TOCCATA：一个定制的碳全相关谱 NMR 代谢组学数据库。
TOCCATA: a customized carbon total correlation spectroscopy NMR metabolomics database.
机构信息
Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, United States.
出版信息
Anal Chem. 2012 Nov 6;84(21):9395-401. doi: 10.1021/ac302197e. Epub 2012 Oct 11.
Abstract
A customized metabolomics NMR database, TOCCATA, is introduced, which uses (13)C chemical shift information for the reliable identification of metabolites, their spin systems, and isomeric states. TOCCATA, whose information was derived from the BMRB and HMDB databases and the literature, currently contains 463 compounds and 801 spin systems, and it can be used through a publicly accessible web server. TOCCATA allows the identification of metabolites in the submillimolar concentration range from (13)C-(13)C total correlation spectroscopy experiments of complex mixtures, which is demonstrated for an Escherichia coli cell lysate, a carbohydrate mixture, and an amino acid mixture, all of which were uniformly (13)C-labeled.
摘要
引入了一个定制的代谢组学 NMR 数据库 TOCCATA，它利用 (13)C 化学位移信息来可靠地鉴定代谢物、它们的自旋系统和同分异构体状态。TOCCATA 的信息来自 BMRB 和 HMDB 数据库以及文献，目前包含 463 种化合物和 801 个自旋系统，可通过公共访问的网络服务器使用。TOCCATA 允许从复杂混合物的 (13)C-(13)C 全相关光谱实验中鉴定亚毫摩尔浓度范围内的代谢物，这在大肠杆菌细胞裂解物、碳水化合物混合物和氨基酸混合物的实验中得到了证明，所有这些混合物都进行了均匀的 (13)C 标记。
相似文献
1
TOCCATA: a customized carbon total correlation spectroscopy NMR metabolomics database.TOCCATA：一个定制的碳全相关谱 NMR 代谢组学数据库。
Anal Chem. 2012 Nov 6;84(21):9395-401. doi: 10.1021/ac302197e. Epub 2012 Oct 11.
2
Customized metabolomics database for the analysis of NMR ¹H-¹H TOCSY and ¹³C-¹H HSQC-TOCSY spectra of complex mixtures.用于分析复杂混合物的核磁共振¹H-¹H TOCSY和¹³C-¹H HSQC-TOCSY谱的定制代谢组学数据库。
Anal Chem. 2014 Jun 3;86(11):5494-501. doi: 10.1021/ac500979g. Epub 2014 May 20.
3
Unified and isomer-specific NMR metabolomics database for the accurate analysis of (13)C-(1)H HSQC spectra.用于精确分析(13)C-(1)H HSQC谱的统一且异构体特异性的核磁共振代谢组学数据库。
ACS Chem Biol. 2015 Feb 20;10(2):452-9. doi: 10.1021/cb5006382. Epub 2014 Nov 5.
4
Accurate and Efficient Determination of Unknown Metabolites in Metabolomics by NMR-Based Molecular Motif Identification.基于 NMR 分子基元识别的代谢组学中未知代谢物的准确高效测定。
Anal Chem. 2019 Dec 17;91(24):15686-15693. doi: 10.1021/acs.analchem.9b03849. Epub 2019 Dec 3.
5
Accurate Identification of Unknown and Known Metabolic Mixture Components by Combining 3D NMR with Fourier Transform Ion Cyclotron Resonance Tandem Mass Spectrometry.通过结合 3D NMR 和傅里叶变换离子回旋共振串联质谱技术准确鉴定未知和已知代谢混合物成分。
J Proteome Res. 2017 Oct 6;16(10):3774-3786. doi: 10.1021/acs.jproteome.7b00457. Epub 2017 Sep 1.
6
Metabolomics beyond spectroscopic databases: a combined MS/NMR strategy for the rapid identification of new metabolites in complex mixtures.超越光谱数据库的代谢组学：一种用于快速鉴定复杂混合物中新代谢物的质谱/核磁共振联用策略。
Anal Chem. 2015 Apr 7;87(7):3864-70. doi: 10.1021/ac504633z. Epub 2015 Mar 12.
7
MetaboHunter: an automatic approach for identification of metabolites from 1H-NMR spectra of complex mixtures.MetaboHunter：一种从复杂混合物的 1H-NMR 光谱中自动识别代谢物的方法。
BMC Bioinformatics. 2011 Oct 14;12:400. doi: 10.1186/1471-2105-12-400.
8
Web server based complex mixture analysis by NMR.基于网络服务器的核磁共振复杂混合物分析
Anal Chem. 2008 May 15;80(10):3606-11. doi: 10.1021/ac702530t. Epub 2008 Apr 19.
9
COLMARppm: A Web Server Tool for the Accurate and Rapid Prediction of H and C NMR Chemical Shifts of Organic Molecules and Metabolites.COLMARppm：一个用于准确快速预测有机分子和代谢物的 H 和 C NMR 化学位移的网络服务器工具。
Anal Chem. 2024 Jan 16;96(2):701-709. doi: 10.1021/acs.analchem.3c03677. Epub 2023 Dec 29.
10
Comprehensive Metabolite Identification Strategy Using Multiple Two-Dimensional NMR Spectra of a Complex Mixture Implemented in the COLMARm Web Server.综合代谢物鉴定策略：在 COLMARm 网络服务器中使用复杂混合物的多个二维 NMR 图谱实现。
Anal Chem. 2016 Dec 20;88(24):12411-12418. doi: 10.1021/acs.analchem.6b03724. Epub 2016 Dec 6.
