LC-MS/MS for Proteome Research

• Subject Area: Biological Chemistry and Food Chemistry
• Term: Funded in 2020
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 452419311

The applicant proposes to acquire a high-resolution mass spectrometer and associated high-performance chromatography system for the large-scale qualitative and quantitative analysis of proteins. More specifically, the instrument should initially support two major projects in the laboratory of the applicant.1. The crop proteome atlas (CPA): As part of the Collaborative Research Center SFB924 (Molecular mechanisms regulating yield and yield stability in plants), the applicant plans to generate a crop proteome atlas that i) contains 20 ‘chapters’ covering the crop species that collectively represent ~80% of the world’s plant-based food production according to the Food and Agriculture Organization of the United Nations; ii) incorporates 10 further chapters on crops that are more important to regional nutritional landscapes and iii) additional thematic chapters on biotic and abiotic stress experiments in crop plants. The main aims of the project are: 1) to provide high-quality protein level data to the plant research community for a diverse but economically important set of plants; 2) to provide the computational tools via ProteomicsDB that allow sharing and mining of the CPA; 3) to demonstrate the utility of this molecular resource by pertinent examples from crop research including questions related to yield, stress or basic biological mechanisms. And 4) to demonstrate that applying mass spectrometry-based proteomics to the plant sciences can reduce the lack of research reagents (such as antibodies).2. Exploiting the Tumor Proteome Activity Status for Future Cancer Therapies (TOPAS): As part of an ERC Advanced Grant, the applicants plan to establish the TOPAS of individual cancer patients as an evidence-based criterion for treatment recommendations by molecular tumor boards. To achieve this, the applicant will i) measure the response of the phosphoproteome of 10 model cancer cell lines to >100 current cancer drug; ii) profile the phosphoproteomes of cancer patients and iii) build computational tools to integrate the experimental data. The research program is guided by three cross-disciplinary objectives: 1) to show that modulating the TOPAS of cancer models by kinase inhibitors functionalizes the phosphoproteome and reveals the cellular mechanisms of action of these important medicines; 2) to develop and validate drug-, protein- and pathway-centric TOPAS scores able to make treatment suggestions based on the proteomes and phosphoproteomes of cancer cell lines and patients and 3) to demonstrate that phosphoproteomic analysis and TOPAS scoring of sarcoma patients complements information from genomic profiling and aids in decision making by molecular tumor boards.

• DFG Programme: Major Research Instrumentation
• Major Instrumentation: LC-MS/MS für die Proteomforschung
• Instrumentation Group: 1700 Massenspektrometer
• Applicant Institution: Technische Universität München (TUM)
• Leader: Professor Dr. Bernhard Küster