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Çiçek SS, Moreno Cardenas C, Girreser U. Determination of Total Sennosides and Sennosides A, B, and A 1 in Senna Leaflets, Pods, and Tablets by Two-Dimensional qNMR. Molecules 2022; 27:7349. [PMID: 36364175 PMCID: PMC9656819 DOI: 10.3390/molecules27217349] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 10/23/2022] [Accepted: 10/26/2022] [Indexed: 03/20/2024] Open
Abstract
In the present work, a two-dimensional qNMR method for the determination of sennosides was established. Using band-selective HSQC and the cross correlations of the characteristic 10-10' bonds, we quantified the total amount of the value-determining dianthranoids in five minutes, thus, rendering the method not only fast, but also specific and stability indicating. The validation of the method revealed excellent accuracy (recovery rates of 98.5 to 103%), precision (RSD values of 3.1%), and repeatability (2.2%) and demonstrated the potential of 2D qNMR in the quality control of medicinal plants. In a second method, the use of 2D qNMR for the single analysis of sennosides A, B, and A1 was evaluated with acceptable measurement times (31 min), accuracy (93.8%), and repeatability (5.4% and 5.6%) for the two major purgatives sennoside A and B. However, the precision for sennoside B and A1 was not satisfactory, mainly due to the low resolution of the HSQC signals of the two compounds.
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Affiliation(s)
- Serhat Sezai Çiçek
- Pharmazeutisches Institut, Abteilung Pharmazeutische Biologie, Christian-Albrechts-Universität zu Kiel, Gutenbergstraße 76, 24118 Kiel, Germany
| | - Calisto Moreno Cardenas
- Pharmazeutisches Institut, Abteilung Pharmazeutische Biologie, Christian-Albrechts-Universität zu Kiel, Gutenbergstraße 76, 24118 Kiel, Germany
| | - Ulrich Girreser
- Pharmazeutisches Institut, Abteilung Pharmazeutische und Medizinische Chemie, Christian-Albrechts-Universität zu Kiel, Gutenbergstraße 76, 24118 Kiel, Germany
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2
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Migdadi L, Telfah A, Hergenröder R, Wöhler C. Novelty Detection for Metabolic Dynamics Established On Breast Cancer Tissue Using 2D NMR TOCSY Spectra. Comput Struct Biotechnol J 2022; 20:2965-2977. [PMID: 35782733 PMCID: PMC9213235 DOI: 10.1016/j.csbj.2022.05.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/26/2022] [Accepted: 05/26/2022] [Indexed: 11/30/2022] Open
Abstract
Automatic novelty detection of metabolites of 2D-TOCSY NMR spectra. Metabolic profiling of the dynamics changes in Breast cancer tissue sample. Accurate and fast automatic multicomponent peak assignment of 2D NMR spectrum. One- and multi- novelty detection of metabolites.
Most metabolic profiling approaches focus only on identifying pre-known metabolites on NMR TOCSY spectrum using configured parameters. However, there is a lack of tasks dealing with automating the detection of new metabolites that might appear during the dynamic evolution of biological cells. Novelty detection is a category of machine learning that is used to identify data that emerge during the test phase and were not considered during the training phase. We propose a novelty detection system for detecting novel metabolites in the 2D NMR TOCSY spectrum of a breast cancer-tissue sample. We build one- and multi-class recognition systems using different classifiers such as, Kernel Null Foley-Sammon Transform, Kernel Density Estimation, and Support Vector Data Description. The training models were constructed based on different sizes of training data and are used in the novelty detection procedure. Multiple evaluation measures were applied to test the performance of the novelty detection methods. Depending on the training data size, all classifiers were able to achieve 0% false positive rates and total misclassification error in addition to 100% true positive rates. The median total time for the novelty detection process varies between 1.5 and 20 seconds, depending on the classifier and the amount of training data. The results of our novel metabolic profiling method demonstrate its suitability, robustness and speed in automated metabolic research.
