Hybrid ESI/MALDI mass spectrometer with trapped ion mobility spectrometry

该申请旨在为申请人在转化/临床蛋白质组学和质谱成像方面的研究项目提供足够的仪器。翻译/临床蛋白质组学部门采用液相色谱（LC）电喷雾电离（ESI）串联质谱（MS/MS），而质谱成像部门采用基质辅助激光解吸/电离（MALDI）。为了促进这两种方法的协同作用，提高仪器的使用效率，优化空间足迹和成本效益，提出了一种ESI/MALDI混合系统。申请者包括一个已建立的和一个初级研究小组，以及一个蛋白质组学核心设施。作为外科病理研究所翻译蛋白质组学的Heisenberg教授，首席申请人是培养高通量临床蛋白质组学的理想人选。选定的研究项目旨在描述实体瘤的蛋白质组生物学特征，以进行风险分层和病理机制理解。研究项目还包括血清蛋白质组分析。提供了概念验证数据。临床标本的稀缺和研究大患者队列的需要需要敏感的蛋白质组学和快速的通量。MALDI成像可以在接近单细胞分辨率的情况下更好地了解肿瘤病理生物学中的组织异质性。MALDI成像通过直接从患者组织中提供空间蛋白质组生物学的见解，无缝集成到临床蛋白质组学研究中。初级研究小组“MALDI Imaging”将研究高度侵袭性实体肿瘤的空间分解分子过程。这包括表征肿瘤内部异质性，揭示肿瘤内部的病理生物学过程和肿瘤微环境，以及用于诊断和预后患者分层的空间分子标记的鉴定。空间组学分析将包括小分子成像，如代谢物、脂质、药物和药物代谢物。对于这些小分子，MALDI成像允许无标签，多路空间分辨测量。核心设施使蛋白质组学能够进入更广泛的科学界，重点是临床科学家。为了成功完成转化/临床蛋白质组学的研究计划，包括空间多组学，需要最先进的质谱分析，并具有以下主要特点：•混合系统覆盖LC-ESI-MS/MS和MALDI-MS•捕获离子迁移谱法（TIMS）用于改善原位MALDI成像•平行积累序列碎片（PASEF）用于从稀缺临床样品中有效利用离子•快速采集速度用于提高大型临床样品队列的通量；•快速激光频率和高空间分辨率的MALDI成像•真空MALDI，以建立在既定的研究计划。

The application aims to provide adequate instrumentation for the applicants’ research program in translational/clinical proteomics and in mass spectrometry imaging. The translational/clinical proteomics arm employs liquid chromatography (LC) electrospray ionization (ESI) tandem mass spectrometry (MS/MS) while the mass spectrometry imaging arm employs matrix assisted laser desorption/ionization (MALDI). In order to foster synergies of the two approaches as well as for efficient instrument usage and to optimize spatial footprint and cost effectiveness, a hybrid ESI/MALDI system is proposed. The applicants include an established and a junior research group as well as a proteomic core facility. As Heisenberg Professor for Translational Proteomics at the Institute of Surgical Pathology, the lead applicant is ideally positioned to foster high-throughput clinical proteomics. Selected research projects aim to characterize the proteome biology of solid tumors for risk stratification and pathomechanistic understanding. Research projects also include serum proteome profiling. Proof-of-concept data is provided. The scarcity of clinical specimens and the need to study large patient cohorts necessitate sensitive proteomics and fast throughput. MALDI imaging serves to better understand tissue heterogeneity in tumor pathobiology at close to single-cell resolution. MALDI imaging seamlessly integrates into clinical proteomics studies by providing insights into spatial proteome biology directly from patient tissues. The junior research group ‘MALDI Imaging’ will investigate spatially resolved molecular processes in highly aggressive solid tumors. This includes characterization of intra-tumor heterogeneity, unraveling pathobiological processes inside the tumor and tumor microenvironment as well as the identification of spatio-molecular markers for diagnostic and prognostic patient stratification. Spatial omics analyses will include imaging of small molecules such as metabolites, lipids, drugs, and drug metabolites. For these small molecules, MALDI imaging allows label-free, multiplexed spatially resolved measurements. The Core Facility makes proteomics accessible to the wider scientific community with a focus on clinical scientists. To successfully accomplish the research programme in translational/clinical proteomics, including spatial multi-omics, state-of-the-art mass spectrometry is required with the following key features: • Hybrid system to cover LC-ESI-MS/MS and MALDI-MS • Trapped Ion Mobility Spectrometry (TIMS) for improved in situ MALDI imaging • Parallel Accumulation Serial Fragmentation (PASEF) for efficient ion usage from scarce clinical samples •Fast acquisition speed for improved throughput of large clinical sample cohorts, achieved by running shorter gradients while maintaining high proteome coverage • Fast laser frequency and high spatial resolution for MALDI imaging • Vacuum MALDI in order to build on the established research program.