Metabolomics for Bioscience Research

全球对用于生物化学科学的基因组学和蛋白质组学工具的重大投资，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理解迅速增加。然而，对代谢的下游影响仍未得到充分研究，但非常重要，因为它们可以在能量产生、细胞维持、增殖和信号传导的变化中表现出来。在代谢组中，也发生了与外部环境的直接界面。代谢组学旨在提供从细胞到整个生物体的生物样品的整个小分子成分的综合分析。综合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学表达的影响，以及环境输入对细胞代谢的影响。在牛津化学，我们最近开创了使用离子交换色谱-质谱法的中心能量代谢代谢组学。虽然非常有效，但它只能用于生理离子和高极性代谢物，并没有给予广泛的代谢物覆盖。此外，它还为医学和临床科学提供资金，并被大量用于此。牛津大学的生物科学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，代谢分析将有利于研究植物与病原体的分子关系和正常功能的共生关系，包括固氮细菌的相互作用。同时研究植物代谢网络的行为和功能，以提高作物产量和抗病性。在生理方面，代谢组学将用于研究酮类代谢、饲料生产性能反应、肠道激素分泌和感染代谢。在基础生物学和化学生物学中，代谢组学将在理解蔗糖信号传导机制、藻类对缺氧的反应、氧化还原平衡的相互作用和基因研究中发挥关键作用，解释DNA修饰对细胞通路功能和人工DNA合成的影响，以了解体内核酸化学、开发治疗干预和理解表观遗传调控。我们建议收购最先进的离子迁移质谱联用超高效液相色谱（LC-IMS-MS/MS）系统。该平台具有良好的低极性代谢物覆盖范围，包括脂质和植物次生代谢物，使用反相色谱法。离子迁移能力将提高代谢组覆盖范围，增加化合物鉴定的信心。因此，该仪器将为全代谢组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级分析成为可能。拟议的仪器不会重叠，而是将与现有的能力协同，使来自生物科学领域的当前和未来的BBSRC研究人员能够在系统生物学、化学生物学、生理和植物科学的知识前沿前进。新仪器将被整合到牛津大学化学系现有的质谱实验室（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有专门的访问权限。该仪器将支持跨越一系列BBSRC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计划的集成设备，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.