Proteomics

Training material for proteomics workflows in Galaxy

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 Input dataset Workflows Galaxy tour
Introduction to proteomics, protein identification, quantification and statistical modelling
slides / video

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

Postprocessing of proteomics data

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

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

Special proteomics techniques

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

Lesson Slides Hands-on Input dataset Workflows Galaxy tour
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 Input dataset Workflows Galaxy tour
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 Input dataset Workflows Galaxy tour
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 AvatarClemens Blank AvatarMarie Crane AvatarPraveen Kumar AvatarRay Sajulga

References