Connecting the neuronal proteome: Unraveling protein dynamics in neurons using Mass Spectrometry-based proteomics

Similarly to the amazon rainforest which is formed by a multitude of different trees, many of them growing around and on top of each other with their branches and roots tightly interconnected, the human brain is composed by approximately 100 billion neurons organized into a complex matrix of connections and packed into highly specialized layers. In order to establish and maintain neuronal connections, neurons must be able to sort and deliver proteins to specific compartments with extreme precision. In fact, the protein composition of each single neuronal compartment not only determines its unique architectural morphology and function but has also a more profound effect on the formation of the neuronal network which is the essence of our brain. In this perspective, it is essential to study the primary building blocks of life, the proteins, alongside with their interactions and the molecular mechanisms regulating their functions. A key concept of modern biology is that proteins participate in complex, interconnected networks, rather than linear pathways. In the field of neurobiology, proteomics has recently started to showcase its full potential as a powerful methodology able to outperform classical biochemical approaches by allowing a more global understanding of protein dynamics and a more detailed characterization of intracellular protein networks and complexes. This thesis describes our efforts in advancing the understanding of selected mechanisms in neurons by using Mass Spectrometry (MS)-based proteomics applications. Latest MS techniques have been widely used to investigate neuronal differentiation, kinesin-mediated neuronal transport and protein-interaction networks in physiological or pathological condition.