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Affiliation(s)
- Lubaba Migdadi
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, 44139 Dortmund, Germany
- Image Analysis Group, TU Dortmund, 44227 Dortmund, Germany
- Corresponding author.
| | - Ahmad Telfah
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, 44139 Dortmund, Germany
| | - Roland Hergenröder
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, 44139 Dortmund, Germany
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Honrao C, Teissier N, Zhang B, Powers R, O’Day EM. Gadolinium-Based Paramagnetic Relaxation Enhancement Agent Enhances Sensitivity for NUS Multidimensional NMR-Based Metabolomics. Molecules 2021; 26:molecules26175115. [PMID: 34500549 PMCID: PMC8433644 DOI: 10.3390/molecules26175115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 01/03/2023] Open
Abstract
Gadolinium is a paramagnetic relaxation enhancement (PRE) agent that accelerates the relaxation of metabolite nuclei. In this study, we noted the ability of gadolinium to improve the sensitivity of two-dimensional, non-uniform sampled NMR spectral data collected from metabolomics samples. In time-equivalent experiments, the addition of gadolinium increased the mean signal intensity measurement and the signal-to-noise ratio for metabolite resonances in both standard and plasma samples. Gadolinium led to highly linear intensity measurements that correlated with metabolite concentrations. In the presence of gadolinium, we were able to detect a broad array of metabolites with a lower limit of detection and quantification in the low micromolar range. We also observed an increase in the repeatability of intensity measurements upon the addition of gadolinium. The results of this study suggest that the addition of a gadolinium-based PRE agent to metabolite samples can improve NMR-based metabolomics.
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Affiliation(s)
| | | | - Bo Zhang
- Olaris, Inc., Waltham, MA 02451, USA; (C.H.); (N.T.); (B.Z.)
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
- Correspondence: (R.P.); (E.M.O.)
| | - Elizabeth M. O’Day
- Olaris, Inc., Waltham, MA 02451, USA; (C.H.); (N.T.); (B.Z.)
- Correspondence: (R.P.); (E.M.O.)
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4
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Hoyt L, O'Day EM. Perspective: A potential role for NUS in metabolite-based in vitro diagnostics. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:257-263. [PMID: 32997360 DOI: 10.1002/mrc.5104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/17/2020] [Accepted: 09/25/2020] [Indexed: 06/11/2023]
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Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a major analytical method used in the growing field of metabolomics. Although NMR is relatively less sensitive than mass spectrometry, this analytical platform has numerous characteristics including its high reproducibility and quantitative abilities, its nonselective and noninvasive nature, and the ability to identify unknown metabolites in complex mixtures and trace the downstream products of isotope labeled substrates ex vivo, in vivo, or in vitro. Metabolomic analysis of highly complex biological mixtures has benefitted from the advances in both NMR data acquisition and analysis methods. Although metabolomics applications span a wide range of disciplines, a majority has focused on understanding, preventing, diagnosing, and managing human diseases. This chapter describes NMR-based methods relevant to the rapidly expanding metabolomics field.
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Evaluation of Non-Uniform Sampling 2D 1H- 13C HSQC Spectra for Semi-Quantitative Metabolomics. Metabolites 2020; 10:metabo10050203. [PMID: 32429340 PMCID: PMC7281502 DOI: 10.3390/metabo10050203] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/04/2020] [Accepted: 05/12/2020] [Indexed: 12/16/2022] Open
Abstract
Metabolomics is the comprehensive study of metabolism, the biochemical processes that sustain life. By comparing metabolites between healthy and disease states, new insights into disease mechanisms can be uncovered. NMR is a powerful analytical method to detect and quantify metabolites. Standard one-dimensional (1D) 1H-NMR metabolite profiling is informative but challenged by significant chemical shift overlap. Multi-dimensional NMR can increase resolution, but the required long acquisition times lead to limited throughput. Non-uniform sampling (NUS) is a well-accepted mode of acquiring multi-dimensional NMR data, enabling either reduced acquisition times or increased sensitivity in equivalent time. Despite these advantages, the technique is not widely applied to metabolomics. In this study, we evaluated the utility of NUS 1H–13C heteronuclear single quantum coherence (HSQC) for semi-quantitative metabolomics. We demonstrated that NUS improved sensitivity compared to uniform sampling (US). We verified that the NUS measurement maintains linearity, making it possible to detect metabolite changes across samples and studies. Furthermore, we calculated the lower limit of detection and quantification (LOD/LOQ) of common metabolites. Finally, we demonstrate that the measurements are repeatable on the same system and across different systems. In conclusion, our results detail the analytical capability of NUS and, in doing so, empower the future use of NUS 1H–13C HSQC in metabolomic studies.
