Training material for proteomics workflows in Galaxy
Before diving into this topic, we recommend you to have a look at:
|Lesson||Slides||Hands-on||Input dataset||Workflows||Galaxy tour||Galaxy instances|
|Detection and quantitation of N-termini (degradomics) via N-TAILS||tutorial Toggle Dropdown||workflow||instances|
|Label-free versus Labelled - How to Choose Your Quantitation Method||tutorial Toggle Dropdown||workflow||instances|
|Mass spectrometry imaging 1: Loading and exploring MSI data||tutorial Toggle Dropdown||zenodo_link|
|Metaproteomics tutorial||tutorial Toggle Dropdown||zenodo_link||workflow|
|Peptide and Protein ID using OpenMS tools||tutorial Toggle Dropdown||zenodo_link||workflow||interactive_tour||instances|
|Peptide and Protein ID using SearchGUI and PeptideShaker||tutorial Toggle Dropdown||zenodo_link||workflow||interactive_tour|
|Peptide and Protein Quantification via Stable Isotope Labelling (SIL)||tutorial Toggle Dropdown||zenodo_link||workflow||interactive_tour||instances|
|Protein FASTA Database Handling||tutorial Toggle Dropdown||workflow||interactive_tour||instances|
|Proteogenomics 1: Database Creation||tutorial Toggle Dropdown||zenodo_link||workflow|
|Proteogenomics 2: Database Search||tutorial Toggle Dropdown||zenodo_link||workflow||instances|
|Proteogenomics 3: Novel peptide analysis||tutorial Toggle Dropdown||zenodo_link||workflow|
|Secretome Prediction||tutorial Toggle Dropdown||zenodo_link||workflow||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.
This material is maintained by:
For any question related to this topic and the content, you can contact them or visit our Gitter channel.
This material was contributed to by:
- Florian Christoph Sigloch
- Björn Grüning
- Melanie Foell
- Timothy J. Griffin
- Pratik Jagtap
- James Johnson
- Clemens Blank
- Subina Mehta
- Ray Sajulga
- Kumar D, Yadav AK and Dash D: Choosing an Optimal Database for Protein Identification from Tandem Mass Spectrometry Data.
Vaudel M, et al.: Shedding light on black boxes in protein identification.
An extensive tutorial for peptide and protein identification, available at http://compomics.com/bioinformatics-for-proteomics. The material is completely based on freely available and open-source tools.
Cappadona S, et al.: Current challenges in software solutions for mass spectrometry-based quantitative proteomics
A comprehensive review of current quantitative techniques, their advantages and pitfalls.
Tholen S, et al.: Limited and Degradative Proteolysis in the Context of Posttranslational Regulatory Networks: Current Technical and Conceptional Advances
Review on LC-MS/MS based proteomic methods to identify neo-N-termini, e.g. generated by protease cleavage.