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
Detection and quantitation of N-termini (degradomics) via N-TAILS tutorial workflow
Label-free versus Labelled - How to Choose Your Quantitation Method tutorial workflow
Mass spectrometry imaging 1: Loading and exploring MSI data tutorial zenodo_link
Metaproteomics tutorial tutorial zenodo_link workflow
Peptide and Protein ID using OpenMS tools tutorial zenodo_link workflow interactive_tour
Peptide and Protein ID using SearchGUI and PeptideShaker tutorial zenodo_link workflow interactive_tour
Peptide and Protein Quantification via Stable Isotope Labelling (SIL) tutorial zenodo_link workflow interactive_tour
Protein FASTA Database Handling 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 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 -d -p 8080:80 quay.io/galaxy/proteomics-training

It will launch a flavored Galaxy instance available on http://localhost:8080.

Maintainers

This material is maintained by:

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:

References