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Girreser U, Ugolini T, Çiçek SS. Quality control of Aloe vera (Aloe barbadensis) and Aloe ferox using band-selective quantitative heteronuclear single quantum correlation spectroscopy (bs-qHSQC). Talanta 2019; 205:120109. [DOI: 10.1016/j.talanta.2019.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/27/2019] [Accepted: 07/01/2019] [Indexed: 01/20/2023]
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Çiçek SS, Ugolini T, Girreser U. Two-dimensional qNMR of anthraquinones in Frangula alnus (Rhamnus frangula) using surrogate standards and delay time adaption. Anal Chim Acta 2019; 1081:131-137. [DOI: 10.1016/j.aca.2019.06.046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/20/2019] [Accepted: 06/23/2019] [Indexed: 01/09/2023]
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Ranjan R, Sinha N. Nuclear magnetic resonance (NMR)-based metabolomics for cancer research. NMR IN BIOMEDICINE 2019; 32:e3916. [PMID: 29733484 DOI: 10.1002/nbm.3916] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 02/01/2018] [Accepted: 02/12/2018] [Indexed: 06/08/2023]
Abstract
Nuclear magnetic resonance (NMR) has emerged as an effective tool in various spheres of biomedical research, amongst which metabolomics is an important method for the study of various types of disease. Metabolomics has proved its stronghold in cancer research by the development of different NMR methods over time for the study of metabolites, thus identifying key players in the aetiology of cancer. A plethora of one-dimensional and two-dimensional NMR experiments (in solids, semi-solids and solution phases) are utilized to obtain metabolic profiles of biofluids, cell extracts and tissue biopsy samples, which can further be subjected to statistical analysis. Any alteration in the assigned metabolite peaks gives an indication of changes in metabolic pathways. These defined changes demonstrate the utility of NMR in the early diagnosis of cancer and provide further measures to combat malignancy and its progression. This review provides a snapshot of the trending NMR techniques and the statistical analysis involved in the metabolomics of diseases, with emphasis on advances in NMR methodology developed for cancer research.
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Affiliation(s)
- Renuka Ranjan
- Centre of Biomedical Research, SGPGIMS Campus, Raebarelly Road, Lucknow, India
- School of Biotechnology, Institute of Science Banaras Hindu University, Varanasi, India
| | - Neeraj Sinha
- Centre of Biomedical Research, SGPGIMS Campus, Raebarelly Road, Lucknow, India
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Abstract
The fast-growing field of metabolomics is impacting numerous areas of basic and life sciences. In metabolomics, analytical methods play a pivotal role, and nuclear magnetic resonance (NMR) and mass spectrometry (MS) have proven to be the most suitable and powerful methods. Although NMR exhibits lower sensitivity and resolution compared to MS, NMR's numerous important characteristics far outweigh its limitations. Some of its characteristics include excellent reproducibility and quantitative accuracy, the capability to analyze intact biospecimens, an unparalleled ability to identify unknown metabolites, the ability to trace in-cell and in-organelle metabolism in real time, and the capacity to trace metabolic pathways atom by atom using 2H, 13C, or 15N isotopes. Each of these characteristics has been exploited extensively in numerous studies. In parallel, the field has witnessed significant progress in instrumentation, methods development, databases, and automation that are focused on higher throughput and alleviating the limitations of NMR, in particular, resolution and sensitivity. Despite the advances, however, the high complexity of biological mixtures combined with the limitations in sensitivity and resolution continues to pose major challenges. These challenges need to be dealt with effectively to better realize the potential of metabolomics, in general. As a result, multifaceted efforts continue to focus on addressing the challenges as well as reaping the benefits of NMR-based metabolomics. This chapter highlights the current status with emphasis on the opportunities and challenges in NMR-based metabolomics.
