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
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tutorial Toggle Dropdown | zenodo_link | workflow | ||
Biomarker candidate identification
|
tutorial Toggle Dropdown | workflow | |||
Detection and quantitation of N-termini (degradomics) via N-TAILS
|
tutorial Toggle Dropdown | workflow | |||
Label-free versus Labelled - How to Choose Your Quantitation Method
|
tutorial Toggle Dropdown | ||||
Mass spectrometry imaging: Loading and exploring MSI data
level level level
|
tutorial Toggle Dropdown | zenodo_link | workflow | ||
Metaproteomics tutorial
|
tutorial Toggle Dropdown | zenodo_link | workflow | interactive_tour | |
Peptide and Protein ID using OpenMS tools
|
tutorial Toggle Dropdown | zenodo_link | workflow | interactive_tour | |
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)
level level level
|
tutorial Toggle Dropdown | zenodo_link | workflow | interactive_tour | |
Protein FASTA Database Handling
level level level
|
tutorial Toggle Dropdown | workflow | interactive_tour | ||
Proteogenomics 1: Database Creation
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tutorial Toggle Dropdown | zenodo_link | workflow | ||
Proteogenomics 2: Database Search
|
tutorial Toggle Dropdown | zenodo_link | workflow | ||
Proteogenomics 3: Novel peptide analysis
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tutorial Toggle Dropdown | zenodo_link | workflow | ||
Secretome Prediction
|
tutorial Toggle Dropdown | 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 admin to access everything.
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
- 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.