Integrative Approaches in Shotgun Proteomics : From sample preparation to multifaceted data analysis

Sammanfattning: Bottom-up proteomics mass-spectrometry gives an opportunity to shed light on var-ious biological aspects/characteristics such as protein composition, its modifications,interactions, and dynamics. Its applications span a wide range of biological sciencesaiming to eventually answer fundamental disease related questions or evaluate drugperformance and predict adverse effects.Bottom-up proteomics experiments are worth the time and effort because it is a comprehensive and multi-level approach to address research questions from a single dataset. Hence, we can gain a thorough understanding of the processes in the studied system and their interconnected changes, thereby confirming results from different perspectives. While the majority of research is focused on the improvement of analytical techniques, it remains challenging to derive meaningful biological insights from the data.This Ph.D. thesis contributes to various proteomics challenges, including the development of a high-throughput micro-scale proteomic workflow and comprehensive multifaceted analysis. In particular, the data on the thermal proteome profiling of melanocyte-stimulating hormone interactions with melanocortin receptors was analyzed using a newly developed workflow. This workflow uniquely combines thermal stabilization data, inferred transcription factor activity, and pathway analysis. Additionally, this thesis integrates omics approaches such as metabolomics and proteomics. Another dimension to the dataset was added by combining metabolic mass spectrometry imaging with region-specific proteomics for the characterization of cocaine’s neurotoxicity.