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Borges RM, das Neves Costa F, Chagas FO, Teixeira AM, Yoon J, Weiss MB, Crnkovic CM, Pilon AC, Garrido BC, Betancur LA, Forero AM, Castellanos L, Ramos FA, Pupo MT, Kuhn S. Data Fusion-based Discovery (DAFdiscovery) pipeline to aid compound annotation and bioactive compound discovery across diverse spectral data. PHYTOCHEMICAL ANALYSIS : PCA 2023; 34:48-55. [PMID: 36191930 DOI: 10.1002/pca.3178] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
INTRODUCTION Data Fusion-based Discovery (DAFdiscovery) is a pipeline designed to help users combine mass spectrometry (MS), nuclear magnetic resonance (NMR), and bioactivity data in a notebook-based application to accelerate annotation and discovery of bioactive compounds. It applies Statistical Total Correlation Spectroscopy (STOCSY) and Statistical HeteroSpectroscopy (SHY) calculation in their data using an easy-to-follow Jupyter Notebook. METHOD Different case studies are presented for benchmarking, and the resultant outputs are shown to aid natural products identification and discovery. The goal is to encourage users to acquire MS and NMR data from their samples (in replicated samples and fractions when available) and to explore their variance to highlight MS features, NMR peaks, and bioactivity that might be correlated to accelerated bioactive compound discovery or for annotation-identification studies. RESULTS Different applications were demonstrated using data from different research groups, and it was shown that DAFdiscovery reproduced their findings using a more straightforward method. CONCLUSION DAFdiscovery has proven to be a simple-to-use method for different situations where data from different sources are required to be analyzed together.
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Affiliation(s)
- Ricardo Moreira Borges
- Instituto de Pesquisas de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Brazil
| | - Fernanda das Neves Costa
- Instituto de Pesquisas de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Brazil
| | - Fernanda O Chagas
- Instituto de Pesquisas de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Brazil
| | - Andrew Magno Teixeira
- Instituto de Pesquisas de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Brazil
| | - Jaewon Yoon
- Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Brazil
| | | | | | - Alan Cesar Pilon
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Brazil
| | - Bruno C Garrido
- Chemical Metrology Division, Organic Analysis Laboratory, Inmetro, Brazil
| | - Luz Adriana Betancur
- Departamento de Química, Edificio Orlando Sierra, Universidad de Caldas, Caldas, Colombia
| | - Abel M Forero
- Departamento de Química, Universidad Nacional de Colombia, Sede Bogotá, Bogotá, Colombia
- Departamento de Química, Facultad de Ciencias and Centro de Investigacions Científicas Avanzadas (CI-CA) Universidade de A Coruña, Coruña, Spain
| | - Leonardo Castellanos
- Departamento de Química, Universidad Nacional de Colombia, Sede Bogotá, Bogotá, Colombia
| | - Freddy A Ramos
- Departamento de Química, Universidad Nacional de Colombia, Sede Bogotá, Bogotá, Colombia
| | - Mônica T Pupo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Brazil
| | - Stefan Kuhn
- School of Computer Science and Informatics, De Montfort University, UK
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2
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Zhao XJG, Cao H. Linking research of biomedical datasets. Brief Bioinform 2022; 23:6712704. [PMID: 36151775 DOI: 10.1093/bib/bbac373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/03/2022] [Accepted: 08/08/2022] [Indexed: 12/14/2022] Open
Abstract
Biomedical data preprocessing and efficient computing can be as important as the statistical methods used to fit the data; data processing needs to consider application scenarios, data acquisition and individual rights and interests. We review common principles, knowledge and methods of integrated research according to the whole-pipeline processing mechanism diverse, coherent, sharing, auditable and ecological. First, neuromorphic and native algorithms integrate diverse datasets, providing linear scalability and high visualization. Second, the choice mechanism of different preprocessing, analysis and transaction methods from raw to neuromorphic was summarized on the node and coordinator platforms. Third, combination of node, network, cloud, edge, swarm and graph builds an ecosystem of cohort integrated research and clinical diagnosis and treatment. Looking forward, it is vital to simultaneously combine deep computing, mass data storage and massively parallel communication.
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Affiliation(s)
- Xiu-Ju George Zhao
- Wuhan Institute of Physics and Mathematics (WIPM), China.,Wuhan Polytechnic University, China
| | - Hui Cao
- Wuhan Polytechnic University, China
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3
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Chandra K, Al-Harthi S, Almulhim F, Emwas AH, Jaremko Ł, Jaremko M. The robust NMR toolbox for metabolomics. Mol Omics 2021; 17:719-724. [PMID: 34636383 DOI: 10.1039/d1mo00118c] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here, we implemented and validated a suite of selective and non-selective CPMG-filtered 1D and 2D TOCSY/HSQC experiments for metabolomics research. They facilitated the unambiguous identification of metabolites embedded in broad lipid and protein signals. The 2D spectra improved non-targeted analysis by removing the background broad signals of macromolecules.
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Affiliation(s)
- Kousik Chandra
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Samah Al-Harthi
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Fatimah Almulhim
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Abdul-Hamid Emwas
- Core Laboratories, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Łukasz Jaremko
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Mariusz Jaremko
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
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Loo RL, Chan Q, Antti H, Li JV, Ashrafian H, Elliott P, Stamler J, Nicholson JK, Holmes E, Wist J. Strategy for improved characterization of human metabolic phenotypes using a COmbined Multi-block Principal components Analysis with Statistical Spectroscopy (COMPASS). Bioinformatics 2021; 36:5229-5236. [PMID: 32692809 PMCID: PMC7850059 DOI: 10.1093/bioinformatics/btaa649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 06/13/2020] [Accepted: 07/15/2020] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Large-scale population omics data can provide insight into associations between gene-environment interactions and disease. However, existing dimension reduction modelling techniques are often inefficient for extracting detailed information from these complex datasets. RESULTS Here, we present an interactive software pipeline for exploratory analyses of population-based nuclear magnetic resonance spectral data using a COmbined Multi-block Principal components Analysis with Statistical Spectroscopy (COMPASS) within the R-library hastaLaVista framework. Principal component analysis models are generated for a sequential series of spectral regions (blocks) to provide more granular detail defining sub-populations within the dataset. Molecular identification of key differentiating signals is subsequently achieved by implementing Statistical TOtal Correlation SpectroscopY on the full spectral data to define feature patterns. Finally, the distributions of cross-correlation of the reference patterns across the spectral dataset are used to provide population statistics for identifying underlying features arising from drug intake, latent diseases and diet. The COMPASS method thus provides an efficient semi-automated approach for screening population datasets. AVAILABILITY AND IMPLEMENTATION Source code is available at https://github.com/cheminfo/COMPASS. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ruey Leng Loo
- Centre for Computational and Systems Medicine, Perth, WA 6150, Australia.,The Australian National Phenome Centre, Health Futures Institute, Murdoch University, Perth, WA 6150, Australia
| | - Queenie Chan
- Department of Epidemiology and Biostatistics, London W2 1PG, UK.,MRC Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Henrik Antti
- Department of Chemistry, Umea Universitet, 901 87 Umeå, Sweden
| | - Jia V Li
- Department of Surgery and Cancer, Imperial College London, London W2 1PG, UK
| | - H Ashrafian
- Department of Surgery and Cancer, Imperial College London, London W2 1PG, UK
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, London W2 1PG, UK.,MRC Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Jeremiah Stamler
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Jeremy K Nicholson
- Centre for Computational and Systems Medicine, Perth, WA 6150, Australia.,The Australian National Phenome Centre, Health Futures Institute, Murdoch University, Perth, WA 6150, Australia
| | - Elaine Holmes
- Centre for Computational and Systems Medicine, Perth, WA 6150, Australia.,The Australian National Phenome Centre, Health Futures Institute, Murdoch University, Perth, WA 6150, Australia.,Department of Surgery and Cancer, Imperial College London, London W2 1PG, UK
| | - Julien Wist
- Chemistry Department, Universidad del Valle, Cali, Colombia
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5
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Identifying unknown metabolites using NMR-based metabolic profiling techniques. Nat Protoc 2020; 15:2538-2567. [PMID: 32681152 DOI: 10.1038/s41596-020-0343-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 04/20/2020] [Indexed: 01/20/2023]
Abstract
Metabolic profiling of biological samples provides important insights into multiple physiological and pathological processes but is hindered by a lack of automated annotation and standardized methods for structure elucidation of candidate disease biomarkers. Here we describe a system for identifying molecular species derived from nuclear magnetic resonance (NMR) spectroscopy-based metabolic phenotyping studies, with detailed information on sample preparation, data acquisition and data modeling. We provide eight different modular workflows to be followed in a recommended sequential order according to their level of difficulty. This multi-platform system involves the use of statistical spectroscopic tools such as Statistical Total Correlation Spectroscopy (STOCSY), Subset Optimization by Reference Matching (STORM) and Resolution-Enhanced (RED)-STORM to identify other signals in the NMR spectra relating to the same molecule. It also uses two-dimensional NMR spectroscopic analysis, separation and pre-concentration techniques, multiple hyphenated analytical platforms and data extraction from existing databases. The complete system, using all eight workflows, would take up to a month, as it includes multi-dimensional NMR experiments that require prolonged experiment times. However, easier identification cases using fewer steps would take 2 or 3 days. This approach to biomarker discovery is efficient and cost-effective and offers increased chemical space coverage of the metabolome, resulting in faster and more accurate assignment of NMR-generated biomarkers arising from metabolic phenotyping studies. It requires a basic understanding of MATLAB to use the statistical spectroscopic tools and analytical skills to perform solid phase extraction (SPE), liquid chromatography (LC) fraction collection, LC-NMR-mass spectroscopy and one-dimensional and two-dimensional NMR experiments.
