Trapped Ion Mobility Mass-Spectrometer (TIMS)

• Subject Area: Basic Research in Biology and Medicine
• Term: Funded in 2025
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 553171438

Genomic, transcriptomic and epigenomic analyses have substantially contributed to the mechanistic understanding of cancer. However, proteins are the most important functional molecules in cells. Technological advances in mass-spectrometry (MS) have recently enabled global, unbiased and functional analyses of this important class of molecules in clinical samples. Based on these developments, it is the key objective of this proposal to provide sufficient and suitable MS-instrumentation for functional proteomic analyses of pediatric and hematologic cancer. Specifically, we aim at studying the proteome landscape with the focus on uncovering targetable proteome changes, novel biomarkers, development of diagnostic methods for early detection, relapse and minimal residual disease for oncologic and hematologic diseases in children, adolescents and young adults. Among several formats of mass spectrometers, trapped ion mobility spectrometry (TIMS) is the most suitable because of its small size, low voltage requirements, and high efficiency of ion utilization. Ion accumulation prior to time of flight (TOF) overcome traditional limitations, allows greater sensitivity and speed to be leveraged in proteomic workflows. TIMS also effectively limits the amount of debris entering the instrument and making it very robust in daily operation. Further, a recently developed scan mode termed parallel accumulation - serial fragmentation (PASEF), which multiplies the sequencing speed without loss in sensitivity has pushed the TIMS devices to greater sensitivity even in data dependent acquisition scheme. Application to large sample cohorts and to investigate the proteome under sample limited conditions requires robustness, high reproducibility and data completeness, which makes data-independent acquisition (DIA) particularly attractive. The DIA-PASEF technology on a TIMS-instrument uses ion mobility separation to reduce signal interferences and increases sensitivity in proteomic experiments by covering the protein low dynamic range. These advances are key and allow for studying clinical samples when the amount of sample material is typically limited. DIA-PASEF also offers accurate multiplexed proteomics capabilities. We will apply a highly sensitive high-throughput technology that we have recently established and will focus on analyses of phosphoproteomes and workflows enabling the study of other post-translational modifications of clinical samples following antibody-based enrichments. It will thus be possible with this technology to disentangle functional relevance of sample or disease of interest. In addition, approximately 20% of the instrument time will be available to users of the Medical Faculty of Heidelberg University (MFHD) for proteome analyses in commissioned projects according to a core facility concept.

• DFG Programme: Major Research Instrumentation
• Major Instrumentation: Trapped Ion Mobility Massenspektrometer (TIMS)
• Instrumentation Group: 1700 Massenspektrometer
• Applicant Institution: Ruprecht-Karls-Universität Heidelberg
• Leader: Professor Andreas Eckhard Kulozik, Ph.D.