MS instrument for ultra-high resolution & sensitivity quantitative proteomics down to single cells

• Subject Area: Basic Research in Biology and Medicine
• Term: Funded in 2025
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 554068498

In the frame of Prof. Thedieck’s recruitment as Department Head for Metabolism, Senescence and Autophagy at the Research Center One Health Ruhr (RCOH) and University Hospital Essen, we apply in two linked proposals for two high resolution mass spectrometers for integrated proteo-metabolomics. (1) One instrument is for quantitative proteomics and PTM analysis with ultrahigh resolution and sensitivity in enriched samples, small cell populations and single cells. (2) The other instrument enables ultra-fast applications for targeted metabolite quantification and non-targeted metabolomics. Our projects intertwine MS-based proteomics and metabolomics to gain an integrated understanding of metabolic signaling. Our research centers on the kinase network converging on mTOR (mechanistic target of rapamycin), a central controller of cell growth and metabolism. mTOR drives age-related diseases, including cancer, neurodegeneration and metabolic disorders, and rare congenital conditions such as Tuberous Sclerosis Complex (TSC) and other mTORopathies. We study metabolic regulation through mTOR by means of biochemistry, proteomics, metabolomics, cell biology and systems approaches. Interactome studies reveal new mTOR regulators, phosphoproteomics discover new downstream effectors, and interplay with other signaling routes comprises protein methylation or acetylation. Our metabolomics studies encompass mTOR-driven metabolic processes including amino acid and central metabolism. In patient-centered studies, we investigate proteome and metabolic alterations in cell and animal models and patient cohorts. A major focus, funded by an ERC Advanced Grant, is the regulation of the mTOR network by stress granule proteins, stress-induced protein-RNA complexes, under non-stress metabolic conditions. Funded by the RCOH and EU projects, we investigate interference of environmental metabolic disruptors with mTOR signaling and cancer therapy. The present proposal is for instrument (1), an ultra-high resolution and sensitivity mass spectrometer for quantitative proteomics and PTM analysis in enriched samples, small cell populations and single cells. The MS infrastructure needs to meet the following requirements: ultra-high mass resolution, accuracy, sensitivity and flexibility for high-end applications in DDA and DIA mode, including absolute and system-wide quantification of proteins and PTMs (phosphorylation, methylation, acetylation, etc). Systems-wide quantitative high-resolution proteome analysis comprises metabolic label methods, chemical derivatization, and label-free quantification. LC-MS/MS applications require a nano-source and nano-UPLC, and the processing of small scale samples requires a robotic platform for nanoliter volumes. Large scale data analysis demands a server and software for proteomics data processing. This infrastructure is a mandatory prerequisite for our research, and none of it is currently available at the University Hospital Essen.

• DFG Programme: Major Research Instrumentation
• Major Instrumentation: Massenspektrometer für quantitative Proteomik mit ultrahoher Auflösung & Empfindlichkeit
• Instrumentation Group: 1700 Massenspektrometer
• Applicant Institution: Universität Duisburg-Essen
• Leader: Professorin Dr. Kathrin Thedieck