Proteomics

Training material for proteomics workflows in Galaxy

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.

Requirements

Before diving into this topic, we recommend you to have a look at:

Material

Introduction

Start here if you are new to proteomic analysis in Galaxy.

Lesson Slides Hands-on Recordings Input dataset Workflows
Introduction to proteomics, protein identification, quantification and statistical modelling

Protein identification and quantification

These tutorials cover protein identification and/or label-free and label based quantification from data dependent acquisition (DDA) and data independent acquisition (DIA).

Lesson Slides Hands-on Recordings Input dataset Workflows
DIA Analysis using OpenSwathWorkflow
DIA
EncyclopeDIA
DIA
Label-free data analysis using MaxQuant
Label-free versus Labelled - How to Choose Your Quantitation Method
DDA
Library Generation for DIA Analysis
DIA
MaxQuant and MSstats for the analysis of TMT data
MaxQuant and MSstats for the analysis of label-free data
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
DDA

Postprocessing of proteomics data

These tutorial cover statistical analyses and visualizations after protein identification and quantification.

Lesson Slides Hands-on Recordings Input dataset Workflows
Annotating a protein list identified by LC-MS/MS experiments
Biomarker candidate identification
Statistical analysis of DIA data
DIA

Special proteomics techniques

These tutorials focus on special techniques such as N-terminomics and mass spectrometry imaging.

Lesson Slides Hands-on Recordings Input dataset Workflows
Detection and quantitation of N-termini (degradomics) via N-TAILS
Mass spectrometry imaging: Loading and exploring MSI data

Multi-omics analyses

These tutorials combine proteomics with other -omics technologies such as transcriptomics.

Lesson Slides Hands-on Recordings Input dataset Workflows
Metaproteomics tutorial
Proteogenomics 1: Database Creation
Proteogenomics 2: Database Search
Proteogenomics 3: Novel peptide analysis
metaQuantome 1: Data creation
metaQuantome 2: Function
metaQuantome 3: Taxonomy

Prediction of peptide properties

These tutorials explain in-silico analyses of different peptide properties.

Lesson Slides Hands-on Recordings Input dataset Workflows
Machine Learning Modeling of Anticancer Peptides
Peptide Library Data Analysis

Metaproteomics analysis of clinical data

These tutorials are step by step analysis from database generation to the discovery of peptides to verification, quantitation, and interpretation of the results.

Lesson Slides Hands-on Recordings Input dataset Workflows
Clinical-MP-1-Database-Generation
Clinical-MP-2-Discovery
Clinical-MP-3-Verification
Clinical-MP-4-Quantitation
Clinical-MP-5-Data Interpretation

Galaxy instances

You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.

You can also use the following Docker image for these tutorials:

docker run -p 8080:80 quay.io/galaxy/proteomics-training

NOTE: Use the -d flag at the end of the command if you want to automatically download all the data-libraries into the container.

It will launch a flavored Galaxy instance available on http://localhost:8080. This instance will contain all the tools and workflows to follow the tutorials in this topic. Login as admin with password password to access everything.

Frequently Asked Questions

Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.

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Editorial Board

This material is reviewed by our Editorial Board:

orcid logoMelanie Föll avatar Melanie Föllorcid logoSubina Mehta avatar Subina Mehtaorcid logoPratik Jagtap avatar Pratik Jagtaporcid logoBjörn Grüning avatar Björn Grüning

For any question related to this topic and the content, you can contact them or visit our Gitter channel.

Contributors

This material was contributed to by:

Florian Christoph Sigloch avatar Florian Christoph Siglochorcid logoMatthias Fahrner avatar Matthias FahrnerFlorence Combes avatar Florence CombesKatherine Do avatar Katherine Doorcid logoTimothy J. Griffin avatar Timothy J. GriffinDavid Christiany avatar David Christianyorcid logoJayadev Joshi avatar Jayadev Joshiorcid logoMelanie Föll avatar Melanie Föllorcid logoDaniel Blankenberg avatar Daniel BlankenbergPraveen Kumar avatar Praveen Kumarorcid logoSubina Mehta avatar Subina MehtaRay Sajulga avatar Ray SajulgaValentin Loux avatar Valentin Louxorcid logoClemens Blank avatar Clemens BlankKlemens Fröhlich avatar Klemens FröhlichYves Vandenbrouck avatar Yves Vandenbrouckorcid logoPratik Jagtap avatar Pratik JagtapMarie Crane avatar Marie CraneDechen Bhuming avatar Dechen BhumingEmma Leith avatar Emma Leithorcid logoBjörn Grüning avatar Björn GrüningJames Johnson avatar James Johnson

Funding

These individuals or organisations provided funding support for the development of this resource

References