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6
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Yuan B, Zhang X, Kamal GM, Jiang B, Liu M. Accurate estimation of diffusion coefficient for molecular identification in a complex background. Anal Bioanal Chem 2020; 412:4519-4525. [PMID: 32405677 DOI: 10.1007/s00216-020-02693-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 04/22/2020] [Accepted: 05/04/2020] [Indexed: 11/25/2022]
Abstract
To eliminate the effects of complex background signals and to enhance the accuracy of the diffusion coefficient measurement, derivative NMR spectroscopy with negligible loss of the spectral quality is introduced based on the customized Savitzky-Golay method and used to construct diffusion-ordered NMR spectroscopy (DOSY). The criterion of the method was established by simulations. The application of this method on mouse urine and serum showed that the accuracy and precision of diffusion coefficient measurements in a complex background were improved to enhance the identification of molecules. Graphical abstract Diffusion-ordered NMR spectroscopy is a powerful tool for analyzing complex mixtures. To improve the accuracy of diffusion coefficient measurement, the magnitude of complex derivative spectra is introduced as a post-processing method to eliminate the effects of background signals, broad signals, or distorted baseline. And thus, accurate estimate of the diffusion coefficient is ensured to enhance the molecule identification.
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Affiliation(s)
- Bin Yuan
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, Hubei, China
| | - Xu Zhang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, Hubei, China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Ghulam Mustafa Kamal
- Department of Chemistry, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, 64200, Pakistan
| | - Bin Jiang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, Hubei, China.
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, Hubei, China.
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
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Ugata Y, Thomas ML, Mandai T, Ueno K, Dokko K, Watanabe M. Li-ion hopping conduction in highly concentrated lithium bis(fluorosulfonyl)amide/dinitrile liquid electrolytes. Phys Chem Chem Phys 2019; 21:9759-9768. [DOI: 10.1039/c9cp01839e] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Li+ ion hopping conduction through ligand (solvent and anion) exchange emerges in solvent-deficient liquid electrolytes of [Li salt]/[dinitrile] > 1.
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Affiliation(s)
- Yosuke Ugata
- Department of Chemistry and Biotechnology
- Yokohama National University
- Yokohama 240-8501
- Japan
| | - Morgan L. Thomas
- Department of Chemistry and Biotechnology
- Yokohama National University
- Yokohama 240-8501
- Japan
| | - Toshihiko Mandai
- Department of Chemistry and Biological Science Studies in Chemistry
- Iwate University
- Morioka
- Japan
- Center for Green Research on Energy and Environmental Materials
| | - Kazuhide Ueno
- Department of Chemistry and Biotechnology
- Yokohama National University
- Yokohama 240-8501
- Japan
| | - Kaoru Dokko
- Department of Chemistry and Biotechnology
- Yokohama National University
- Yokohama 240-8501
- Japan
- Unit of Elements Strategy Initiative for Catalysts & Batteries (ESICB)
| | - Masayoshi Watanabe
- Department of Chemistry and Biotechnology
- Yokohama National University
- Yokohama 240-8501
- Japan
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8
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Kikuchi J, Ito K, Date Y. Environmental metabolomics with data science for investigating ecosystem homeostasis. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 104:56-88. [PMID: 29405981 DOI: 10.1016/j.pnmrs.2017.11.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 11/19/2017] [Accepted: 11/19/2017] [Indexed: 05/08/2023]
Abstract
A natural ecosystem can be viewed as the interconnections between complex metabolic reactions and environments. Humans, a part of these ecosystems, and their activities strongly affect the environments. To account for human effects within ecosystems, understanding what benefits humans receive by facilitating the maintenance of environmental homeostasis is important. This review describes recent applications of several NMR approaches to the evaluation of environmental homeostasis by metabolic profiling and data science. The basic NMR strategy used to evaluate homeostasis using big data collection is similar to that used in human health studies. Sophisticated metabolomic approaches (metabolic profiling) are widely reported in the literature. Further challenges include the analysis of complex macromolecular structures, and of the compositions and interactions of plant biomass, soil humic substances, and aqueous particulate organic matter. To support the study of these topics, we also discuss sample preparation techniques and solid-state NMR approaches. Because NMR approaches can produce a number of data with high reproducibility and inter-institution compatibility, further analysis of such data using machine learning approaches is often worthwhile. We also describe methods for data pretreatment in solid-state NMR and for environmental feature extraction from heterogeneously-measured spectroscopic data by machine learning approaches.
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Affiliation(s)
- Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Bioagricultural Sciences, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya, Aichi 464-0810, Japan.
| | - Kengo Ito
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yasuhiro Date
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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9
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Yang FC, Chou KH, Kuo CY, Lin YY, Lin CP, Wang SJ. The pathophysiology of episodic cluster headache: Insights from recent neuroimaging research. Cephalalgia 2017; 38:970-983. [DOI: 10.1177/0333102417716932] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Background Cluster headache is a disorder characterized by intermittent, severe unilateral head pain accompanied by cranial autonomic symptoms. Most cases of CH are episodic, manifesting as “in-bout” periods of frequent headache separated by month-to-year-long “out-of-bout” periods of remission. Previous imaging studies have implicated the hypothalamus and pain matrix in the pathogenesis of episodic CH. However, the pathophysiology driving the transition between in- and out-of-bout periods remains unclear. Methods The present study provides a narrative review of previous neuroimaging studies on the pathophysiology of episodic CH, addressing alterations in brain structures, metabolism, and structural and functional connectivity occurring between bout periods. Results Although the precise brain structures responsible for episodic CH are unknown, major roles are indicated for the posterior hypothalamus (especially in acute attacks), the pain neuromatrix with an emphasis on central descending pain modulation, and non-traditional pain processing networks including the occipital, cerebellar, and salience networks. These areas are potentially related to dynamic transitioning between in- and out-of-bout periods. Conclusion Recent progress in magnetic resonance imaging of episodic CH has provided additional insights into dynamic bout-associated structural and functional connectivity changes in the brain, especially in non-traditional pain processing network areas. These areas warrant future investigations as targets for neuromodulation in patients with CH.
