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 (slides) and tutorial (tutorial) buttons below.


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



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

    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 tutorial
  • Biomarker candidate identification tutorial
    Secretome Prediction tutorial
    Statistical analysis of DIA data

    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 tutorial

    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 tutorial
  • Proteogenomics 1: Database Creation tutorial
  • Proteogenomics 2: Database Search tutorial
  • Proteogenomics 3: Novel peptide analysis tutorial
  • metaQuantome 1: Data creation tutorial
    metaQuantome 2: Function tutorial
    metaQuantome 3: Taxonomy tutorial

    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 tutorial
    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

    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.


    This material is maintained by:

    orcid logoAvatarMelanie Föllorcid logoAvatarSubina Mehtaorcid logoAvatarPratik Jagtaporcid logoAvatarBjörn Grüning

    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:

    AvatarMarie CraneAvatarKlemens FröhlichAvatarJames JohnsonAvatarValentin Louxorcid logoAvatarPratik JagtapAvatarPraveen Kumarorcid logoAvatarMelanie FöllAvatarEmma Leithorcid logoAvatarSubina Mehtaorcid logoAvatarBjörn Grüningorcid logoAvatarTimothy J. GriffinAvatarFlorian Christoph Siglochorcid logoAvatarDaniel BlankenbergAvatarDavid ChristianyAvatarFlorence Combesorcid logoAvatarMatthias FahrnerAvatarClemens Blankorcid logoAvatarJayadev JoshiAvatarRay SajulgaAvatarYves Vandenbrouck