Mass spectrometry-based proteomics and metabolomics in neuroscience

This doctoral thesis investigates how mass spectrometry (MS) supports proteomic and metabolomic studies in neuroscience. It describes the design, optimisation and validation of end-to-end LC-MS workflows, both targeted and untargeted, applied to clinically relevant questions in neurology. Emphasis is placed on performance controls from pre-analytics through chromatography, ionisation, acquisition, to computational analysis, ensuring that molecular evidence reflects biology rather than analytical artefact. In proteomics, the work covers targeted drug biodistribution, cell-type profiling, epigenetic mapping, and protein-vector characterisation. A bottom-up microLC-HRMS/MS workflow for a compassionate-use biotherapeutic in Lafora disease was developed and validated to assess exposure and biodistribution. Furthermore, to define disease-relevant protein signatures in Lafora disease, a standardised untargeted microLC-HRMS protocol for peripheral blood mononuclear cells was optimised. Analytical groundwork for epigenetic studies in Alzheimer’s disease was established by developing complementary top-down and bottom-up LC-MS workflows to profile histone post-translational modifications in astrocyte lines. MicroLC-HRMS/MS supported a live-delivery proof-of-concept, confirming expression and secretion of a TATκ–GFP fusion protein by Lactococcus lactis in vitro and providing peptide-level confirmation in murine tissues after oral dosing. In metabolomics, applications range from untargeted characterisation for differential diagnosis to clinic-ready microsampling. Untargeted plasma LC-HRMS workflows were optimised to support differential diagnosis of parkinsonian syndromes. For therapeutic drug monitoring of antiseizure medications, patient self-collected volumetric absorptive microsampling (VAMS) was analytically validated through UHPLC-MS/MS, showing feasibility for routine care and telemedicine. Using the same microsampling technique, a targeted UHPLC-MS/MS method for lyso-Gb3 in Fabry disease was developed and clinically validated to enable minimally invasive diagnosis. A quantitative dried blood spot UHPLC-MS/MS method for antiseizure medications was developed and validated to enable remote care. Research stay at the Precision Proteomics Center Davos (SIAF, University of Zurich) focused on refining data-independent acquisition plasma proteomics, benchmarking sample-preparation and data-analysis protocols to improve depth, reproducibility, and clinical readiness.