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Affiliation(s)
- Fu-Chi Yang
- Department of Neurology, Tri-Service General Hospital, National Defense Medical Center, Taiwan
| | - Kun-Hsien Chou
- Brain Research Center, National Yang-Ming University, Taiwan
- Institute of Neuroscience, National Yang-Ming University, Taiwan
| | - Chen-Yuan Kuo
- Department of Biomedical Imaging and Radiological Sciences, National Yang-Ming University, Taiwan
| | - Yung-Yang Lin
- Brain Research Center, National Yang-Ming University, Taiwan
- Institute of Brain Science, National Yang-Ming University, Taiwan
- Faculty of Medicine, National Yang-Ming University School of Medicine, Taiwan
- Neurological Institute, Taipei Veterans General Hospital, Taiwan
| | - Ching-Po Lin
- Brain Research Center, National Yang-Ming University, Taiwan
- Institute of Neuroscience, National Yang-Ming University, Taiwan
- Department of Biomedical Imaging and Radiological Sciences, National Yang-Ming University, Taiwan
- Institute of Brain Science, National Yang-Ming University, Taiwan
| | - Shuu-Jiun Wang
- Brain Research Center, National Yang-Ming University, Taiwan
- Institute of Brain Science, National Yang-Ming University, Taiwan
- Faculty of Medicine, National Yang-Ming University School of Medicine, Taiwan
- Neurological Institute, Taipei Veterans General Hospital, Taiwan
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10
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Yuan B, Ding Y, Kamal GM, Shao L, Zhou Z, Jiang B, Sun P, Zhang X, Liu M. Reconstructing diffusion ordered NMR spectroscopy by simultaneous inversion of Laplace transform. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 278:1-7. [PMID: 28301804 DOI: 10.1016/j.jmr.2017.03.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Revised: 03/04/2017] [Accepted: 03/06/2017] [Indexed: 06/06/2023]
Abstract
2D diffusion-ordered NMR spectroscopy (DOSY) has been widely recognized as a powerful tool for analyzing mixtures and probing inter-molecular interactions in situ. But it is difficult to differentiate molecules with similar diffusion coefficients in presence of overlapped spectra. Its performance is susceptible to the number of chemical components, and usually gets worse when the number of components increases. Here, to alleviate the problem, numerical simultaneous inversion of Laplace transform (SILT) of many related variables is proposed for reconstructing DOSY spectrum (SILT-DOSY). The advantage of the proposed method in comparison to other methods is that it is capable of estimating the number of analytes more accurately and deriving corresponding component spectra, which in turn leads to the more reliable identification of the components.
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Affiliation(s)
- Bin Yuan
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yiming Ding
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Ghulam M Kamal
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Limin Shao
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Zhiming Zhou
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Bin Jiang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Peng Sun
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Xu Zhang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
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11
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Pagès G, Gilard V, Martino R, Malet-Martino M. Pulsed-field gradient nuclear magnetic resonance measurements (PFG NMR) for diffusion ordered spectroscopy (DOSY) mapping. Analyst 2017; 142:3771-3796. [DOI: 10.1039/c7an01031a] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The advent of Diffusion Ordered SpectroscopY (DOSY) NMR has enabled diffusion coefficients to be routinely measured and used to characterize chemical systems in solution. Indeed, DOSY NMR allows the separation of the chemical entities present in multicomponent systems and provides information on their intermolecular interactions as well as on their size and shape.
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Affiliation(s)
- G. Pagès
- INRA
- AgroResonance – UR370 Qualité des Produits Animaux
- Saint Genès Champanelle
- France
| | - V. Gilard
- Groupe de RMN Biomédicale
- Laboratoire de Synthèse et Physicochimie de Molécules d'Intérêt Biologique
- UMR CNRS 5068
- Université de Toulouse
- 31062 Toulouse cedex 9
| | - R. Martino
- Groupe de RMN Biomédicale
- Laboratoire de Synthèse et Physicochimie de Molécules d'Intérêt Biologique
- UMR CNRS 5068
- Université de Toulouse
- 31062 Toulouse cedex 9
| | - M. Malet-Martino
- Groupe de RMN Biomédicale
- Laboratoire de Synthèse et Physicochimie de Molécules d'Intérêt Biologique
- UMR CNRS 5068
- Université de Toulouse
- 31062 Toulouse cedex 9
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12
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Metabolic phenotyping for discovery of urinary biomarkers of diet, xenobiotics and blood pressure in the INTERMAP Study: an overview. Hypertens Res 2016; 40:336-345. [PMID: 28003647 DOI: 10.1038/hr.2016.164] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 10/03/2016] [Accepted: 10/07/2016] [Indexed: 12/27/2022]
Abstract
The etiopathogenesis of cardiovascular diseases (CVDs) is multifactorial. Adverse blood pressure (BP) is a major independent risk factor for epidemic CVD affecting ~40% of the adult population worldwide and resulting in significant morbidity and mortality. Metabolic phenotyping of biological fluids has proven its application in characterizing low-molecular-weight metabolites providing novel insights into gene-environmental-gut microbiome interaction in relation to a disease state. In this review, we synthesize key results from the INTERnational study of MAcro/micronutrients and blood Pressure (INTERMAP) Study, a cross-sectional epidemiologic study of 4680 men and women aged 40-59 years from Japan, the People's Republic of China, the United Kingdom and the United States. We describe the advancements we have made regarding the following: (1) analytical techniques for high-throughput metabolic phenotyping; (2) statistical analyses for biomarker identification; (3) discovery of unique food-specific biomarkers; and (4) application of metabolome-wide association studies to gain a better understanding into the molecular mechanisms of cross-cultural and regional BP differences.
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Akhter M, Dutta Majumdar R, Fortier-McGill B, Soong R, Liaghati-Mobarhan Y, Simpson M, Arhonditsis G, Schmidt S, Heumann H, Simpson AJ. Identification of aquatically available carbon from algae through solution-state NMR of whole 13C-labelled cells. Anal Bioanal Chem 2016; 408:4357-70. [DOI: 10.1007/s00216-016-9534-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 03/24/2016] [Accepted: 03/30/2016] [Indexed: 11/28/2022]
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Nestor G, Eriksson J, Sandström C, Malmlöf K. Nuclear Magnetic Resonance-Based Blood Metabolic Profiles of Rats Exposed to Short-Term Caloric Restriction. ANAL LETT 2015. [DOI: 10.1080/00032719.2015.1041028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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15
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Nagana Gowda GA, Raftery D. Can NMR solve some significant challenges in metabolomics? JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 260:144-60. [PMID: 26476597 PMCID: PMC4646661 DOI: 10.1016/j.jmr.2015.07.014] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Revised: 07/17/2015] [Accepted: 07/18/2015] [Indexed: 05/04/2023]
Abstract
The field of metabolomics continues to witness rapid growth driven by fundamental studies, methods development, and applications in a number of disciplines that include biomedical science, plant and nutrition sciences, drug development, energy and environmental sciences, toxicology, etc. NMR spectroscopy is one of the two most widely used analytical platforms in the metabolomics field, along with mass spectrometry (MS). NMR's excellent reproducibility and quantitative accuracy, its ability to identify structures of unknown metabolites, its capacity to generate metabolite profiles using intact bio-specimens with no need for separation, and its capabilities for tracing metabolic pathways using isotope labeled substrates offer unique strengths for metabolomics applications. However, NMR's limited sensitivity and resolution continue to pose a major challenge and have restricted both the number and the quantitative accuracy of metabolites analyzed by NMR. Further, the analysis of highly complex biological samples has increased the demand for new methods with improved detection, better unknown identification, and more accurate quantitation of larger numbers of metabolites. Recent efforts have contributed significant improvements in these areas, and have thereby enhanced the pool of routinely quantifiable metabolites. Additionally, efforts focused on combining NMR and MS promise opportunities to exploit the combined strength of the two analytical platforms for direct comparison of the metabolite data, unknown identification and reliable biomarker discovery that continue to challenge the metabolomics field. This article presents our perspectives on the emerging trends in NMR-based metabolomics and NMR's continuing role in the field with an emphasis on recent and ongoing research from our laboratory.
