Proteomics

Training material for proteomics workflows in Galaxy

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides () and tutorial () buttons below.

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 Recordings Input dataset Workflows Galaxy servers
Introduction to proteomics, protein identification, quantification and statistical modelling

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 Recordings Input dataset Workflows Galaxy servers
DIA Analysis using OpenSwathWorkflow
DIA
EncyclopeDIA
DIA
    • Label-free data analysis using MaxQuant
    Label-free versus Labelled - How to Choose Your Quantitation Method
    DDA
    Library Generation for DIA Analysis
    DIA
    MaxQuant and MSstats for the analysis of label-free data
    • MaxQuant and MSstats for the analysis of TMT data
    Peptide and Protein ID using OpenMS tools
    DDA
    Peptide and Protein ID using SearchGUI and PeptideShaker
    DDA
    Peptide and Protein Quantification via Stable Isotope Labelling (SIL)
    Protein FASTA Database Handling
    DDA

    Postprocessing of proteomics data

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

    Lesson Slides Hands-on Recordings Input dataset Workflows Galaxy servers
    Annotating a protein list identified by LC-MS/MS experiments
    • Biomarker candidate identification
    Secretome Prediction
    Statistical analysis of DIA data
    DIA

    Special proteomics techniques

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

    Lesson Slides Hands-on Recordings Input dataset Workflows Galaxy servers
    Detection and quantitation of N-termini (degradomics) via N-TAILS
    Mass spectrometry imaging: Loading and exploring MSI data

    Multi-omics analyses

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

    Lesson Slides Hands-on Recordings Input dataset Workflows Galaxy servers
    Metaproteomics tutorial
    • metaQuantome 1: Data creation
    metaQuantome 2: Function
    metaQuantome 3: Taxonomy
    Proteogenomics 1: Database Creation
    • Proteogenomics 2: Database Search
    • Proteogenomics 3: Novel peptide analysis

    • Prediction of peptide properties

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

    Lesson Slides Hands-on Recordings Input dataset Workflows Galaxy servers
    Machine Learning Modeling of Anticancer Peptides
    Peptide Library Data Analysis

    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:

    orcid logoAvatarMelanie Föll orcid logoAvatarSubina Mehta AvatarPratik Jagtap orcid logoAvatarBjörn 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:

    orcid logoAvatarMelanie Föll AvatarValentin Loux AvatarFlorence Combes AvatarDavid Christiany AvatarYves Vandenbrouck AvatarFlorian Christoph Sigloch orcid logoAvatarBjörn Grüning orcid logoAvatarMatthias Fahrner AvatarEmma Leith orcid logoAvatarSubina Mehta AvatarJames Johnson AvatarPratik Jagtap AvatarTimothy J. Griffin orcid logoAvatarJayadev Joshi orcid logoAvatarDaniel Blankenberg AvatarKlemens Fröhlich AvatarClemens Blank AvatarMarie Crane AvatarPraveen Kumar AvatarRay Sajulga

    References