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
plain text

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
tutorial
EncyclopeDIA
DIA
tutorial
Label-free data analysis using MaxQuant tutorial
Label-free versus Labelled - How to Choose Your Quantitation Method
DDA
tutorial
Library Generation for DIA Analysis
DIA
tutorial
MaxQuant and MSstats for the analysis of label-free data tutorial
MaxQuant and MSstats for the analysis of TMT data tutorial
Peptide and Protein ID using OpenMS tools
DDA
tutorial
Peptide and Protein ID using SearchGUI and PeptideShaker
DDA
tutorial
Peptide and Protein Quantification via Stable Isotope Labelling (SIL) tutorial
Protein FASTA Database Handling
DDA
tutorial

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 tutorial
Biomarker candidate identification tutorial
Secretome Prediction tutorial
Statistical analysis of DIA data
DIA
tutorial

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
tutorial
Mass spectrometry imaging: Loading and exploring MSI data tutorial

Multi-omics analyses

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

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

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 tutorial
Peptide Library Data Analysis
tutorial

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.

Maintainers

This material is maintained by:

AvatarMelanie Föll AvatarSubina Mehta AvatarPratik Jagtap AvatarBjörn 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:

AvatarMelanie Föll AvatarValentin Loux AvatarFlorence Combes AvatarDavid Christiany AvatarYves Vandenbrouck AvatarFlorian Christoph Sigloch AvatarBjörn Grüning AvatarMatthias Fahrner AvatarEmma Leith AvatarSubina Mehta AvatarJames Johnson AvatarPratik Jagtap AvatarTimothy J. Griffin AvatarJayadev Joshi AvatarDaniel Blankenberg AvatarKlemens Fröhlich AvatarClemens Blank AvatarMarie Crane AvatarPraveen Kumar AvatarRay Sajulga

References