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.