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Affiliation(s)
- G A Nagana Gowda
- Northwest Metabolomics Research Center, Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98109, United States
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98109, United States; Department of Chemistry, University of Washington, Seattle, WA 98195, United States; Fred Hutchinson Cancer Research Center, Seattle, WA 98109, United States.
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16
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Arnold JM, Choi WT, Sreekumar A, Maletić-Savatić M. Analytical strategies for studying stem cell metabolism. ACTA ACUST UNITED AC 2015. [PMID: 26213533 DOI: 10.1007/s11515-015-1357-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Owing to their capacity for self-renewal and pluripotency, stem cells possess untold potential for revolutionizing the field of regenerative medicine through the development of novel therapeutic strategies for treating cancer, diabetes, cardiovascular and neurodegenerative diseases. Central to developing these strategies is improving our understanding of biological mechanisms responsible for governing stem cell fate and self-renewal. Increasing attention is being given to the significance of metabolism, through the production of energy and generation of small molecules, as a critical regulator of stem cell functioning. Rapid advances in the field of metabolomics now allow for in-depth profiling of stem cells both in vitro and in vivo, providing a systems perspective on key metabolic and molecular pathways which influence stem cell biology. Understanding the analytical platforms and techniques that are currently used to study stem cell metabolomics, as well as how new insights can be derived from this knowledge, will accelerate new research in the field and improve future efforts to expand our understanding of the interplay between metabolism and stem cell biology.
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Affiliation(s)
- James M Arnold
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - William T Choi
- Program in Developmental Biology and Medical Scientist Training Program, Baylor College of Medicine; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Arun Sreekumar
- Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mirjana Maletić-Savatić
- Program in Developmental Biology and Medical Scientist Training Program, Baylor College of Medicine; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA ; Departments of Pediatrics-Neurology and Neuroscience, and Program in Structural and Computational Biology and Molecular Biophysics Baylor College of Medicine, Houston, TX 77030, USA
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Toumi I, Caldarelli S, Torrésani B. A review of blind source separation in NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2014; 81:37-64. [PMID: 25142734 DOI: 10.1016/j.pnmrs.2014.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 06/12/2014] [Indexed: 05/22/2023]
Abstract
Fourier transform is the data processing naturally associated to most NMR experiments. Notable exceptions are Pulse Field Gradient and relaxation analysis, the structure of which is only partially suitable for FT. With the revamp of NMR of complex mixtures, fueled by analytical challenges such as metabolomics, alternative and more apt mathematical methods for data processing have been sought, with the aim of decomposing the NMR signal into simpler bits. Blind source separation is a very broad definition regrouping several classes of mathematical methods for complex signal decomposition that use no hypothesis on the form of the data. Developed outside NMR, these algorithms have been increasingly tested on spectra of mixtures. In this review, we shall provide an historical overview of the application of blind source separation methodologies to NMR, including methods specifically designed for the specificity of this spectroscopy.
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Affiliation(s)
- Ichrak Toumi
- Aix Marseille Université, Centrale Marseille, CNRS, iSm2 UMR 7313, 13397 Marseille, France
| | - Stefano Caldarelli
- Aix Marseille Université, Centrale Marseille, CNRS, iSm2 UMR 7313, 13397 Marseille, France.
| | - Bruno Torrésani
- Aix-Marseille Université, CNRS, Centrale Marseille I2M, UMR 7373, 13453 Marseille, France
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18
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Urbańczyk M, Koźmiński W, Kazimierczuk K. Accelerating Diffusion‐Ordered NMR Spectroscopy by Joint Sparse Sampling of Diffusion and Time Dimensions. Angew Chem Int Ed Engl 2014; 53:6464-7. [DOI: 10.1002/anie.201402049] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 03/05/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Mateusz Urbańczyk
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, Warsaw, 02‐089 (Poland)
| | - Wiktor Koźmiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, Warsaw, 02‐089 (Poland)
| | - Krzysztof Kazimierczuk
- Centre of New Technologies, University of Warsaw, Żwirki iWigury 93, Warsaw, 02‐089 (Poland)
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19
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Urbańczyk M, Koźmiński W, Kazimierczuk K. Accelerating Diffusion‐Ordered NMR Spectroscopy by Joint Sparse Sampling of Diffusion and Time Dimensions. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Mateusz Urbańczyk
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, Warsaw, 02‐089 (Poland)
| | - Wiktor Koźmiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, Warsaw, 02‐089 (Poland)
| | - Krzysztof Kazimierczuk
- Centre of New Technologies, University of Warsaw, Żwirki iWigury 93, Warsaw, 02‐089 (Poland)
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20
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Ala-Korpela M. Potential role of body fluid1H NMR metabonomics as a prognostic and diagnostic tool. Expert Rev Mol Diagn 2014; 7:761-73. [DOI: 10.1586/14737159.7.6.761] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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21
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Nagana Gowda G, Raftery D. Advances in NMR-Based Metabolomics. FUNDAMENTALS OF ADVANCED OMICS TECHNOLOGIES: FROM GENES TO METABOLITES 2014. [DOI: 10.1016/b978-0-444-62651-6.00008-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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22
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Toumi I, Torrésani B, Caldarelli S. Effective Processing of Pulse Field Gradient NMR of Mixtures by Blind Source Separation. Anal Chem 2013; 85:11344-51. [DOI: 10.1021/ac402085x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Ichrak Toumi
- Aix Marseille Université, CNRS, Centrale
Marseille, iSm2 UMR 7313, 13397, Marseille, France
| | - Bruno Torrésani
- Aix Marseille Université, CNRS, Centrale Marseille, LATP
UMR 7353, 13453, Marseille, France
| | - Stefano Caldarelli
- Aix Marseille Université, CNRS, Centrale
Marseille, iSm2 UMR 7313, 13397, Marseille, France
- CNRS UPR 2301 ICSN 91190, Gif-sur-Yvette, France
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Trifonova O, Lokhov P, Archakov A. Postgenomics diagnostics: metabolomics approaches to human blood profiling. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2013; 17:550-9. [PMID: 24044364 DOI: 10.1089/omi.2012.0121] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We live in exciting times with the prospects of postgenomics diagnostics. Metabolomics is a novel "omics" data-intensive science that is accelerating the development of postgenomics diagnostics, particularly with use of accessible peripheral tissue compartments. Metabolomics involves the study of a comprehensive set of low molecular weight substances (metabolites) present in biological systems. The metabolite profiles represent the molecular phenotype of biological systems and reflect the information encoded at the genomic level and implemented at the transcriptomic and proteomic levels. Analysis of the human blood metabolite profile is a universal and highly promising tool for clinical postgenomics applications because it reflects both the endogenous and exogenous (environmental) factors influencing an individual organism. This article presents a critical synthesis and original analysis of both the technical implementation of metabolic profiling of blood and statistical analysis of metabolite profiles for effective disease diagnostics and risk assessment in the present postgenomics era.