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Çiçek SS, Pfeifer Barbosa AL, Girreser U. Quantification of diterpene acids in Copaiba oleoresin by UHPLC-ELSD and heteronuclear two-dimensional qNMR. J Pharm Biomed Anal 2018; 160:126-134. [DOI: 10.1016/j.jpba.2018.07.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/17/2018] [Accepted: 07/18/2018] [Indexed: 02/06/2023]
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Gołowicz D, Urbańczyk M, Shchukina A, Kazimierczuk K. SCoT: Swept coherence transfer for quantitative heteronuclear 2D NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2018; 294:1-6. [PMID: 29960129 DOI: 10.1016/j.jmr.2018.06.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/08/2018] [Accepted: 06/17/2018] [Indexed: 06/08/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is frequently applied in quantitative chemical analysis (qNMR). It is easy to measure one-dimensional (1D) NMR spectra in a quantitative regime (with appropriately long relaxation delays and acquisition times); however, their applicability is limited in the case of complex samples with severe peak overlap. Two-dimensional (2D) NMR solves the overlap problem, but at the cost of biasing peak intensities and hence quantitativeness. This is partly due to the uneven coherence transfer between excited/detected 1H nuclei and the heteronuclei coupled to them (typically 13C). In the traditional approach, the transfer occurs via the evolution of a spin system state under the J-coupling Hamiltonian during a delay of a fixed length. The delay length is set on the basis of the predicted average coupling constant in the sample. This leads to disturbances for pairs of nuclei with coupling constants deviating from this average. Here, we present a novel approach based on non-standard processing of the data acquired in experiments, where the coherence transfer delay is co-incremented with non-uniformly sampled evolution time. This method allows us to obtain the optimal transfer for all resonances, which improves quantitativeness. We demonstrate the concept for the coherence transfer and multiplicity-edit delays in a heteronuclear single-quantum correlation experiment (HSQC).
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Affiliation(s)
- Dariusz Gołowicz
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland; Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland
| | - Mateusz Urbańczyk
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland
| | - Alexandra Shchukina
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097 Warsaw, Poland; Institute for Spectroscopy, Russian Academy of Sciences, Fizicheskaya 5, Troitsk, 108840 Moscow, Russia
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13
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Schlippenbach TV, Oefner PJ, Gronwald W. Systematic Evaluation of Non-Uniform Sampling Parameters in the Targeted Analysis of Urine Metabolites by 1H, 1H 2D NMR Spectroscopy. Sci Rep 2018; 8:4249. [PMID: 29523811 PMCID: PMC5844889 DOI: 10.1038/s41598-018-22541-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 02/23/2018] [Indexed: 11/15/2022] Open
Abstract
Non-uniform sampling (NUS) allows the accelerated acquisition of multidimensional NMR spectra. The aim of this contribution was the systematic evaluation of the impact of various quantitative NUS parameters on the accuracy and precision of 2D NMR measurements of urinary metabolites. Urine aliquots spiked with varying concentrations (15.6-500.0 µM) of tryptophan, tyrosine, glutamine, glutamic acid, lactic acid, and threonine, which can only be resolved fully by 2D NMR, were used to assess the influence of the sampling scheme, reconstruction algorithm, amount of omitted data points, and seed value on the quantitative performance of NUS in 1H,1H-TOCSY and 1H,1H-COSY45 NMR spectroscopy. Sinusoidal Poisson-gap sampling and a compressed sensing approach employing the iterative re-weighted least squares method for spectral reconstruction allowed a 50% reduction in measurement time while maintaining sufficient quantitative accuracy and precision for both types of homonuclear 2D NMR spectroscopy. Together with other advances in instrument design, such as state-of-the-art cryogenic probes, use of 2D NMR spectroscopy in large biomedical cohort studies seems feasible.
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Affiliation(s)
- Trixi von Schlippenbach
- Institute of Functional Genomics, University of Regensburg, Am BioPark 9, 93053, Regensburg, Germany
| | - Peter J Oefner
- Institute of Functional Genomics, University of Regensburg, Am BioPark 9, 93053, Regensburg, Germany
| | - Wolfram Gronwald
- Institute of Functional Genomics, University of Regensburg, Am BioPark 9, 93053, Regensburg, Germany.
