank"><i class="fa fa-share-alt" aria-hidden="true"></i></a></td>
<td><a href="https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/protein-quant-sil/tours/" target="_blank"><i class="fa fa-magic" aria-hidden="true"></i></a></td>
</tr>
<tr>
<td>Protein FASTA Database Handling</td>
<td><a href="https://galaxyproject.github.io/training-material/topics/proteomics/tutorials/database-handling/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a></td>
<td> </td>
<td><a href="https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/database-handling/workflows/" target="_blank"><i class="fa fa-share-alt" aria-hidden="true"></i></a></td>
<td><a href="https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/database-handling/tours/" target="_blank"><i class="fa fa-magic" aria-hidden="true"></i></a></td>
</tr>
<tr>
<td>Proteogenomics 1: Database Creation</td>
<td><a href="https://galaxyproject.github.io/training-material/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a></td>
<td><a href="https://doi.org/10.5281/zenodo.1489208" target="_blank"><i class="fa fa-files-o" aria-hidden="true"></i></a></td>
<td><a href="https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/proteogenomics-dbcreation/workflows/" target="_blank"><i class="fa fa-share-alt" aria-hidden="true"></i></a></td>
<td> </td>
</tr>
<tr>
<td>Proteogenomics 2: Database Search</td>
<td><a href="https://galaxyproject.github.io/training-material/topics/proteomics/tutorials/proteogenomics-dbsearch/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a></td>
<td><a href="https://doi.org/10.5281/zenodo.1489208" target="_blank"><i class="fa fa-files-o" aria-hidden="true"></i></a></td>
<td><a href="https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/proteogenomics-dbsearch/workflows/" target="_blank"><i class="fa fa-share-alt" aria-hidden="true"></i></a></td>
<td> </td>
</tr>
<tr>
<td>Proteogenomics 3: Novel peptide analysis</td>
<td><a href="https://galaxyproject.github.io/training-material/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a></td>
<td><a href="https://doi.org/10.5281/zenodo.1489208" target="_blank"><i class="fa fa-files-o" aria-hidden="true"></i></a></td>
<td><a href="https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/workflows/" target="_blank"><i class="fa fa-share-alt" aria-hidden="true"></i></a></td>
<td> </td>
</tr>
<tr>
<td>Secretome Prediction</td>
<td><a href="https://galaxyproject.github.io/training-material/topics/proteomics/tutorials/secretome-prediction/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a></td>
<td><a href="https://zenodo.org/record/519260" target="_blank"><i class="fa fa-files-o" aria-hidden="true"></i></a></td>
<td><a href="https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/secretome-prediction/workflows/" target="_blank"><i class="fa fa-share-alt" aria-hidden="true"></i></a></td>
<td><a href="https://github.com/galaxyproject/training-material/tree/master/topics/proteomics/tutorials/secretome-prediction/tours/" target="_blank"><i class="fa fa-magic" aria-hidden="true"></i></a></td>
</tr>
</tbody>
</table>
<hr />
<h1 id="gateways">Gateways</h1>
<p>Other specialized Galaxy servers curated by the Galaxy-P team containing tools, workflows, and hands-on/video tutorials.</p>
<table class="table table-striped tooltable">
<thead>
<tr>
<th>Server</th>
<th>Tutorial(s)</th>
<th>Video</th>
</tr>
</thead>
<tbody>
<tr>
<td><a href="http://z.umn.edu/proteogenomicsgateway" target="_blank">Proteogenomics Gateway</a></td>
<td><a href="https://galaxyproject.github.io/training-material/topics/proteomics/tutorials/proteogenomics-dbcreation/tutorial.html" target="_blank">Proteogenomics 1: Database creation</a><br /><a href="https://galaxyproject.github.io/training-material/topics/proteomics/tutorials/proteogenomics-dbsearch/tutorial.html" target="_blank">Proteogenomics 2: Database search</a><br /><a href="https://galaxyproject.github.io/training-material/topics/proteomics/tutorials/proteogenomics-novel-peptide-analysis/tutorial.html" target="_blank">Proteogenomics 3: Novel peptide analysis</a></td>
