Metabolomics for Bioscience Research

全球对用于生化科学的基因组和蛋白质组工具的重大投资使我们对细胞功能的遗传基础和遗传变化对蛋白质组的影响的了解迅速增加。然而，下游对新陈代谢的影响仍然被严重低估，但非常重要，因为它们可以表现为能量产生、细胞维持、增殖和信号传递的变化。也正是在代谢组中，与外部环境发生了直接的接口。代谢组学的目的是提供从细胞到整个生物体的整个生物样本小分子成分的全面分析。全面的代谢组学可以作为一种发现工具来评估上游改变对遗传和蛋白质组表达的影响，以及环境输入对细胞代谢的影响。在牛津化学，我们最近开创了中枢能量代谢的代谢组学，它使用了离子交换色谱-质谱仪。虽然非常有效，但它只能用于生理离子和高极性代谢物，不能提供广泛的代谢组覆盖。此外，它还为医学和临床科学提供资金，并为此投入了大量资金。牛津大学生物科学的研究人员迫切需要一个专门的代谢组学平台，以专注于基础生物学、植物科学和生理学。例如，在申请人的植物科学研究中，代谢图谱将有助于研究植物与病原菌的分子关系和正常功能的共生关系，包括固氮菌之间的相互作用。还研究植物代谢网络的行为和功能，以提高作物产量和抗病能力。在生理学方面，代谢组学将用于研究酮代谢、饮食性能反应、肠道激素分泌和感染的代谢。在基础生物学和化学生物学中，代谢组学将在了解蔗糖信号机制、藻类对低氧的反应、氧化还原平衡的相互作用以及解释DNA修饰对细胞途径功能和人工DNA合成的影响的遗传学研究中发挥关键作用，以了解体内的核酸化学、开发治疗干预措施和了解表观遗传调节。我们建议收购一套最先进的离子迁移质谱学系统，并与超性能液相色谱(LC-IMS-MS/MS)联用。该平台使用反相色谱对低极性代谢物进行了极好的覆盖，包括重要的脂类和植物次生代谢物。离子迁移能力将增强新陈代谢组的覆盖面，并增加对化合物鉴定的信心。因此，该仪器将为代谢组范围的分析提供一个特殊的平台。此外，这将补充致力于生物科学研究的其他非代谢组学能力，使从基因组表达到代谢组覆盖的系统水平分析成为可能。拟议的仪器不会重叠，而是将与现有能力协同，使来自生物科学领域的当前和未来的BBSRC研究人员能够推进系统生物学、化学生物学以及生理和植物科学的知识前沿。新仪器将被整合到牛津大学化学系现有的质谱仪实验室(MS-SRF)中。它将是多用户的，使BBSRC资助的牛津和英国的研究小组能够拥有专用访问权限。该仪器将支持BBSRC一系列战略研究优先领域的研究项目，并将成为跨学科生物科学博士培训方案的一个综合设备，使其可供牛津布鲁克斯大学和钻石光源等其他地点的研究人员使用。

The significant global investment in genomic and proteomic tools for biochemical sciences has led to a rapid increase in our understanding of the genetic basis of cellular function and the influence of genetic changes on the proteome. However, downstream effects on metabolism remain significantly under-investigated but hugely important as they can manifest in changes to energy production, cell maintenance, proliferation and signalling. It is also in the metabolome that a direct interface with the external environment takes place. Metabolomics aims to provide comprehensive analysis of the entire small molecule component of biological samples from cells to whole organisms. Comprehensive metabolomics can be used as a discovery tool to assess the impact of upstream alterations to genetic and proteomic expression as well as the effects of environmental inputs on cellular metabolism. In Oxford Chemistry we have recently pioneered metabolomics of central energy metabolism which uses ion-exchange chromatography-mass spectrometry. Although very effective it can only be used for physiologically ionic and highly polar metabolites and does not give wide metabolome coverage. Furthermore it is funded for medical and clinical sciences and very heavily used for this. Researchers in the biosciences at Oxford desperately need a dedicated metabolomics platform to focus on fundamental biology, plant science and physiology. For example in the applicant's research in plant sciences metabolic profiling will benefit the investigation of plant-pathogen molecular relationships and normal functioning symbiotic relationships including nitrogen fixing bacteria interactions. Also studying the behaviour and functioning of plant metabolic networks to increase crop yield and resistance to disease. In physiology metabolomics will be used to study ketone metabolism, dietary performance response, hormone secretion by the gut and metabolism of infection. In fundamental biology and chemical biology metabolomics will play a key role in understanding mechanisms of sucrose signalling, algal responses to hypoxia, the interaction of redox balance and genetic studies interpreting the effects of DNA modifications on cellular pathway function and on artificial DNA synthesis to understand nucleic acid chemistry in vivo, develop therapeutic interventions and understand epigenetic regulation. We propose acquisition of a state-of-the-art Ion Mobility Mass Spectrometry system coupled to Ultra-Performance Liquid Chromatography (LC-IMS-MS/MS). This platform has excellent metabolite coverage of lower polarity metabolites including, importantly, lipids and plant secondary metabolites, using reversed phase chromatography. Ion-mobility capabilities will enhance metabolome coverage and increase confidence in compound identifications. The instrument will therefore provide an exceptional platform for metabolome-wide profiling. Furthermore this will complement other non-metabolomics capabilities dedicated to research in the biosciences enabling systems level analyses from genome expression to metabolome coverage. The proposed instrument does not overlap, but instead will be synergistic with existing capabilities enabling current and future BBSRC researchers from across the biosciences to move forward the frontiers of knowledge in systems biology, chemical biology, and the physiological and plant sciences. The new instrument will be integrated into the existing mass spectrometry laboratories (MS-SRF) in the Department of Chemistry in Oxford. It will be multi-user, enabling BBSRC-funded research groups in Oxford and the UK, to have dedicated access. The instrument will support research projects spanning a range of BBSRC strategic research priority areas, and will become an integrated piece of equipment in the Interdisciplinary Biosciences Doctoral Training Programme, making it available to researchers at other sites including Oxford Brookes University and the Diamond Light Source.