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Rapid two-dimensional ALSOFAST-HSQC experiment for metabolomics and fluxomics studies: application to a 13C-enriched cancer cell model treated with gold nanoparticles. Anal Bioanal Chem 2018; 410:2793-2804. [PMID: 29480388 DOI: 10.1007/s00216-018-0961-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 02/01/2018] [Accepted: 02/09/2018] [Indexed: 02/05/2023]
Abstract
Isotope labeling enables the use of 13C-based metabolomics techniques with strongly improved resolution for a better identification of relevant metabolites and tracing of metabolic fluxes in cell and animal models, as required in fluxomics studies. However, even at high NMR-active isotope abundance, the acquisition of one-dimensional 13C and classical two-dimensional 1H,13C-HSQC experiments remains time consuming. With the aim to provide a shorter, more efficient alternative, herein we explored the ALSOFAST-HSQC experiment with its rapid acquisition scheme for the analysis of 13C-labeled metabolites in complex biological mixtures. As an initial step, the parameters of the pulse sequence were optimized to take into account the specific characteristics of the complex samples. We then applied the fast two-dimensional experiment to study the effect of different kinds of antioxidant gold nanoparticles on a HeLa cancer cell model grown on 13C glucose-enriched medium. As a result, 1H,13C-2D correlations could be obtained in a couple of seconds to few minutes, allowing a simple and reliable identification of various 13C-enriched metabolites and the determination of specific variations between the different sample groups. Thus, it was possible to monitor glucose metabolism in the cell model and study the antioxidant effect of the coated gold nanoparticles in detail. Finally, with an experiment time of only half an hour, highly resolved 1H,13C-HSQC spectra using the ALSOFAST-HSQC pulse sequence were acquired, revealing the isotope-position-patterns of the corresponding 13C-nuclei from carbon multiplets. Graphical abstract Fast NMR applied to metabolomics and fluxomics studies with gold nanoparticles.
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Sharma R, Gogna N, Singh H, Dorai K. Fast profiling of metabolite mixtures using chemometric analysis of a speeded-up 2D heteronuclear correlation NMR experiment. RSC Adv 2017. [DOI: 10.1039/c7ra04032f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
One-dimensional (1D) NMR spectra of mixtures of metabolites suffer from severe overlap of spectral resonances and hence recent research in NMR-based metabolomics focuses on using two-dimensional (2D) NMR experiments for metabolite fingerprinting.
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Affiliation(s)
- Rakesh Sharma
- Department of Physical Sciences
- Indian Institute of Science Education & Research (IISER) Mohali
- India
| | - Navdeep Gogna
- Department of Physical Sciences
- Indian Institute of Science Education & Research (IISER) Mohali
- India
| | - Harpreet Singh
- Department of Physical Sciences
- Indian Institute of Science Education & Research (IISER) Mohali
- India
| | - Kavita Dorai
- Department of Physical Sciences
- Indian Institute of Science Education & Research (IISER) Mohali
- India
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16
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Walker LR, Hoyt DW, Walker SM, Ward JK, Nicora CD, Bingol K. Unambiguous metabolite identification in high-throughput metabolomics by hybrid 1D 1 H NMR/ESI MS 1 approach. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2016; 54:998-1003. [PMID: 27539910 DOI: 10.1002/mrc.4503] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/08/2016] [Accepted: 08/15/2016] [Indexed: 06/06/2023]
Affiliation(s)
- Lawrence R Walker
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - David W Hoyt
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - S Michael Walker
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
| | - Joy K Ward
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
| | - Carrie D Nicora
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Kerem Bingol
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
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Smirnov KS, Maier TV, Walker A, Heinzmann SS, Forcisi S, Martinez I, Walter J, Schmitt-Kopplin P. Challenges of metabolomics in human gut microbiota research. Int J Med Microbiol 2016; 306:266-279. [PMID: 27012595 DOI: 10.1016/j.ijmm.2016.03.006] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/08/2016] [Accepted: 03/09/2016] [Indexed: 01/17/2023] Open
Abstract
The review highlights the role of metabolomics in studying human gut microbial metabolism. Microbial communities in our gut exert a multitude of functions with huge impact on human health and disease. Within the meta-omics discipline, gut microbiome is studied by (meta)genomics, (meta)transcriptomics, (meta)proteomics and metabolomics. The goal of metabolomics research applied to fecal samples is to perform their metabolic profiling, to quantify compounds and classes of interest, to characterize small molecules produced by gut microbes. Nuclear magnetic resonance spectroscopy and mass spectrometry are main technologies that are applied in fecal metabolomics. Metabolomics studies have been increasingly used in gut microbiota related research regarding health and disease with main focus on understanding inflammatory bowel diseases. The elucidated metabolites in this field are summarized in this review. We also addressed the main challenges of metabolomics in current and future gut microbiota research. The first challenge reflects the need of adequate analytical tools and pipelines, including sample handling, selection of appropriate equipment, and statistical evaluation to enable meaningful biological interpretation. The second challenge is related to the choice of the right animal model for studies on gut microbiota. We exemplified this using NMR spectroscopy for the investigation of cross-species comparison of fecal metabolite profiles. Finally, we present the problem of variability of human gut microbiota and metabolome that has important consequences on the concepts of personalized nutrition and medicine.
