Galaxy Proteomics

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

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	Watch video
Metaproteomics Gateway	Metaproteomics tutorial	Watch video

Research Projects

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

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

News and Events

Galaxy 2026 update published in Nucleic Acids Research

News More news

The European Galaxy Project Website Is Now Fully Served by the Galaxy Hub
After ten years on a Jekyll-on-GitHub setup, galaxyproject.eu is now completely powered by the Galaxy Hub — a fast, metadata-driven home that any Galaxy community can reuse.
Galaxy 26.1 is here!
Galaxy 26.1 introduces Galaxy Notebooks, context-aware GalaxyAI agents, Model Context Protocol support, bulk dataset storage migration, a modern workflow extraction interface, favorite and recent tools, and clearer workflow execution monitoring. Explore the user release notes.
The European Galaxy Project Website Is Now Fully Served by the Galaxy Hub
After ten years on a Jekyll-on-GitHub setup, galaxyproject.eu is now completely powered by the Galaxy Hub — a fast, metadata-driven home that any Galaxy community can reuse.
Galaxy for Accessible, Reproducible, and Collaborative Data Analyses: 2026 Update
The latest Galaxy update in Nucleic Acids Research highlights major advances in the platform’s interface, workflows, data management, visualizations, infrastructure, and global community.
Galaxy Newsletter July 2026
From GCC2026 and GTA2026 highlights to a major new Galaxy publication, Galaxy 26.0, and community-curated research environments, explore what the Galaxy community accomplished in the second quarter of 2026.

Events More events

Small Scale Galaxy Admins Meeting
Aug 20 · Online, Global
microGalaxy / Microbiology Community Meeting
Sep 9 · online

Join us on September 9th to explore how BioDIGs is collaboratively bridging soil microbiomes, the environment, and health and how we can collaborate!
Small Scale Galaxy Admins Meeting
Sep 17 · Online, Global
ESG4Stars kick-off meeting
Oct 5 - Oct 6 · Department of Computer Science, University of Freiburg

Our new EU-funded research infrastructure project to reduce the environmental footprint of scientific computing on platforms like Galaxy will begin in October.
ASM Conference on Rapid Applied Microbial NGS and Bioinformatic Pipelines
Oct 11 · Washington, DC, USA

Join the ASM NGS conference to explore the latest in microbial genomics and bioinformatics.

Contributors

Our Data Policy

Registered Users	Unregistered Users	FTP Data	GDPR Compliance
For all different storage options, for detailed explanations of data retention policies, and ways how to increase your quota please refer to our dedicated storage site.	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.