DDA and DIA proteomic analysis in Galaxy
Galaxy enables researchers without bioinformatics expertise to perform computational analyses through the web. This hands-on workshop aims to familiarize you with the Galaxy user interface & execute (label-free) proteomics data-analysis.
The first part of this hands-on workshop will introduce the participants to the Galaxy platform. Basic tasks such as importing data, running tools, working with histories, creating workflows, and sharing of the work will be handled.
For the proteomics analysis, MaxQuant will be used to analyse 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.
Secondarily, a complete analysis workflow for data independent acquisition (DIA) will be performed 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. More info and registration.
This course is organised by the VIB Bioinformatics Core and ELIXIR Belgium. The instructors are Melanie Föll and Matthias Fahrner from the Institute of Molecular Medicine and Cell Research from the University of Freiburg.