Proteomics

Training material for proteomics workflows in Galaxy

Requirements

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

Material

Lesson Slides Hands-on Input dataset Workflows Galaxy tour Galaxy instances
Annotating a protein list identified by LC-MS/MS experiments
tutorial zenodo_link workflow
Biomarker candidate identification
tutorial workflow
Detection and quantitation of N-termini (degradomics) via N-TAILS
level level level
tutorial workflow
Label-free data analysis using MaxQuant
level level level
tutorial zenodo_link workflow
Label-free versus Labelled - How to Choose Your Quantitation Method
level level level
tutorial
Mass spectrometry imaging: Loading and exploring MSI data
level level level
tutorial zenodo_link workflow
Metaproteomics tutorial
tutorial zenodo_link workflow interactive_tour
metaQuantome Data creation tutorial
tutorial zenodo_link workflow
Peptide and Protein ID using OpenMS tools
level level level
tutorial zenodo_link workflow interactive_tour
Peptide and Protein ID using SearchGUI and PeptideShaker
level level level
tutorial zenodo_link workflow interactive_tour
Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
level level level
tutorial zenodo_link workflow interactive_tour
Protein FASTA Database Handling
level level level
tutorial workflow interactive_tour
Proteogenomics 1: Database Creation
tutorial zenodo_link workflow
Proteogenomics 2: Database Search
tutorial zenodo_link workflow
Proteogenomics 3: Novel peptide analysis
tutorial zenodo_link workflow
Secretome Prediction
level level level
tutorial zenodo_link workflow

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.

Maintainers

This material is maintained by:

Florian Christoph SiglochFlorian Christoph Sigloch, Björn GrüningBjörn Grüning, Clemens BlankClemens Blank

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:

Valentin LouxValentin Loux, Florence CombesFlorence Combes, David ChristianyDavid Christiany, Yves VandenbrouckYves Vandenbrouck, Florian Christoph SiglochFlorian Christoph Sigloch, Björn GrüningBjörn Grüning, Melanie FöllMelanie Föll, Matthias FahrnerMatthias Fahrner, Timothy J. GriffinTimothy J. Griffin, Pratik JagtapPratik Jagtap, James JohnsonJames Johnson, Clemens BlankClemens Blank, Subina MehtaSubina Mehta, Emma LeithEmma Leith, Marie CraneMarie Crane, Ray SajulgaRay Sajulga, Praveen KumarPraveen Kumar

References