Trapped ion mobility-resolved mass spectrometry-based phosphoproteomics of Arbovirus infection

• Applicants: Professor Dr. Florian Meier-Rosar; Dr. Pietro Scaturro
• Subject Area: Analytical Chemistry ; Biochemistry
• Term: since 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 528559282

Mass spectrometry-based proteomics has become the method of choice to study virus-host interactions, and as witnessed also during the ongoing SARS-CoV-2 pandemic, enables the identification of novel cellular targets of RNA viruses and rationalizes the development of repurposed antiviral agents. Arboviruses have gained considerable public health relevance, due to their widespread diffusion and the lack of broad-spectrum antivirals for prophylactic or therapeutic use. The most clinically-relevant arboviral species include members of the Flaviviridae (such as Dengue virus or Zika virus), Alphaviridae (such as Chikungunya or Sindbis virus) and Bunyaviridae (such as LaCrosse virus or Rift Valley Fever virus) families, associated with high mortality and a wide spectrum of co-morbidities ranging from neurotropic to visceral diseases. Here, we aim to define the concerted host response to arboviral infections on the proteome and phosphoproteome levels across virus families. Building on our recent development of parallel accumulation – serial fragmentation (PASEF) acquisition modes on a trapped ion mobility (TIMS) mass spectrometer, we aim to extend the capabilities of mass spectrometry-based (phospho)-proteomics by ion mobility-enhanced data-independent acquisition (dia-PASEF). We will develop and optimize sample preparation and acquisition methods, leveraging the unique advantages of ion mobility mass-spectrometry, data-independent acquisition and high-throughput liquid chromatography. The increased analytical depth of these new high-throughput methods will be exploited to profile global perturbations on the host proteome and phosphoproteome by 17 individual viruses spanning three arbovirus families in a time-resolved manner. Identified host proteins and pathways will be integrated using stringent bioinformatics pipelines and prioritized targets will be further validated using orthogonal biochemical methods and functional genetic screens. Altogether, this study will shed light on unique and conserved arboviral targets, identifying critical host proteins with therapeutic or drug repurposing potential. Importantly, it will establish a novel high-throughput ion mobility phosphoproteomics platform, empowering a myriad of applications in biomedical research.

• DFG Programme: Research Grants