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Affiliation(s)
- Kirill S Smirnov
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Tanja V Maier
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Alesia Walker
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Silke S Heinzmann
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Sara Forcisi
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany
| | - Inés Martinez
- Department of Agriculture, Food and Nutritional Science, University of Alberta, T6G 2E1 Edmonton, AB, Canada
| | - Jens Walter
- Department of Agriculture, Food and Nutritional Science, University of Alberta, T6G 2E1 Edmonton, AB, Canada
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstraße 1, Neuherberg, 85764, Germany; Chair of Analytical Food Chemistry, Technische Universität München, Alte Akademie 10, 85354 Freising, Germany; ZIEL, Institute for Food & Health, Weihenstephaner Berg 1, 85354 Freising, Germany.
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18
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Emwas AH, Roy R, McKay RT, Ryan D, Brennan L, Tenori L, Luchinat C, Gao X, Zeri AC, Gowda GAN, Raftery D, Steinbeck C, Salek RM, Wishart DS. Recommendations and Standardization of Biomarker Quantification Using NMR-Based Metabolomics with Particular Focus on Urinary Analysis. J Proteome Res 2016; 15:360-73. [PMID: 26745651 PMCID: PMC4865177 DOI: 10.1021/acs.jproteome.5b00885] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
NMR-based metabolomics has shown considerable promise in disease diagnosis and biomarker discovery because it allows one to nondestructively identify and quantify large numbers of novel metabolite biomarkers in both biofluids and tissues. Precise metabolite quantification is a prerequisite to move any chemical biomarker or biomarker panel from the lab to the clinic. Among the biofluids commonly used for disease diagnosis and prognosis, urine has several advantages. It is abundant, sterile, and easily obtained, needs little sample preparation, and does not require invasive medical procedures for collection. Furthermore, urine captures and concentrates many "unwanted" or "undesirable" compounds throughout the body, providing a rich source of potentially useful disease biomarkers; however, incredible variation in urine chemical concentrations makes analysis of urine and identification of useful urinary biomarkers by NMR challenging. We discuss a number of the most significant issues regarding NMR-based urinary metabolomics with specific emphasis on metabolite quantification for disease biomarker applications and propose data collection and instrumental recommendations regarding NMR pulse sequences, acceptable acquisition parameter ranges, relaxation effects on quantitation, proper handling of instrumental differences, sample preparation, and biomarker assessment.
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Affiliation(s)
- Abdul-Hamid Emwas
- Imaging and Characterization Core Lab, KAUST , Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Raja Roy
- Centre of Biomedical Research, formerly, Centre of Biomedical Magnetic Resonance, Sanjay Gandhi Post-Graduate Institute of Medical Sciences Campus , Lucknow, Uttar Pradesh, India
| | - Ryan T McKay
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada
| | - Danielle Ryan
- School of Agricultural and Wine Sciences, Charles Sturt University , Bathurst, New South Wales, Australia
| | - Lorraine Brennan
- UCD Insitute of Food and Health, UCD , Belfield, Dublin, Ireland
| | - Leonardo Tenori
- FiorGen Foundation , 50019 Sesto Fiorentino, Florence, Italy
| | - Claudio Luchinat
- Centro Risonanze Magnetiche - CERM, University of Florence , Florence, Italy
| | - Xin Gao
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Ana Carolina Zeri
- Brazilian Biosciences National Laboratory, LNBio , Campinas, São Paulo, Brazil
| | - G A Nagana Gowda
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington , 850 Republican Street, Seattle, Washington 98109, United States
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington , 850 Republican Street, Seattle, Washington 98109, United States.,Fred Hutchinson Cancer Research Center , 1100 Fairview Avenue, Seattle, Washington 98109, United States
