Proteomics

Training material for proteomics workflows in Galaxy

Requirements

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

Material

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

Introduction

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

Lesson Slides Hands-on Recordings Input dataset Workflows
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
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 TMT data
MaxQuant and MSstats for the analysis of label-free data
Peptide and Protein ID using OpenMS tools
Peptide and Protein ID using SearchGUI and PeptideShaker
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
Annotating a protein list identified by LC-MS/MS experiments
Biomarker candidate identification
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
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
Metaproteomics tutorial
Proteogenomics 1: Database Creation
Proteogenomics 2: Database Search
Proteogenomics 3: Novel peptide analysis
metaQuantome 1: Data creation
metaQuantome 2: Function
metaQuantome 3: Taxonomy

Prediction of peptide properties

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

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

Metaproteomics analysis of clinical data

These tutorials are step by step analysis from database generation to the discovery of peptides to verification, quantitation, and interpretation of the results.

Lesson Slides Hands-on Recordings Input dataset Workflows
Clinical Metaproteiomics 1: Database-Generation
Clinical Metaproteomics 2: Discovery
Clinical Metaproteomics 3: Verification
Clinical Metaproteomics 4: Quantitation
Clinical Metaproteomics 5: Data Interpretation

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.

Follow topic updates rss-feed with our RSS Feed

Editorial Board

This material is reviewed by our Editorial Board:

orcid logoMelanie Föll avatar Melanie Föllorcid logoSubina Mehta avatar Subina Mehtaorcid logoPratik Jagtap avatar Pratik Jagtaporcid logoBjörn Grüning avatar Björn Grüning

Contributors

This material was contributed to by:

Florian Christoph Sigloch avatar Florian Christoph SiglochJames Johnson avatar James JohnsonEmma Leith avatar Emma LeithRay Sajulga avatar Ray SajulgaPraveen Kumar avatar Praveen KumarYves Vandenbrouck avatar Yves Vandenbrouckorcid logoPratik Jagtap avatar Pratik Jagtaporcid logoJayadev Joshi avatar Jayadev JoshiDechen Bhuming avatar Dechen BhumingValentin Loux avatar Valentin Louxorcid logoDaniel Blankenberg avatar Daniel Blankenbergorcid logoTimothy J. Griffin avatar Timothy J. GriffinKlemens Fröhlich avatar Klemens Fröhlichorcid logoSubina Mehta avatar Subina MehtaFlorence Combes avatar Florence CombesDavid Christiany avatar David Christianyorcid logoMelanie Föll avatar Melanie FöllMarie Crane avatar Marie CraneKatherine Do avatar Katherine Doorcid logoClemens Blank avatar Clemens Blankorcid logoBjörn Grüning avatar Björn Grüningorcid logoMatthias Fahrner avatar Matthias Fahrner

Funding

These individuals or organisations provided funding support for the development of this resource

References