On December 3 and 4, we ran a 2-day Galaxy Proteomics data analysis workshop organized by ELIXIR Belgium. Therefore, most of the 20 participants were from Belgium, but others were from all around Europe, the US and Australia.

The course covered the analysis of two common proteomics methods: data-dependent acquisition (DDA) and data-independent acquisition method (DIA). The latter is a more recently developed proteomics method that comes with many advantages, but due to its complexity and file sizes, also with new challenges. In particular, the reproducibility and robustness (multiple software needed), as well as the limited accessibility due to the required computational resources, has been challenging in DIA data analysis. All these issues could be overcome by using Galaxy. This course has been our first time covering the data analysis of both, the most commonly used (DDA) and the more innovative mass spectrometry method (DIA).

We held lectures and demos of the respective GTN material in the morning until noon while answering questions and discussing details of the involved analysis steps. In the afternoon, the participants had time to go through the training at their own pace using the GTN material, and asking questions in a shared google doc as well as live in a zoom meeting. Due to the designated computational resources, the waiting time was minimized and we were able to track the progress of our participants through the Training Infrastructure as a Service (TIaaS) Dashboard. Many thanks to the Galaxy TIaaS, without which this course would not have been such a success!

Matthias Fahrner & Melanie Föll