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24
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Bouatra S, Aziat F, Mandal R, Guo AC, Wilson MR, Knox C, Bjorndahl TC, Krishnamurthy R, Saleem F, Liu P, Dame ZT, Poelzer J, Huynh J, Yallou FS, Psychogios N, Dong E, Bogumil R, Roehring C, Wishart DS. The human urine metabolome. PLoS One 2013; 8:e73076. [PMID: 24023812 PMCID: PMC3762851 DOI: 10.1371/journal.pone.0073076] [Citation(s) in RCA: 929] [Impact Index Per Article: 84.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 07/09/2013] [Indexed: 02/07/2023] Open
Abstract
Urine has long been a "favored" biofluid among metabolomics researchers. It is sterile, easy-to-obtain in large volumes, largely free from interfering proteins or lipids and chemically complex. However, this chemical complexity has also made urine a particularly difficult substrate to fully understand. As a biological waste material, urine typically contains metabolic breakdown products from a wide range of foods, drinks, drugs, environmental contaminants, endogenous waste metabolites and bacterial by-products. Many of these compounds are poorly characterized and poorly understood. In an effort to improve our understanding of this biofluid we have undertaken a comprehensive, quantitative, metabolome-wide characterization of human urine. This involved both computer-aided literature mining and comprehensive, quantitative experimental assessment/validation. The experimental portion employed NMR spectroscopy, gas chromatography mass spectrometry (GC-MS), direct flow injection mass spectrometry (DFI/LC-MS/MS), inductively coupled plasma mass spectrometry (ICP-MS) and high performance liquid chromatography (HPLC) experiments performed on multiple human urine samples. This multi-platform metabolomic analysis allowed us to identify 445 and quantify 378 unique urine metabolites or metabolite species. The different analytical platforms were able to identify (quantify) a total of: 209 (209) by NMR, 179 (85) by GC-MS, 127 (127) by DFI/LC-MS/MS, 40 (40) by ICP-MS and 10 (10) by HPLC. Our use of multiple metabolomics platforms and technologies allowed us to identify several previously unknown urine metabolites and to substantially enhance the level of metabolome coverage. It also allowed us to critically assess the relative strengths and weaknesses of different platforms or technologies. The literature review led to the identification and annotation of another 2206 urinary compounds and was used to help guide the subsequent experimental studies. An online database containing the complete set of 2651 confirmed human urine metabolite species, their structures (3079 in total), concentrations, related literature references and links to their known disease associations are freely available at http://www.urinemetabolome.ca.
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Affiliation(s)
- Souhaila Bouatra
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Farid Aziat
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Rupasri Mandal
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - An Chi Guo
- Department of Computing Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Michael R. Wilson
- Department of Computing Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Craig Knox
- Department of Computing Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Trent C. Bjorndahl
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | | | - Fozia Saleem
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Philip Liu
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Zerihun T. Dame
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Jenna Poelzer
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Jessica Huynh
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Faizath S. Yallou
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Nick Psychogios
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Edison Dong
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | | | | | - David S. Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Department of Computing Sciences, University of Alberta, Edmonton, Alberta, Canada
- National Institute for Nanotechnology, Edmonton, Alberta, Canada
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25
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Robinette SL, Lindon JC, Nicholson JK. Statistical spectroscopic tools for biomarker discovery and systems medicine. Anal Chem 2013; 85:5297-303. [PMID: 23614579 DOI: 10.1021/ac4007254] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Metabolic profiling based on comparative, statistical analysis of NMR spectroscopic and mass spectrometric data from complex biological samples has contributed to increased understanding of the role of small molecules in affecting and indicating biological processes. To enable this research, the development of statistical spectroscopy has been marked by early beginnings in applying pattern recognition to nuclear magnetic resonance data and the introduction of statistical total correlation spectroscopy (STOCSY) as a tool for biomarker identification in the past decade. Extensions of statistical spectroscopy now compose a family of related tools used for compound identification, data preprocessing, and metabolic pathway analysis. In this Perspective, we review the theory and current state of research in statistical spectroscopy and discuss the growing applications of these tools to medicine and systems biology. We also provide perspectives on how recent institutional initiatives are providing new platforms for the development and application of statistical spectroscopy tools and driving the development of integrated "systems medicine" approaches in which clinical decision making is supported by statistical and computational analysis of metabolic, phenotypic, and physiological data.
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Affiliation(s)
- Steven L Robinette
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, UK
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26
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Mallol R, Rodriguez MA, Brezmes J, Masana L, Correig X. Human serum/plasma lipoprotein analysis by NMR: application to the study of diabetic dyslipidemia. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 70:1-24. [PMID: 23540574 DOI: 10.1016/j.pnmrs.2012.09.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 07/26/2012] [Indexed: 06/02/2023]
Affiliation(s)
- Roger Mallol
- Department of Electronic Engineering, Universitat Rovira i Virgili, Tarragona, Spain
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27
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Kirwan GM, Fernandez DI, Niere JO, Adams MJ. General and hybrid correlation nuclear magnetic resonance analysis of phosphorus in Phytophthora palmivora. Anal Biochem 2012; 429:1-7. [DOI: 10.1016/j.ab.2012.06.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 06/21/2012] [Accepted: 06/22/2012] [Indexed: 10/28/2022]
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28
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NMR and pattern recognition methods in metabolomics: From data acquisition to biomarker discovery: A review. Anal Chim Acta 2012; 750:82-97. [DOI: 10.1016/j.aca.2012.05.049] [Citation(s) in RCA: 303] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 05/25/2012] [Accepted: 05/26/2012] [Indexed: 01/09/2023]
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29
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Okushita K, Chikayama E, Kikuchi J. Solubilization mechanism and characterization of the structural change of bacterial cellulose in regenerated states through ionic liquid treatment. Biomacromolecules 2012; 13:1323-30. [PMID: 22489745 DOI: 10.1021/bm300537k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A statistical approach was used to characterize the heterogeneous structures of bacterial cellulose samples pretreated with four kinds of ionic liquids (ILs). The structural heterogeneity of these samples was measured by Fourier transform infrared spectroscopy as well as solid-state NMR methods such as cross-polarization magic-angle spinning and dipolar-assisted rotational resonance. The obtained data matrices were then evaluated by principal components analysis. The measured 1-D data clearly revealed the modification of crystalline cellulose; in addition, the statistical approach revealed subtle structural changes that occurred upon pretreatment with different kinds of ILs. To investigate whether such regenerated structural changes occurred because of solubilization, we examined the intermolecular nuclear Overhauser effect between cellulose and an IL. Our results clarify how the nucleophilic imidazole is attacked and suggest that the cation of the IL is associated with the collapse of hydrogen bonds in cellulose.
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Affiliation(s)
- Keiko Okushita
- RIKEN Plant Science Center, RIKEN Research Cluster for Innovation, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 235-0045, Japan
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30
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Sonkar K, Purusottam RN, Sinha N. Metabonomic Study of Host–Phage Interaction by Nuclear Magnetic Resonance- and Statistical Total Correlation Spectroscopy-Based Analysis. Anal Chem 2012; 84:4063-70. [DOI: 10.1021/ac300096j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Kanchan Sonkar
- Centre of Biomedical Magnetic Resonance, SGPGIMS Campus,
Raebareli Road, Lucknow 226014, India
| | - Rudra N. Purusottam
- Centre of Biomedical Magnetic Resonance, SGPGIMS Campus,
Raebareli Road, Lucknow 226014, India
| | - Neeraj Sinha
- Centre of Biomedical Magnetic Resonance, SGPGIMS Campus,
Raebareli Road, Lucknow 226014, India
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31
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Gowda GAN, Shanaiah N, Raftery D. Isotope enhanced approaches in metabolomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 992:147-64. [PMID: 23076583 DOI: 10.1007/978-94-007-4954-2_8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The rapidly growing area of "metabolomics," in which a large number of metabolites from body fluids, cells or tissue are detected quantitatively, in a single step, promises immense potential for a number of disciplines including early disease diagnosis, therapy monitoring, systems biology, drug discovery and nutritional science. Because of its ability to detect a large number of metabolites in intact biological samples reproducibly and quantitatively, nuclear magnetic resonance (NMR) spectroscopy has emerged as one of the most powerful analytical techniques in metabolomics. NMR spectroscopy of biological samples with isotope labeling of metabolites using nuclei such as (2)H, (13)C, (15)N and (31)P, either in vivo or ex vivo, has dramatically improved our ability to identify low concentrated metabolites and trace important metabolic pathways. Considering the somewhat limited sensitivity and high complexity of NMR spectra of biological samples, efforts have been made to increase sensitivity and selectivity through isotope labeling methods, which pave novel avenues to unravel biological complexity and understand cellular functions in health and various disease conditions. This chapter describes current developments in isotope labeling of metabolites in vivo as well as ex vivo, and their potential metabolomics applications.
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Affiliation(s)
- G A Nagana Gowda
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98109, USA.
