DDA and DIA proteomic analysis in Galaxy

DDA and DIA proteomic analysis in Galaxy

basic bioinformatics
ELIXIR
Location:

Online

Start date:

03 December 2020

General context

Galaxy software framework is an open-source application. It is a system that enables researchers without informatics expertise to perform computational biology analyses through the web. 

This hands-on workshop aims to familiarize you with the Galaxy user interface & execute (label-free) proteomics data-analysis. The course will be taught by Melanie Föll and Matthias Fahrner from the Institute of Molecular Medicine and Cell Research from the University of Freiburg. 

Objectives

At the beginning of the course we will introduce you to the Galaxy platform and teach you how to perform basic tasks such as importing data, running tools, working with histories, creating workflows, and sharing your work. 

Then, we will dive into proteomic analyses which are split up into two parts.

First, we will use MaxQuant to analyze classical proteomic shotgun (label-free data dependent acquisition = DDA) data. MaxQuant is a standalone tool that enables peptide and protein identification as well as quantification. 

In the second part we will perform a complete analysis workflow for data independent acquisition (DIA) data using a variety of open-source tools (including diapysef, OpenSwath, Pyprophet, MSstats). This includes generating a peptide library, refining the library and utilizing the library to identify and quantify peptides in DIA data. 

Event intended for

Biologists and other life science researchers who would like an introduction to Galaxy, its workflows and use it for proteomics analysis.

Required skills

No prior bioinformatics knowledge is required, however a basic understanding of mass spectrometry based proteomics experiments is definitely helpful to get more out of the course.  

Trainers

Melanie Föll
Institute for Surgical Pathology in Freiburg, Germany

Melanie Föll is a postdoctoral researcher working in translational metabolomics, proteomics and mass spectrometry imaging in Oliver Schilling's lab at the Institute for Surgical Pathology in Freiburg, Germany. She performed her PhD thesis in the same lab working on translational cancer tissue proteomic and did a PostDoc in the Vitek Lab at Northeastern University. 

Matthias Fahrner
Institute for Surgical Pathology in Freiburg, Germany

Matthias Fahrner is a PhD student in Oliver Schilling's lab at the Institute for Surgical Pathology in Freiburg, Germany. Matthias is focusing on proteomic characterizations of different tumor entities using mass spectrometry approaches. 

Program

Working with Galaxy user interface

Label-free data dependent analysis

Label-free data independent acquisition analysis