引用本文的文献
1
PyINETA: Open-Source Platform for INADEQUATE-JRES Integration in NMR Metabolomics.PyINETA：核磁共振代谢组学中用于INADEQUATE-JRES集成的开源平台。
Anal Chem. 2024 Dec 3;96(48):19029-19037. doi: 10.1021/acs.analchem.4c03966. Epub 2024 Nov 19.
2
Problems, principles and progress in computational annotation of NMR metabolomics data.计算注释 NMR 代谢组学数据中的问题、原则和进展。
Metabolomics. 2022 Dec 5;18(12):102. doi: 10.1007/s11306-022-01962-z.
3
NMR-Based Approaches in the Study of Foods.基于 NMR 的食品研究方法。
Molecules. 2022 Nov 15;27(22):7906. doi: 10.3390/molecules27227906.
4
Leveraging the HMBC to Facilitate Metabolite Identification.利用 HMBC 促进代谢产物鉴定。
Anal Chem. 2022 Nov 29;94(47):16308-16318. doi: 10.1021/acs.analchem.2c02902. Epub 2022 Nov 14.
5
Variable-temperature NMR spectroscopy for metabolite identification in biological materials.用于生物材料中代谢物鉴定的变温核磁共振光谱法。
RSC Adv. 2021 Nov 3;11(56):35321-35325. doi: 10.1039/d1ra05626c. eCollection 2021 Oct 28.
6
The exposome paradigm to predict environmental health in terms of systemic homeostasis and resource balance based on NMR data science.基于核磁共振数据科学，从系统稳态和资源平衡角度预测环境卫生的暴露组范式。
RSC Adv. 2021 Sep 13;11(48):30426-30447. doi: 10.1039/d1ra03008f. eCollection 2021 Sep 6.
7
Phosphorus NMR and Its Application to Metabolomics.磷核磁共振及其在代谢组学中的应用。
Anal Chem. 2020 Jul 21;92(14):9536-9545. doi: 10.1021/acs.analchem.0c00591. Epub 2020 Jun 29.
8
Metabolomics in the Context of Plant Natural Products Research: From Sample Preparation to Metabolite Analysis.植物天然产物研究背景下的代谢组学：从样品制备到代谢物分析
Metabolites. 2020 Jan 15;10(1):37. doi: 10.3390/metabo10010037.
9
InterSpin: Integrated Supportive Webtools for Low- and High-Field NMR Analyses Toward Molecular Complexity.InterSpin：用于低场和高场核磁共振分析以研究分子复杂性的集成支持网络工具
ACS Omega. 2019 Feb 14;4(2):3361-3369. doi: 10.1021/acsomega.8b02714. eCollection 2019 Feb 28.
10
C Labeling of Nematode Worms to Improve Metabolome Coverage by Heteronuclear Nuclear Magnetic Resonance Experiments.通过异核核磁共振实验对线虫进行标记以提高代谢组覆盖度
Front Mol Biosci. 2019 Apr 26;6:27. doi: 10.3389/fmolb.2019.00027. eCollection 2019.
本文引用的文献
1
Carbon backbone topology of the metabolome of a cell.细胞代谢组的碳骨架拓扑结构。
J Am Chem Soc. 2012 May 30;134(21):9006-11. doi: 10.1021/ja3033058. Epub 2012 May 17.
2
NMR in metabolomics and natural products research: two sides of the same coin.代谢组学和天然产物研究中的 NMR：同一枚硬币的两面。
Acc Chem Res. 2012 Feb 21;45(2):288-97. doi: 10.1021/ar2001606. Epub 2011 Sep 2.
3
Deconvolution of chemical mixtures with high complexity by NMR consensus trace clustering.通过 NMR 一致轨迹聚类对高复杂度化学混合物进行解卷积。
Anal Chem. 2011 Oct 1;83(19):7412-7. doi: 10.1021/ac201464y. Epub 2011 Aug 30.
4
Statistical indices for simultaneous large-scale metabolite detections for a single NMR spectrum.用于单个 NMR 光谱同时大规模代谢物检测的统计指标。
Anal Chem. 2010 Mar 1;82(5):1653-8. doi: 10.1021/ac9022023.
5
Web server suite for complex mixture analysis by covariance NMR.基于协方差 NMR 的复杂混合物分析用网络服务器套件。
Magn Reson Chem. 2009 Dec;47 Suppl 1(Suppl 1):S118-22. doi: 10.1002/mrc.2486.
6
HMDB: a knowledgebase for the human metabolome.HMDB：人类代谢组知识库。
Nucleic Acids Res. 2009 Jan;37(Database issue):D603-10. doi: 10.1093/nar/gkn810. Epub 2008 Oct 25.
7
Web server based complex mixture analysis by NMR.基于网络服务器的核磁共振复杂混合物分析
Anal Chem. 2008 May 15;80(10):3606-11. doi: 10.1021/ac702530t. Epub 2008 Apr 19.
8
Metabolite identification via the Madison Metabolomics Consortium Database.通过麦迪逊代谢组学联盟数据库进行代谢物鉴定。
Nat Biotechnol. 2008 Feb;26(2):162-4. doi: 10.1038/nbt0208-162.
9
BioMagResBank.生物磁共振数据库
Nucleic Acids Res. 2008 Jan;36(Database issue):D402-8. doi: 10.1093/nar/gkm957. Epub 2007 Nov 4.
10
Robust deconvolution of complex mixtures by covariance TOCSY spectroscopy.通过协方差全相关谱对复杂混合物进行稳健的反褶积
Angew Chem Int Ed Engl. 2007;46(15):2639-42. doi: 10.1002/anie.200604599.
Zotero 插件