Proteomics

Training material for proteomics workflows in Galaxy

Requirements

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

Material

Introduction

Start here if you are new to proteomic analysis in Galaxy.

Lesson Slides Hands-on Input dataset Workflows Galaxy tour Galaxy instances
Introduction to proteomics, protein identification, quantification and statistical modelling
slides / video

Protein identification and quantification

These tutorials cover protein identification and/or label-free and label based quantification from data dependent acquisition (DDA) and data independent acquisition (DIA).

Lesson Slides Hands-on Input dataset Workflows Galaxy tour Galaxy instances
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
MaxQuant and MSstats for the analysis of label-free data
level level level
tutorial 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

Postprocessing of proteomics data

These tutorial cover statistical analyses and visualizations after protein identification and quantification.

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
Secretome Prediction
level level level
tutorial zenodo_link workflow

Special proteomics techniques

These tutorials focus on special techniques such as N-terminomics and mass spectrometry imaging.

Lesson Slides Hands-on Input dataset Workflows Galaxy tour Galaxy instances
Detection and quantitation of N-termini (degradomics) via N-TAILS
level level level
tutorial workflow
Mass spectrometry imaging: Loading and exploring MSI data
level level level
tutorial zenodo_link workflow

Multi-omics analyses

These tutorials combine proteomics with other -omics technologies such as transcriptomics.

Lesson Slides Hands-on Input dataset Workflows Galaxy tour Galaxy instances
Metaproteomics tutorial
tutorial zenodo_link workflow interactive_tour
metaQuantome 1: Data creation
level level level
tutorial zenodo_link workflow
metaQuantome 2: Function
level level level
tutorial zenodo_link workflow
metaQuantome 3: Taxonomy
level level level
tutorial zenodo_link workflow
Proteogenomics 1: Database Creation
level level level
tutorial zenodo_link workflow
Proteogenomics 2: Database Search
level level level
tutorial zenodo_link workflow
Proteogenomics 3: Novel peptide analysis
level level level
tutorial zenodo_link workflow

Prediction of peptide properties

These tutorials explain in-silico analyses of different peptide properties.

Lesson Slides Hands-on Input dataset Workflows Galaxy tour Galaxy instances
Machine Learning Modeling of Anticancer Peptides
level level level
tutorial zenodo_link workflow
Peptide Library Data Analysis
level level level
tutorial 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.

Frequently Asked Questions

Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.

Maintainers

This material is maintained by:

Melanie FöllMelanie Föll Subina MehtaSubina Mehta Pratik JagtapPratik Jagtap Björn GrüningBjörn Grüning

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:

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

References