LC-MS system for proteomics

• Subject Area: Biological Chemistry and Food Chemistry
• Term: Funded in 2025
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 574898102

Mass spectrometry-based proteomics is nowadays an essential technology in chemical-biology and (cellular) molecular biology research. At the Faculty of Biology and the University of Duisburg-Essen (UDE), this methodology is made available to interested users from research via the Analytics Core Facility Essen (ACE). To this end, the ACE hosts two mass spectrometers for proteomics that are operated in parallel. However, the older of the two MS systems neither meets the current state of the art nor can it still be operated in an economic fashion due to frequent malfunctions and necessary maintenance. Therefore, this application aims at a replacement of this MS system with a modern, high-performance MS system. The new system should consist of a state-of-the-art mass spectrometer, i.e., an MS device with high resolution, sensitivity, mass accuracy, and scan rates, as well as a compatible ultra-high-performance liquid chromatography system (UHPLC). Since today’s MS systems also generate very large amounts of data during measurement and data analysis, which also need to be stored long-term, we are also applying for file server expansions. These will be integrated into the existing Ceph cluster of the Faculty of Biology, significantly expanding its storage capacity. Finally, to efficiently process the large data volumes, we will also procure a high-performance data analysis workstation (192 threads, 768 GB RAM, at least 16 TB of fast M.2 storage). The requested MS system will primarily be used for label-free MS applications (label-free comparison of differently treated proteomes) in DDA (data-dependent acquisition) or DIA (data-independent acquisition, e.g., for comparative proteomic analyses) modes. Additionally, it is planned to use the system for structural elucidation and interaction studies (main applications here will be cross-linking MS and proximity-dependent biotinylation). The new MS system will be integrated into the ACE and thus making it available to all interested users at the Faculty of Biology and UDE.

• DFG Programme: Major Research Instrumentation
• Major Instrumentation: Proteomik-fähiges LC-MS-System
• Instrumentation Group: 1700 Massenspektrometer
• Applicant Institution: Universität Duisburg-Essen
• Leader: Professor Dr. Markus Kaiser