<td><a href="https://www.youtube.com/watch?v=Xwks5qKApj8&t=4s" target="_blank"><img src="https://img.youtube.com/vi/Xwks5qKApj8/0.jpg" alt="proteogenomics thumbnail" /></a></td>
</tr>
<tr>
<td><a href="http://z.umn.edu/metaproteomicsgateway" target="_blank">Metaproteomics Gateway</a></td>
<td><a href="https://galaxyproject.github.io/training-material/topics/proteomics/tutorials/metaproteomics/tutorial.html" target="_blank">Metaproteomics tutorial</a></td>
<td><a href="https://www.youtube.com/watch?v=Vywt_-D5Kek&t=1s" target="_blank"><img src="https://img.youtube.com/vi/Vywt_-D5Kek/0.jpg" alt="metaproteomics thumbnail" /></a></td>
</tr>
</tbody>
</table>
<hr />
<h1 id="research-projects">Research Projects</h1>
<p>Featured Galaxy-P tools supported with manuscripts, visualization plugins, docker containers, and hands-on tutorials.</p>
<table class="table table-striped tooltable">
<thead>
<tr>
<th>Tool</th>
<th>Description</th>
<th>Paper</th>
<th>Tutorial</th>
<th>Docker</th>
</tr>
</thead>
<tbody>
<tr>
<td>CRAVAT-P</td>
<td>Stands for Cancer Related Analysis of Variants Toolkit for Proteogenomics. Submits, checks for, and retrieves data for cancer annotation</td>
<td><a href="https://pubs.acs.org/doi/10.1021/acs.jproteome.8b00404" target="_blank">Sajulga et. al 2018</a></td>
<td><a href="https://pubs.acs.org/doi/suppl/10.1021/acs.jproteome.8b00404/suppl_file/pr8b00404_si_001.pdf" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a></td>
<td><a href="http://z.umn.edu/gpcravatdocker" target="_blank"><img src="https://cdn3.iconfinder.com/data/icons/social-media-2169/24/social_media_social_media_logo_docker-128.png" alt="docker-icon" /></a></td>
</tr>
<tr>
<td>QuanTP</td>
<td>Correlation between protein and transcript</td>
<td><a href="https://pubs.acs.org/doi/10.1021/acs.jproteome.8b00727" target="_blank">Kumar et. al 2019</a></td>
<td><a href="https://pubs.acs.org/doi/suppl/10.1021/acs.jproteome.8b00404/suppl_file/pr8b00404_si_001.pdf" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a></td>
<td><a href="http://z.umn.edu/quantpdocker" target="_blank"><img src="https://cdn3.iconfinder.com/data/icons/social-media-2169/24/social_media_social_media_logo_docker-128.png" alt="docker-icon" /></a></td>
</tr>
<tr>
<td>MetaQuantome</td>
<td>Quantitative analysis of the function and taxonomy of microbiomes and their interaction</td>
<td> </td>
<td><a href="https://galaxyproteomics.github.io/metaquantome_mcp_analysis/galaxy_tutorial/tutorial.html" target="_blank"><i class="fa fa-laptop" aria-hidden="true"></i></a></td>
<td> </td>
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<h2 class="display-3">Acknowledgements</h2>
<p>We are aiming to maintain high competency and provide high-quality data analysis
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<p>Individuals who have contributed to the project, but whose contributions
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acknowledgements section of the manuscript as follows:</p>
<blockquote>
<p>The authors acknowledge the support of the Freiburg Galaxy Team:
Person X and Prof. Rolf Backofen, Bioinformatics, University of Freiburg,
Germany funded by <a href="http://www.sfb992.uni-freiburg.de">Collaborative
Research Centre 992 Medical Epigenetics</a> (<a href="http://www.dfg.de">DFG</a>
grant SFB 992/1 2012) and the German Federal Ministry of Education and Research
(<a href="http://www.bmbf.de/">BMBF</a> grant 031 A538A <a href="https://www.denbi.de">de.NBI</a>-RBC).
</p>
</blockquote>
<p>Additional funding of projects and/or provision of material expenses are welcome as well, to help
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<td>< 5 minutes</td><td>possibly without notice</td>
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