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32
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Ebbels TMD, Lindon JC, Coen M. Processing and modeling of nuclear magnetic resonance (NMR) metabolic profiles. Methods Mol Biol 2011; 708:365-88. [PMID: 21207301 DOI: 10.1007/978-1-61737-985-7_21] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Modern nuclear magnetic resonance (NMR) spectroscopy generates complex and information-rich metabolic profiles. These require robust, accurate, and often sophisticated statistical techniques to yield the maximum meaningful knowledge. In this chapter, we describe methods typically used to analyze such data. We begin by describing seven goals of metabolic profile analysis, ranging from production of a data table to multi-omic integration for systems biology. Methods for preprocessing and pretreatment are then presented, including issues such as instrument-level spectral processing, data reduction and deconvolution, normalization, scaling, and transformations of the data. We then discuss methods for exploratory modeling and exemplify three techniques: principal components analysis, hierarchical clustering, and self-organizing maps. Moving to predictive modeling, we focus our discussion on partial least squares regression, orthogonal partial least squares regression, and genetic algorithm approaches. A typical set of in vitro metabolic profiles is used where possible to compare and contrast the methods. The importance of validating statistical models is highlighted, and standard techniques for doing so, such as training/test set and cross-validation are described. Finally, we discuss the contributions of statistical techniques such as statistical total correlation spectroscopy, and other correlation-based methods have made to the process of structural characterization for unknown metabolites.
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Affiliation(s)
- Timothy M D Ebbels
- Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College, London, UK.
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Sands CJ, Coen M, Ebbels TMD, Holmes E, Lindon JC, Nicholson JK. Data-driven approach for metabolite relationship recovery in biological 1H NMR data sets using iterative statistical total correlation spectroscopy. Anal Chem 2011; 83:2075-82. [PMID: 21323345 DOI: 10.1021/ac102870u] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Statistical total correlation spectroscopy (STOCSY) is a well-established and valuable method in the elucidation of both inter- and intrametabolite correlations in NMR metabonomic data sets. Here, the STOCSY approach is extended in a novel Iterative-STOCSY (I-STOCSY) tool in which correlations are calculated initially from a driver peak of interest and subsequently for all peaks identified as correlating with a correlation coefficient greater than a set threshold. Consequently, in a single automated run, the majority of information contained in multiple STOCSY calculations from all peaks recursively correlated to the original user defined driver peak of interest are recovered. In addition, highly correlating peaks are clustered into putative structurally related sets, and the results are presented in a fully interactive plot where each set is represented by a node; node-to-node connections are plotted alongside corresponding spectral data colored by the strength of connection, thus allowing the intuitive exploration of both inter- and intrametabolite connections. The I-STOCSY approach has been here applied to a (1)H NMR data set of 24 h postdose aqueous liver extracts from rats treated with the model hepatotoxin galactosamine and has been shown both to recover the previously deduced major metabolic effects of treatment and to generate new hypotheses even on this well-studied model system. I-STOCSY, thus, represents a significant advance in correlation based analysis and visualization, providing insight into inter- and intrametabolite relationships following metabolic perturbations.
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Affiliation(s)
- Caroline J Sands
- Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, SW7 2AZ, United Kingdom
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Coen M. A metabonomic approach for mechanistic exploration of pre-clinical toxicology. Toxicology 2010; 278:326-40. [DOI: 10.1016/j.tox.2010.07.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 07/29/2010] [Accepted: 07/30/2010] [Indexed: 12/17/2022]
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35
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Forseth RR, Schroeder FC. NMR-spectroscopic analysis of mixtures: from structure to function. Curr Opin Chem Biol 2010; 15:38-47. [PMID: 21071261 DOI: 10.1016/j.cbpa.2010.10.010] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Accepted: 10/08/2010] [Indexed: 12/22/2022]
Abstract
NMR spectroscopy as a particularly information-rich method offers unique opportunities for improving the structural and functional characterization of metabolomes, which will be essential for advancing the understanding of many biological processes. Whereas traditionally NMR spectroscopy was mostly relegated to the characterization of pure compounds, the past few years have seen a surge of interest in using NMR-spectroscopic techniques for characterizing complex metabolite mixtures. Development of new methods was motivated partly by the realization that using NMR for the analysis of metabolite mixtures can help identify otherwise inaccessible small molecules, for example compounds that are prone to chemical decomposition and thus cannot be isolated. Furthermore, comparative metabolomics and statistical analyses of NMR spectra have proven highly effective at identifying novel and known metabolites that correlate with changes in genotype or phenotype. In this review, we provide an overview of the range of NMR-spectroscopic techniques recently developed for characterizing metabolite mixtures, including methods used in discovery-oriented natural product chemistry, in the study of metabolite biosynthesis and function, or for comparative analyses of entire metabolomes.
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Affiliation(s)
- Ry R Forseth
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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Novoa-Carballal R, Fernandez-Megia E, Jimenez C, Riguera R. NMR methods for unravelling the spectra of complex mixtures. Nat Prod Rep 2010; 28:78-98. [PMID: 20936238 DOI: 10.1039/c005320c] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The main methods for the simplification of the NMR of complex mixtures by selective attenuation/suppression of the signals of certain components are presented. The application of relaxation, diffusion and PSR filters and other techniques to biological samples, pharmaceuticals, foods, living organisms and natural products are illustrated with examples.
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Affiliation(s)
- Ramon Novoa-Carballal
- Department of Organic Chemistry and Centre for Research in Biological Chemistry and Molecular Materials, University of Santiago de Compostela, Santiago de Compostela, Spain
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37
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Alves AC, Rantalainen M, Holmes E, Nicholson JK, Ebbels TMD. Analytic properties of statistical total correlation spectroscopy based information recovery in 1H NMR metabolic data sets. Anal Chem 2010; 81:2075-84. [PMID: 19220030 DOI: 10.1021/ac801982h] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Structural assignment of resonances is an important problem in NMR spectroscopy, and statistical total correlation spectroscopy (STOCSY) is a useful tool aiding this process for small molecules in complex mixture analysis and metabolic profiling studies. STOCSY delivers intramolecular information (delineating structural connectivity) and in metabolism studies can generate information on pathway-related correlations. To understand further the behavior of STOCSY for structural assignment, we analyze the statistical distribution of structural and nonstructural correlations from 1050 (1)H NMR spectra of normal rat urine samples. We find that the distributions of structural/nonstructural correlations are significantly different (p < 10(-112)). From the area under the curve of the receiver operating characteristic (ROC AUC) we show that structural correlations exceed nonstructural correlations with probability AUC = 0.98. Through a bootstrap resampling approach, we demonstrate that sample size has a surprisingly small effect (e.g., AUC = 0.97 for a sample size of 50). We identify specific signatures in the correlation maps resulting from small matrix-derived variations in peak positions but find that their effect on discrimination of structural and nonstructural correlations is negligible for most metabolites. A correlation threshold of r > 0.89 is required to assign two peaks to the same metabolite with high probability (positive predictive value, PPV = 0.9), whereas sensitivity and specificity are equal at 93% for r = 0.22. To assess the wider applicability of our results, we analyze (1)H NMR spectra of urine from rats treated with 115 model toxins or physiological stressors. Across the data sets, we find that the thresholds required to obtain PPV = 0.9 are not significantly different and the degree of overlap between the structural and nonstructural distributions is always small (median AUC = 0.97). The STOCSY method is effective for structural characterization under diverse biological conditions and sample sizes provided the degree of correlation resulting from nonstructural associations (e.g., from nonstationary processes) is small. This study validates the use of the STOCSY approach in the routine assignment of signals in NMR metabolic profiling studies and provides practical benchmarks against which researchers can interpret the results of a STOCSY analysis.