| | - Christoph Steinbeck
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Reza M Salek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - David S Wishart
- Department of Biological Sciences, University of Alberta , Edmonton, Alberta, Canada
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19
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Le Guennec A, Dumez JN, Giraudeau P, Caldarelli S. Resolution-enhanced 2D NMR of complex mixtures by non-uniform sampling. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:913-20. [PMID: 26053155 DOI: 10.1002/mrc.4258] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 03/28/2015] [Accepted: 04/08/2015] [Indexed: 05/20/2023]
Abstract
NMR is a powerful tool for the analysis of complex mixtures and the identification of individual components. Two-dimensional (2D) NMR potentially offers a wealth of information, but resolution is often sacrificed in order to contain experimental times. We explore the use of non-uniform sampling (NUS) to increase substantially the resolution of 2D NMR spectra of complex mixtures of small molecules, with no increase in experimental time. Two common pulse sequences for metabolomics applications are analysed, HSQC and TOCSY. Specific attention is paid to sensitivity in resolution-enhanced NUS spectra, using the signal-to-maximum-noise ratio as a metric. With a careful choice of sampling schedule and reconstruction algorithm, resolution in the (13) C dimension for HSQC is increased by a factor of at least 32, with no loss in sensitivity and no spurious peaks. For TOCSY, multiplets can be resolved in the indirect dimension in a reasonable experimental time. These properties should increase the usefulness of 2D NMR for metabolomics applications by, for example, increasing the chances of metabolite identification.
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Affiliation(s)
- Adrien Le Guennec
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Avenue de la Terrasse, 91190, Gif-sur-Yvette, France
- Université de Nantes, CNRS, CEISAM UMR 6230, BP92208, 2, rue de la Houssinière, F-44322, Nantes Cedex 03, France
| | - Jean-Nicolas Dumez
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Avenue de la Terrasse, 91190, Gif-sur-Yvette, France
| | - Patrick Giraudeau
- Université de Nantes, CNRS, CEISAM UMR 6230, BP92208, 2, rue de la Houssinière, F-44322, Nantes Cedex 03, France
- Institut Universitaire de France, 103 Boulevard St. Michel, 75005, Paris Cedex 5, France
| | - Stefano Caldarelli
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Avenue de la Terrasse, 91190, Gif-sur-Yvette, France
- Aix Marseille Université, Centrale Marseille, CNRS, iSm2 UMR 7313, 13397, Marseille, France
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20
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Worley B, Powers R. Generalized adaptive intelligent binning of multiway data. CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS : AN INTERNATIONAL JOURNAL SPONSORED BY THE CHEMOMETRICS SOCIETY 2015; 146:42-46. [PMID: 26052171 PMCID: PMC4456038 DOI: 10.1016/j.chemolab.2015.05.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
NMR metabolic fingerprinting methods almost exclusively rely upon the use of one-dimensional (1D) 1H NMR data to gain insights into chemical differences between two or more experimental classes. While 1D 1H NMR spectroscopy is a powerful, highly informative technique that can rapidly and nondestructively report details of complex metabolite mixtures, it suffers from significant signal overlap that hinders interpretation and quantification of individual analytes. Two-dimensional (2D) NMR methods that report heteronuclear connectivities can reduce spectral overlap, but their use in metabolic fingerprinting studies is limited. We describe a generalization of Adaptive Intelligent binning that enables its use on multidimensional datasets, allowing the direct use of nD NMR spectroscopic data in bilinear factorizations such as principal component analysis (PCA) and partial least squares (PLS).
