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Welcome to Galaxy Proteomics

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| --- | --- GalaxyP logo{:target="_blank"}

This European Galaxy branches off from the main
usegalaxy.eu{:target="_blank"} server and focuses on one specific
domain: Proteomics.

Galaxy Proteomics is a multiple-'omics' data-analysis
platform with particular emphasis on mass
spectrometry-based proteomics. It is hosted by
GalaxyEU and maintained by the GalaxyP team{:target="_blank"} from
the University of Minnesota, USA.

GalaxyP Resources:
About Us{:target="_blank"}
Publications{:target="_blank"}
Conference presentations{:target="_blank"}
Workshops{:target="_blank"} | Tweets by usegalaxyp <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>* {:.table}

Content

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  1. TOC {:toc}

Tutorials

Are you new to Galaxy, or returning after a long time, and looking for help to get started? Take a guided tour{:target="_blank"} through Galaxy's user interface.

Want to learn more about proteomics? Check out the following lesson tutorials from the Galaxy Training Network{:target="_blank"}:

Lesson Hands-on Input dataset Workflows Galaxy tour
Detection and quantitation of N-termini degradomics via N-TAILS {:target="_blank"} {:target="_blank"} {:target="_blank"}
Label-free versus Labelled - How to Choose Your Quantitation Method {:target="_blank"} {:target="_blank"}
Mass spectrometry imaging 1: Loading and exploring MSI data {:target="_blank"} {:target="_blank"} {:target="_blank"}
Metaproteomics tutorial {:target="_blank"} {:target="_blank"} {:target="_blank"}
Peptide and Protein ID using OpenMS tools {:target="_blank"} {:target="_blank"} {:target="_blank"} {:target="_blank"}
Peptide and Protein ID using SearchGUI and PeptideShaker {:target="_blank"} {:target="_blank"} {:target="_blank"} {:target="_blank"}
Peptide and Protein Quantification via Stable Isotope Labelling (SIL) {:target="_blank"} {:target="_blank"} {:target="_blank"} {:target="_blank"}
Protein FASTA Database Handling {:target="_blank"} {:target="_blank"} {:target="_blank"}
Proteogenomics 1: Database Creation {:target="_blank"} {:target="_blank"} {:target="_blank"}
Proteogenomics 2: Database Search {:target="_blank"} {:target="_blank"} {:target="_blank"}
Proteogenomics 3: Novel peptide analysis {:target="_blank"} {:target="_blank"} {:target="_blank"}
Secretome Prediction {:target="_blank"} {:target="_blank"} {:target="_blank"} {:target="_blank"}
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Gateways

Other specialized Galaxy servers curated by the Galaxy-P team containing tools, workflows, and hands-on/video tutorials.

Server Tutorial(s) Video
Proteogenomics Gateway{:target="_blank"} Proteogenomics 1: Database creation{:target="_blank"}
Proteogenomics 2: Database search{:target="_blank"}
Proteogenomics 3: Novel peptide analysis{:target="_blank"}		 proteogenomics thumbnail{:target="_blank"}
Metaproteomics Gateway{:target="_blank"} Metaproteomics tutorial{:target="_blank"} metaproteomics thumbnail{:target="_blank"}
{: .table.table-striped .tooltable}

Research Projects

Featured Galaxy-P tools supported with manuscripts, visualization plugins, docker containers, and hands-on tutorials.

Tool Description Paper Tutorial Docker
CRAVAT-P Stands for Cancer Related Analysis of Variants Toolkit for Proteogenomics. Submits, checks for, and retrieves data for cancer annotation Sajulga et. al 2018{:target="_blank"} {:target="_blank"} docker-icon{:target="_blank"}
QuanTP Correlation between protein and transcript Kumar et. al 2019{:target="_blank"} {:target="_blank"} docker-icon{:target="_blank"}
MetaQuantome Quantitative analysis of the function and taxonomy of microbiomes and their interaction {:target="_blank"}
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News and Events

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Contributors