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Affiliation(s)
- Alexessander Couto Alves
- Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, U.K
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38
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Dunn WB, Broadhurst DI, Atherton HJ, Goodacre R, Griffin JL. Systems level studies of mammalian metabolomes: the roles of mass spectrometry and nuclear magnetic resonance spectroscopy. Chem Soc Rev 2010; 40:387-426. [PMID: 20717559 DOI: 10.1039/b906712b] [Citation(s) in RCA: 543] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The study of biological systems in a holistic manner (systems biology) is increasingly being viewed as a necessity to provide qualitative and quantitative descriptions of the emergent properties of the complete system. Systems biology performs studies focussed on the complex interactions of system components; emphasising the whole system rather than the individual parts. Many perturbations to mammalian systems (diet, disease, drugs) are multi-factorial and the study of small parts of the system is insufficient to understand the complete phenotypic changes induced. Metabolomics is one functional level tool being employed to investigate the complex interactions of metabolites with other metabolites (metabolism) but also the regulatory role metabolites provide through interaction with genes, transcripts and proteins (e.g. allosteric regulation). Technological developments are the driving force behind advances in scientific knowledge. Recent advances in the two analytical platforms of mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy have driven forward the discipline of metabolomics. In this critical review, an introduction to metabolites, metabolomes, metabolomics and the role of MS and NMR spectroscopy will be provided. The applications of metabolomics in mammalian systems biology for the study of the health-disease continuum, drug efficacy and toxicity and dietary effects on mammalian health will be reviewed. The current limitations and future goals of metabolomics in systems biology will also be discussed (374 references).
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Affiliation(s)
- Warwick B Dunn
- Manchester Centre for Integrative Systems Biology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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39
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Zhang S, Nagana Gowda GA, Ye T, Raftery D. Advances in NMR-based biofluid analysis and metabolite profiling. Analyst 2010; 135:1490-8. [PMID: 20379603 PMCID: PMC4720135 DOI: 10.1039/c000091d] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Significant improvements in NMR technology and methods have propelled NMR studies to play an important role in a rapidly expanding number of applications involving the profiling of metabolites in biofluids. This review discusses recent technical advances in NMR spectroscopy based metabolite profiling methods, data processing and analysis over the last three years.
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Affiliation(s)
- Shucha Zhang
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - G. A. Nagana Gowda
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Tao Ye
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Daniel Raftery
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
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40
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41
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Sukumaran DK, Garcia E, Hua J, Tabaczynski W, Odunsi K, Andrews C, Szyperski T. Standard operating procedure for metabonomics studies of blood serum and plasma samples using a 1H-NMR micro-flow probe. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2009; 47 Suppl 1:S81-S85. [PMID: 19688872 DOI: 10.1002/mrc.2469] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A standard operating procedure (SOP) is presented for high-throughput metabonomics studies using a 600 MHz NMR spectrometer equipped with a micro-flow probe that is connected to an auto-sampler. The procedure is designed to minimize random and systematic variation of NMR data collection. In addition, a protocol is described to assess the quality of the data acquired by a given NMR spectroscopist to ensure that (i) all researchers involved in the NMR data acquisition of a metabonomics research program perform equally and (ii) operator-associated variation of NMR data collection is statistically not relevant for the interpretation of results obtained from multivariate data analyses.
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Affiliation(s)
- Dinesh K Sukumaran
- Department of Chemistry, The State University of New York at Buffalo, Buffalo, NY, USA
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42
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Abstract
Metabonomics is a new technology providing broad information about dynamic metabolic responses in living systems to pathophysiological stimuli or genetic modification. Nuclear magnetic resonance (NMR) spectroscopy is one of the most powerful methods in metabonomics; it is utilized to establish the metabolic profiles of biofluids, and is practically the only method capable of examining intact tissue samples. Experience with the application of metabonomics in eye research is still limited, yet this method provides the possibility of exploring metabolic processes in the eye in vivo. This article presents a brief background to the usefulness of metabonomics, and the possible applications of an NMR-based technique in eye research and clinical practice.
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Affiliation(s)
- Anna Midelfart
- Department of Ophthalmology, Faculty of Medicine, Institute of Neuroscience, Norwegian University of Science and Technology and University Hospital, Trondheim, Norway.
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43
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Spectroscopic correlation analysis of NMR-based metabonomics in exercise science. Anal Chim Acta 2009; 652:173-9. [DOI: 10.1016/j.aca.2009.07.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Revised: 07/03/2009] [Accepted: 07/03/2009] [Indexed: 11/23/2022]
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Sands CJ, Coen M, Maher AD, Ebbels TMD, Holmes E, Lindon JC, Nicholson JK. Statistical Total Correlation Spectroscopy Editing of 1H NMR Spectra of Biofluids: Application to Drug Metabolite Profile Identification and Enhanced Information Recovery. Anal Chem 2009; 81:6458-66. [DOI: 10.1021/ac900828p] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Caroline J. Sands
- Department of Biomolecular Medicine, Sir Alexander Fleming Building, Division of Surgery, Oncology, Reproductive Biology and Anesthetics, Faculty of Medicine, Imperial College London, SW7 2AZ, United Kingdom
| | - Muireann Coen
- Department of Biomolecular Medicine, Sir Alexander Fleming Building, Division of Surgery, Oncology, Reproductive Biology and Anesthetics, Faculty of Medicine, Imperial College London, SW7 2AZ, United Kingdom
| | - Anthony D. Maher
- Department of Biomolecular Medicine, Sir Alexander Fleming Building, Division of Surgery, Oncology, Reproductive Biology and Anesthetics, Faculty of Medicine, Imperial College London, SW7 2AZ, United Kingdom
| | - Timothy M. D. Ebbels
- Department of Biomolecular Medicine, Sir Alexander Fleming Building, Division of Surgery, Oncology, Reproductive Biology and Anesthetics, Faculty of Medicine, Imperial College London, SW7 2AZ, United Kingdom
| | - Elaine Holmes
- Department of Biomolecular Medicine, Sir Alexander Fleming Building, Division of Surgery, Oncology, Reproductive Biology and Anesthetics, Faculty of Medicine, Imperial College London, SW7 2AZ, United Kingdom
| | - John C. Lindon
- Department of Biomolecular Medicine, Sir Alexander Fleming Building, Division of Surgery, Oncology, Reproductive Biology and Anesthetics, Faculty of Medicine, Imperial College London, SW7 2AZ, United Kingdom
| | - Jeremy K. Nicholson
- Department of Biomolecular Medicine, Sir Alexander Fleming Building, Division of Surgery, Oncology, Reproductive Biology and Anesthetics, Faculty of Medicine, Imperial College London, SW7 2AZ, United Kingdom
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45
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Loo RL, Coen M, Ebbels T, Cloarec O, Maibaum E, Bictash M, Yap I, Elliott P, Stamler J, Nicholson JK, Holmes E. Metabolic profiling and population screening of analgesic usage in nuclear magnetic resonance spectroscopy-based large-scale epidemiologic studies. Anal Chem 2009; 81:5119-29. [PMID: 19489597 PMCID: PMC2726443 DOI: 10.1021/ac900567e] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The application of a (1)H nuclear magnetic resonance (NMR) spectroscopy-based screening method for determining the use of two widely available analgesics (acetaminophen and ibuprofen) in epidemiologic studies has been investigated. We used samples and data from the cross-sectional INTERMAP Study involving participants from Japan (n = 1145), China (n = 839), U.K. (n = 501), and the U.S. (n = 2195). An orthogonal projection to latent structures discriminant analysis (OPLS-DA) algorithm with an incorporated Monte Carlo resampling function was applied to the NMR data set to determine which spectra contained analgesic metabolites. OPLS-DA preprocessing parameters (normalization, bin width, scaling, and input parameters) were assessed systematically to identify an optimal acetaminophen prediction model. Subsets of INTERMAP spectra were examined to verify and validate the presence/absence of acetaminophen/ibuprofen based on known chemical shift and coupling patterns. The optimized and validated acetaminophen model correctly predicted 98.2%, and the ibuprofen model correctly predicted 99.0% of the urine specimens containing these drug metabolites. The acetaminophen and ibuprofen models were subsequently used to predict the presence/absence of these drug metabolites for the remaining INTERMAP specimens. The acetaminophen model identified 415 out of 8436 spectra as containing acetaminophen metabolite signals while the ibuprofen model identified 245 out of 8604 spectra as containing ibuprofen metabolite signals from the global data set after excluding samples used to construct the prediction models. The NMR-based metabolic screening strategy provides a new objective approach for evaluation of self-reported medication data and is extendable to other aspects of population xenometabolome profiling.
