基于元数据的源注释增强非靶向代谢组学。
Enhancing untargeted metabolomics using metadata-based source annotation.
机构信息
Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
出版信息
Nat Biotechnol. 2022 Dec;40(12):1774-1779. doi: 10.1038/s41587-022-01368-1. Epub 2022 Jul 7.
Abstract
Human untargeted metabolomics studies annotate only ~10% of molecular features. We introduce reference-data-driven analysis to match metabolomics tandem mass spectrometry (MS/MS) data against metadata-annotated source data as a pseudo-MS/MS reference library. Applying this approach to food source data, we show that it increases MS/MS spectral usage 5.1-fold over conventional structural MS/MS library matches and allows empirical assessment of dietary patterns from untargeted data.
摘要
人类非靶向代谢组学研究仅能注释约 10%的分子特征。我们引入参考数据驱动的分析方法，将代谢组学串联质谱 (MS/MS) 数据与元数据注释的源数据进行匹配，作为伪 MS/MS 参考库。将这种方法应用于食物源数据，我们发现它使 MS/MS 光谱的使用比传统的结构 MS/MS 库匹配增加了 5.1 倍，并允许从非靶向数据中进行经验性的饮食模式评估。
相似文献
1
Enhancing untargeted metabolomics using metadata-based source annotation.基于元数据的源注释增强非靶向代谢组学。
Nat Biotechnol. 2022 Dec;40(12):1774-1779. doi: 10.1038/s41587-022-01368-1. Epub 2022 Jul 7.
2
Autonomous METLIN-Guided In-source Fragment Annotation for Untargeted Metabolomics.自主 METLIN 引导的内源性碎片注释用于非靶向代谢组学。
Anal Chem. 2019 Mar 5;91(5):3246-3253. doi: 10.1021/acs.analchem.8b03126. Epub 2019 Feb 11.
3
Open access repository-scale propagated nearest neighbor suspect spectral library for untargeted metabolomics.开放获取存储库规模传播的近邻可疑光谱库，用于无目标代谢组学。
Nat Commun. 2023 Dec 20;14(1):8488. doi: 10.1038/s41467-023-44035-y.
4
A Structure-Guided Molecular Network Strategy for Global Untargeted Metabolomics Data Annotation.基于结构导向的分子网络策略进行全局非靶向代谢组学数据注释。
Anal Chem. 2023 Aug 8;95(31):11603-11612. doi: 10.1021/acs.analchem.3c00849. Epub 2023 Jul 26.
5
MARS: A Multipurpose Software for Untargeted LC-MS-Based Metabolomics and Exposomics.MARS：一种基于非靶向 LC-MS 的代谢组学和暴露组学的多功能软件。
Anal Chem. 2024 Jan 30;96(4):1468-1477. doi: 10.1021/acs.analchem.3c03620. Epub 2024 Jan 18.
6
Incorporating In-Source Fragment Information Improves Metabolite Identification Accuracy in Untargeted LC-MS Data Sets.在源碎片信息中加入可提高非靶向 LC-MS 数据集代谢物鉴定准确性。
J Proteome Res. 2019 Feb 1;18(2):791-796. doi: 10.1021/acs.jproteome.8b00601. Epub 2018 Oct 18.
7
[A novel method for efficient screening and annotation of important pathway-associated metabolites based on the modified metabolome and probe molecules].一种基于改良代谢组和探针分子的重要通路相关代谢物高效筛选与注释新方法
Se Pu. 2022 Sep;40(9):788-796. doi: 10.3724/SP.J.1123.2022.03025.
8
Retrieving and Utilizing Hypothetical Neutral Losses from Tandem Mass Spectra for Spectral Similarity Analysis and Unknown Metabolite Annotation.从串联质谱中检索和利用假设中性损失进行光谱相似性分析和未知代谢物注释。
Anal Chem. 2020 Nov 3;92(21):14476-14483. doi: 10.1021/acs.analchem.0c02521. Epub 2020 Oct 19.
9
Customized Consensus Spectral Library Building for Untargeted Quantitative Metabolomics Analysis with Data Independent Acquisition Mass Spectrometry and MetaboDIA Workflow.基于数据非依赖采集质谱和 MetaboDIA 工作流程的靶向定量代谢组学分析的定制共识谱库构建。
Anal Chem. 2017 May 2;89(9):4897-4906. doi: 10.1021/acs.analchem.6b05006. Epub 2017 Apr 18.
10
Enhancing Metabolome Annotation by Electron Impact Excitation of Ions from Organics-Molecular Networking.通过有机物分子网络中离子的电子冲击激发增强代谢组注释。
Anal Chem. 2024 Jan 30;96(4):1444-1453. doi: 10.1021/acs.analchem.3c03443. Epub 2024 Jan 19.
引用本文的文献
1
Longitudinal Fragment Profiles Based on Multi-Collision Energy Tandem Mass Spectra Improve the Accuracy of Metabolite Identification in Untargeted Metabolomics.基于多碰撞能量串联质谱的纵向碎片谱图提高了非靶向代谢组学中代谢物鉴定的准确性。
Anal Chem. 2025 Jul 15;97(27):14349-14360. doi: 10.1021/acs.analchem.5c01414. Epub 2025 Jul 1.
