2020BBSRC-NSF/BIO: Linking Mass Spectrometry Computational Ecosystems to Enhance Biological Insights of Publicly-Available Data

2020BBSRC-NSF/BIO：连接质谱计算生态系统以增强对公开数据的生物学见解

• 批准号: BB/W002345/1
• 负责人: Warwick Dunn
• 金额: $ 81.42万
• 依托单位: University of Liverpool
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2022
• 资助国家: 英国
• 起止时间: 2022 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FW002345%2F1
• 关键词: 2020BBSRC; NSF; BIO; Linking; Mass

All biological systems are composed of important chemicals which help the systems grow, respond to the environment and communicate. The genome is composed of DNA which carries genetic information required for reproduction, growth and development and whose composition remains relatively static throughout a lifetime. The metabolome is composed of metabolites derived from food (e.g. sugars) and the environment (e.g. prescribed drugs) and whose composition is dynamic in relation to which metabolites are present and at what concentration. The scientific research community studies metabolites to understand how we metabolise food and drugs, how we respond dynamically to the environment and also to identify metabolites which are important for a biological system to function. Many of these investigations are discovery studies which apply a scientific technique called metabolomics that can detect hundreds or low thousands of different metabolites in a biological sample. These studies discover new metabolites which then have to be analysed to understand their chemical structure which is essential for biological interpretation. Many metabolomic studies performed across the world are being released to the scientific community so that these data can be re-used and re-analysed to derive new biological information. The data from these studies are stored in data repositories and two examples of these are MetaboLights in the UK and GNPS in the USA. However, many of the metabolites detected and reported in these data repositories do not have a chemical identity assigned to them. Therefore there is an essential requirement to assign chemical structures to as many metabolites as is possible so that the data can be reused and biological information derived from the data. The planned project will further develop and apply computational approaches to all data deposited in MetaboLights and GNPS. This will allow more metabolites to be assigned a chemical identity and for the confidence that the correct structure has been assigned to be increased. When completed, the volume and quality of biological information available in the deposited datasets will be much greater and will allow new research questions to be asked and answered without the need to collect new data.

所有的生物系统都是由重要的化学物质组成的，这些化学物质帮助系统生长，对环境做出反应和交流。基因组由DNA组成，DNA携带生殖、生长和发育所需的遗传信息，其组成在一生中保持相对稳定。代谢物组由来自食物（如糖）和环境（如处方药）的代谢物组成，其组成与代谢物的存在和浓度有关。科学研究界研究代谢物，以了解我们如何代谢食物和药物，我们如何动态地响应环境，并确定对生物系统功能重要的代谢物。这些研究中有许多是发现性研究，它们应用了一种称为代谢组学的科学技术，可以检测生物样品中数百种或数千种不同的代谢物。这些研究发现了新的代谢物，然后必须对其进行分析，以了解其化学结构，这对于生物学解释至关重要。世界各地进行的许多代谢组学研究正在向科学界公布，以便这些数据可以重新使用和重新分析，以获得新的生物信息。这些研究的数据存储在数据库中，其中两个例子是英国的MetaboLights和美国的GNPS。然而，在这些数据储存库中检测和报告的许多代谢物没有指定化学身份。因此，有一个基本的要求，分配化学结构，尽可能多的代谢物是可能的，使数据可以重复使用和生物信息来源于数据。计划中的项目将进一步开发计算方法，并将其应用于MetaboLights和广东核电站储存的所有数据。这将允许更多的代谢物被分配化学身份，并增加已分配正确结构的置信度。完成后，存放的数据集中可用的生物信息的数量和质量将大大增加，并将允许提出和回答新的研究问题，而无需收集新的数据。

项目成果

Critical assessment of chromatographic metadata in publicly available metabolomics data repositories.

• DOI: 10.1007/s11306-022-01956-x
• 发表时间: 2022-11-27
• 期刊: Metabolomics : Official journal of the Metabolomic Society

Providing metabolomics education and training: pedagogy and considerations.

• DOI: 10.1007/s11306-022-01957-w
• 发表时间: 2022-12-13
• 期刊: Metabolomics : Official journal of the Metabolomic Society

Quality assurance and quality control reporting in untargeted metabolic phenotyping: mQACC recommendations for analytical quality management.

• DOI: 10.1007/s11306-022-01926-3
• 发表时间: 2022-08-27
• 期刊: METABOLOMICS
• 影响因子: 3.6
• 作者: Kirwan, Jennifer A.;Gika, Helen;Beger, Richard D.;Bearden, Dan;Dunn, Warwick B.;Goodacre, Royston;Theodoridis, Georgios;Witting, Michael;Yu, Li-Rong;Wilson, Ian D.
• 通讯作者: Wilson, Ian D.

Unlocking the secrets of the microbiome: exploring the dynamic microbial interplay with humans through metabolomics and their manipulation for synthetic biology applications.

• DOI: 10.1042/bcj20210534
• 发表时间: 2023-06-28
• 期刊: BIOCHEMICAL JOURNAL
• 影响因子: 4.1
• 作者: Muhamadali, Howbeer;Winder, Catherine L.;Dunn, Warwick B.;Goodacre, Royston
• 通讯作者: Goodacre, Royston

Single sample pathway analysis in metabolomics: performance evaluation and application.

• DOI: 10.1186/s12859-022-05005-1
• 发表时间: 2022-11-14
• 期刊: BMC BIOINFORMATICS
• 影响因子: 3
• 作者: Wieder, Cecilia;Lai, Rachel P. J.;Ebbels, Timothy M. D.
• 通讯作者: Ebbels, Timothy M. D.