Welcome to Galaxy Proteomics

This European Galaxy branches off from the main usegalaxy.eu 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 from the University of Minnesota, USA.

GalaxyP Resources:
About Us
Publications
Conference presentations
Workshops

Tutorials
Gateways
Research Projects
News and Events
Contributors

Tutorials

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

Want to learn more about proteomics? Check out the following lesson tutorials from the Galaxy Training Network:

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

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	Proteogenomics 1: Database creation Proteogenomics 2: Database search Proteogenomics 3: Novel peptide analysis
Metaproteomics Gateway	Metaproteomics tutorial

Research Projects

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

Tool	Description	Paper
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
QuanTP	Correlation between protein and transcript	Kumar et. al 2019
MetaQuantome	Quantitative analysis of the function and taxonomy of microbiomes and their interaction

News and Events

Contributors

Our Data Policy

Registered Users	Unregistered Users	FTP Data	GDPR Compliance
User data on UseGalaxy.eu (i.e. datasets, histories) will be available as long as they are not deleted by the user. Once marked as deleted the datasets will be permanently removed within 14 days. If the user "purges" the dataset in the Galaxy, it will be removed immediately, permanently. An extended quota can be requested for a limited time period in special cases.	Processed data will only be accessible during one browser session, using a cookie to identify your data. This cookie is not used for any other purposes (e.g. tracking or analytics). If UseGalaxy.eu service is not accessed for 90 days, those datasets will be permanently deleted.	Any user data uploaded to our FTP server should be imported into Galaxy as soon as possible. Data left in FTP folders for more than 3 months, will be deleted.	The Galaxy service complies with the EU General Data Protection Regulation (GDPR). You can read more about this on our Terms and Conditions.