2
From stool to sequence: decoding the human diet with FoodSeq.从粪便到序列：用FoodSeq解码人类饮食。
mSystems. 2025 Jul 22;10(7):e0015825. doi: 10.1128/msystems.00158-25. Epub 2025 Jun 23.
3
The microbiome diversifies long- to short-chain fatty acid-derived N-acyl lipids.微生物群落使长链至短链脂肪酸衍生的N-酰基脂质多样化。
Cell. 2025 Jun 9. doi: 10.1016/j.cell.2025.05.015.
4
Discovering organic reactions with a machine-learning-powered deciphering of tera-scale mass spectrometry data.通过机器学习驱动的太赫兹级质谱数据解析发现有机反应。
Nat Commun. 2025 Mar 16;16(1):2587. doi: 10.1038/s41467-025-56905-8.
5
The International Space Station has a unique and extreme microbial and chemical environment driven by use patterns.国际空间站因使用模式而拥有独特且极端的微生物和化学环境。
Cell. 2025 Apr 3;188(7):2022-2041.e23. doi: 10.1016/j.cell.2025.01.039. Epub 2025 Feb 27.
6
Human Untargeted Metabolomics in High-Throughput Gut Microbiome Research: Ethanol vs Methanol.高通量肠道微生物组研究中的人类非靶向代谢组学：乙醇与甲醇
Anal Chem. 2025 Mar 11;97(9):4945-4953. doi: 10.1021/acs.analchem.4c05142. Epub 2025 Feb 27.
7
To Impute or Not To Impute in Untargeted Metabolomics─That is the Compositional Question.非靶向代谢组学中是否进行插补——这就是成分问题。
J Am Soc Mass Spectrom. 2025 Apr 2;36(4):742-759. doi: 10.1021/jasms.4c00434. Epub 2025 Feb 25.
8
ROASMI: accelerating small molecule identification by repurposing retention data.ROASMI：通过重新利用保留数据加速小分子鉴定
J Cheminform. 2025 Feb 14;17(1):20. doi: 10.1186/s13321-025-00968-8.
9
Introducing "Identification Probability" for Automated and Transferable Assessment of Metabolite Identification Confidence in Metabolomics and Related Studies.介绍用于代谢组学及相关研究中代谢物鉴定置信度的自动化和可转移评估的“鉴定概率”。
Anal Chem. 2025 Jan 14;97(1):1-11. doi: 10.1021/acs.analchem.4c04060. Epub 2024 Dec 19.
10
Effective data visualization strategies in untargeted metabolomics.非靶向代谢组学中的有效数据可视化策略
Nat Prod Rep. 2024 Dec 2. doi: 10.1039/d4np00039k.
本文引用的文献
1
foodMASST a mass spectrometry search tool for foods and beverages.FoodMASST：一种用于食品和饮料的质谱搜索工具。
NPJ Sci Food. 2022 Apr 20;6(1):22. doi: 10.1038/s41538-022-00137-3.
2
Chemically informed analyses of metabolomics mass spectrometry data with Qemistree.使用Qemistree对代谢组学质谱数据进行化学信息分析。
Nat Chem Biol. 2021 Feb;17(2):146-151. doi: 10.1038/s41589-020-00677-3. Epub 2020 Nov 16.
3
All of gene expression (AOE): An integrated index for public gene expression databases.所有基因表达 (AOE)：公共基因表达数据库的综合指标。
PLoS One. 2020 Jan 24;15(1):e0227076. doi: 10.1371/journal.pone.0227076. eCollection 2020.
4
MetaboLights: a resource evolving in response to the needs of its scientific community.代谢组学文献共享资源库（MetaboLights）：一个响应其科研群体需求而不断发展的资源库。
Nucleic Acids Res. 2020 Jan 8;48(D1):D440-D444. doi: 10.1093/nar/gkz1019.
5
Bile acids targeted metabolomics and medication classification data in the ADNI1 and ADNIGO/2 cohorts.ADNI1 和 ADNIGO/2 队列中的胆汁酸靶向代谢组学和药物分类数据。
Sci Data. 2019 Oct 17;6(1):212. doi: 10.1038/s41597-019-0181-8.
6
Perspective: Dietary Biomarkers of Intake and Exposure-Exploration with Omics Approaches.观点：基于组学方法的饮食生物标志物摄入与暴露研究
Adv Nutr. 2020 Mar 1;11(2):200-215. doi: 10.1093/advances/nmz075.
7
Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics.通过将代谢组数据库与质谱化学信息学相结合来鉴定代谢物。
Nat Methods. 2018 Jan;15(1):53-56. doi: 10.1038/nmeth.4512. Epub 2017 Nov 27.
8
Significance estimation for large scale metabolomics annotations by spectral matching.基于谱图匹配的大规模代谢组学注释的显著性估计。
Nat Commun. 2017 Nov 14;8(1):1494. doi: 10.1038/s41467-017-01318-5.
9
RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes.RefEx，一个参考基因表达数据集，作为一个网络工具，用于基因的功能分析。
Sci Data. 2017 Aug 29;4:170105. doi: 10.1038/sdata.2017.105.
10
Lifestyle chemistries from phones for individual profiling.用于个人剖析的手机生活方式化学特征。
Proc Natl Acad Sci U S A. 2016 Nov 29;113(48):E7645-E7654. doi: 10.1073/pnas.1610019113. Epub 2016 Nov 14.
Zotero 插件