DDA and DIA proteomic analysis in Galaxy

DDA and DIA proteomic analysis in Galaxy

basic bioinformatics


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. 


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.  


Melanie Föll
Khoury College of Computer Sciences, Northeastern University, Boston, USA. 

Melanie Föll is a postdoctoral researcher working in mass spectrometry imaging in the lab of Olga Vitek at Northeastern University. During her PhD studies in Oliver Schilling's lab at the Institute for Surgical Pathology in Freiburg, Germany, she established and applied methods for translational cancer tissue proteomics. 

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. 


Working with Galaxy user interface

Label-free data dependent analysis

Label-free data independent acquisition analysis