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
Annotating a protein list identified by LC-MS/MS experiments
Biomarker candidate identification
Detection and quantitation of N-termini (degradomics) via N-TAILS
Label-free versus Labelled - How to Choose Your Quantitation Method
Mass spectrometry imaging: 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

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 admin 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 FoellMelanie Foell, Timothy J. GriffinTimothy J. Griffin, Pratik JagtapPratik Jagtap, James JohnsonJames Johnson, Clemens BlankClemens Blank, Subina MehtaSubina Mehta, MatthiasMatthias, Ray SajulgaRay Sajulga, Praveen KumarPraveen Kumar

References