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Affiliation(s)
- Ruey Leng Loo
- Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics (SORA), Faculty of Medicine, Imperial College London, SW7 2AZ, UK
| | - Muireann Coen
- Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics (SORA), Faculty of Medicine, Imperial College London, SW7 2AZ, UK
| | - Timothy Ebbels
- Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics (SORA), Faculty of Medicine, Imperial College London, SW7 2AZ, UK
| | - Olivier Cloarec
- Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics (SORA), Faculty of Medicine, Imperial College London, SW7 2AZ, UK
| | - Elaine Maibaum
- Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics (SORA), Faculty of Medicine, Imperial College London, SW7 2AZ, UK
| | - Magda Bictash
- Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics (SORA), Faculty of Medicine, Imperial College London, SW7 2AZ, UK
- Department of Epidemiology and Public Health, Imperial College London, St Mary's Campus, London, UK
| | - Ivan Yap
- Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics (SORA), Faculty of Medicine, Imperial College London, SW7 2AZ, UK
- Department of Epidemiology and Public Health, Imperial College London, St Mary's Campus, London, UK
| | - Paul Elliott
- Department of Epidemiology and Public Health, Imperial College London, St Mary's Campus, London, UK
| | - Jeremiah Stamler
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Jeremy K. Nicholson
- Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics (SORA), Faculty of Medicine, Imperial College London, SW7 2AZ, UK
| | - Elaine Holmes
- Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics (SORA), Faculty of Medicine, Imperial College London, SW7 2AZ, UK
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46
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Abstract
Diabetes is characterized by hyperglycemia due to dysfunction of insulin secretion or action. The two most common forms are Type 1 diabetes, in which pancreatic β-cells are destroyed, and Type 2 diabetes, in which a combination of disordered insulin action and secretion results in abnormal carbohydrate, lipid and protein metabolism. Metabonomics employs analytical technologies to measure ‘global’ metabolic responses to a disease state. With the aid of statistical pattern recognition, this can reveal novel insights into the biochemical consequences of diabetes. The metabonomic method can be divided into four stages: sample collection; preparation; data acquisition and processing; and statistical analyses. In this review, we describe the most recent developments at each experimental stage in detail, and comment on specific precautions or improvements that should be taken into account when studying diabetes. Finally, we end with speculations as to where and how the field will develop in the future. Metabonomics provides a logical framework for understanding the global metabolic effects of diabetes. Continuing technological improvements will expand our knowledge of the causes and progression of this disease, and enhance treatment options for individuals.
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47
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Angulo S, García-Pérez I, Legido-Quigley C, Barbas C. The autocorrelation matrix probing biochemical relationships after metabolic fingerprinting with CE. Electrophoresis 2009; 30:1221-7. [DOI: 10.1002/elps.200800554] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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48
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Maher AD, Cloarec O, Patki P, Craggs M, Holmes E, Lindon JC, Nicholson JK. Dynamic biochemical information recovery in spontaneous human seminal fluid reactions via 1H NMR kinetic statistical total correlation spectroscopy. Anal Chem 2009; 81:288-95. [PMID: 19117456 DOI: 10.1021/ac801993m] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Human seminal fluid (HSF) is a complex mixture of reacting glandular metabolite and protein secretions that provides critical support functions in fertilization. We have employed 600-MHz (1)H NMR spectroscopy to compare and contrast the temporal biochemical and biophysical changes in HSF from infertile men with spinal cord injury compared to age-matched controls. We have developed new approaches to data analysis and visualization to facilitate the interpretation of the results, including the first application of the recently published K-STOCSY concept to a biofluid, enhancing the extraction of information on biochemically related metabolites and assignment of resonances from the major seminal protein, semenogelin. Principal components analysis was also applied to evaluate the extent to which macromolecules influence the overall variation in the metabolic data set. The K-STOCSY concept was utilized further to determine the relationships between reaction rates and metabolite levels, revealing that choline, N-acetylglucosamine, and uridine are associated with higher peptidase activity. The novel approach adopted here has the potential to capture dynamic information in any complex mixture of reacting chemicals including other biofluids or cell extracts.
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Affiliation(s)
- Anthony D Maher
- Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics (SORA), Faculty of Medicine, Imperial College London, South Kensington, SW7 2AZ, United Kingdom.
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49
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Veselkov KA, Lindon JC, Ebbels TMD, Crockford D, Volynkin VV, Holmes E, Davies DB, Nicholson JK. Recursive Segment-Wise Peak Alignment of Biological 1H NMR Spectra for Improved Metabolic Biomarker Recovery. Anal Chem 2008; 81:56-66. [DOI: 10.1021/ac8011544] [Citation(s) in RCA: 267] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kirill A. Veselkov
- Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anesthetics (SORA), Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, SW7 2AZ, London, U.K., and Department of Physics, Sevastopol National Technical University, Streletskaya Bay, Crimea, Ukraine
| | - John C. Lindon
- Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anesthetics (SORA), Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, SW7 2AZ, London, U.K., and Department of Physics, Sevastopol National Technical University, Streletskaya Bay, Crimea, Ukraine
| | - Timothy M. D. Ebbels
- Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anesthetics (SORA), Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, SW7 2AZ, London, U.K., and Department of Physics, Sevastopol National Technical University, Streletskaya Bay, Crimea, Ukraine
| | - Derek Crockford
- Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anesthetics (SORA), Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, SW7 2AZ, London, U.K., and Department of Physics, Sevastopol National Technical University, Streletskaya Bay, Crimea, Ukraine
| | - Vladimir V. Volynkin
- Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anesthetics (SORA), Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, SW7 2AZ, London, U.K., and Department of Physics, Sevastopol National Technical University, Streletskaya Bay, Crimea, Ukraine
| | - Elaine Holmes
- Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anesthetics (SORA), Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, SW7 2AZ, London, U.K., and Department of Physics, Sevastopol National Technical University, Streletskaya Bay, Crimea, Ukraine
| | - David B. Davies
- Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anesthetics (SORA), Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, SW7 2AZ, London, U.K., and Department of Physics, Sevastopol National Technical University, Streletskaya Bay, Crimea, Ukraine
| | - Jeremy K. Nicholson
- Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anesthetics (SORA), Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, SW7 2AZ, London, U.K., and Department of Physics, Sevastopol National Technical University, Streletskaya Bay, Crimea, Ukraine
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50
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Nuclear magnetic resonance and liquid chromatography-mass spectrometry combined with an incompleted separation strategy for identifying the natural products in crude extract. Anal Chim Acta 2008; 632:221-8. [PMID: 19110097 DOI: 10.1016/j.aca.2008.11.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2008] [Revised: 10/29/2008] [Accepted: 11/02/2008] [Indexed: 11/23/2022]
Abstract
NMR and LC-MS combined with an incompleted separation strategy were proposed to the simultaneous structure identification of natural products in crude extracts, and a novel method termed as NMR/LC-MS parallel dynamic spectroscopy (NMR/LC-MS PDS) was developed to discover the intrinsic correlation between retention time (Rt), mass/charge (m/z) and chemical shift (delta) data of the same constituent from mixture spectra by the co-analysis of parallelly visualized multispectroscopic datasets from LC-MS and (1)H NMR. The extracted ion chromatogram (XIC) and (1)H NMR signals deriving from the same individual constituent were correlated through fraction ranges and intensity changing profiles in NMR/LC-MS PDS spectrum due to the signal amplitude co-variation resulted from the concentration variation of constituents in a series of incompletely separated fractions. NMR/LC-MS PDS was applied to identify 12 constituents in an active herbal extract including flavonol glycosides, which was separated into a series of fractions by flash column chromatography. The complementary spectral information of the same individual constituent in the crude extract was discovered simultaneously from mixture spectra. Especially, two groups of co-eluted isomers were identified successfully. The results demonstrated that NMR/LC-MS PDS combined with the incompleted separation strategy achieved the similar function of on-line LC-NMR-MS analysis in off-line mode and had the potential for simplifying and accelerating the analytical routes for structure identification of constituents in herbs or their active extracts.
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