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Affiliation(s)
| | - Robert Powers
- To whom correspondence should be addressed Robert Powers University of Nebraska-Lincoln Department of Chemistry 722 Hamilton Hall Lincoln, NE 68588-0304 Phone: (402) 472-3039 Fax: (402) 472-9402
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21
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Bingol K, Brüschweiler R. NMR/MS Translator for the Enhanced Simultaneous Analysis of Metabolomics Mixtures by NMR Spectroscopy and Mass Spectrometry: Application to Human Urine. J Proteome Res 2015; 14:2642-8. [PMID: 25881480 DOI: 10.1021/acs.jproteome.5b00184] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel metabolite identification strategy is presented for the combined NMR/MS analysis of complex metabolite mixtures. The approach first identifies metabolite candidates from 1D or 2D NMR spectra by NMR database query, which is followed by the determination of the masses (m/z) of their possible ions, adducts, fragments, and characteristic isotope distributions. The expected m/z ratios are then compared with the MS(1) spectrum for the direct assignment of those signals of the mass spectrum that contain information about the same metabolites as the NMR spectra. In this way, the mass spectrum can be assigned with very high confidence, and it provides at the same time validation of the NMR-derived metabolites. The method was first demonstrated on a model mixture, and it was then applied to human urine collected from a pool of healthy individuals. A number of metabolites could be detected that had not been reported previously, further extending the list of known urine metabolites. The new analysis approach, which is termed NMR/MS Translator, is fully automated and takes only a few seconds on a computer workstation. NMR/MS Translator synergistically uses the power of NMR and MS, enhancing the accuracy and efficiency of the identification of those metabolites compiled in databases.
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Affiliation(s)
- Kerem Bingol
- †Department of Chemistry and Biochemistry, ‡Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Rafael Brüschweiler
- †Department of Chemistry and Biochemistry, ‡Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
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22
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Emwas AH, Luchinat C, Turano P, Tenori L, Roy R, Salek RM, Ryan D, Merzaban JS, Kaddurah-Daouk R, Zeri AC, Nagana Gowda GA, Raftery D, Wang Y, Brennan L, Wishart DS. Standardizing the experimental conditions for using urine in NMR-based metabolomic studies with a particular focus on diagnostic studies: a review. Metabolomics 2015; 11:872-894. [PMID: 26109927 PMCID: PMC4475544 DOI: 10.1007/s11306-014-0746-7] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 10/27/2014] [Indexed: 02/08/2023]
Abstract
The metabolic composition of human biofluids can provide important diagnostic and prognostic information. Among the biofluids most commonly analyzed in metabolomic studies, urine appears to be particularly useful. It is abundant, readily available, easily stored and can be collected by simple, noninvasive techniques. Moreover, given its chemical complexity, urine is particularly rich in potential disease biomarkers. This makes it an ideal biofluid for detecting or monitoring disease processes. Among the metabolomic tools available for urine analysis, NMR spectroscopy has proven to be particularly well-suited, because the technique is highly reproducible and requires minimal sample handling. As it permits the identification and quantification of a wide range of compounds, independent of their chemical properties, NMR spectroscopy has been frequently used to detect or discover disease fingerprints and biomarkers in urine. Although protocols for NMR data acquisition and processing have been standardized, no consensus on protocols for urine sample selection, collection, storage and preparation in NMR-based metabolomic studies have been developed. This lack of consensus may be leading to spurious biomarkers being reported and may account for a general lack of reproducibility between laboratories. Here, we review a large number of published studies on NMR-based urine metabolic profiling with the aim of identifying key variables that may affect the results of metabolomics studies. From this survey, we identify a number of issues that require either standardization or careful accounting in experimental design and provide some recommendations for urine collection, sample preparation and data acquisition.
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Affiliation(s)
- Abdul-Hamid Emwas
- Imaging and Characterization Core Lab, King Abdullah University of Science and Technology, KSA, Thuwal, Saudi Arabia
| | - Claudio Luchinat
- Centro Risonanze Magnetiche – CERM, University of Florence, Florence, Italy
| | - Paola Turano
- Centro Risonanze Magnetiche – CERM, University of Florence, Florence, Italy
| | | | - Raja Roy
- Centre of Biomedical Research, Formerly known as Centre of Biomedical Magnetic Resonance, Sanjay Gandhi Post-Graduate Institute of Medical Sciences Campus, Lucknow, India
| | - Reza M. Salek
- Department of Biochemistry & Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD UK
| | - Danielle Ryan
- School of Agricultural and Wine Sciences, Charles Sturt University, Wagga Wagga, Australia
| | - Jasmeen S. Merzaban
- Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, KSA, Thuwal, Saudi Arabia
| | - Rima Kaddurah-Daouk
- Pharmacometabolomics Center, School of Medicine, Duke University, Durham, USA
| | - Ana Carolina Zeri
- Brazilian Biosciences National Laboratory, LNBio, Campinas, SP Brazil
| | - G. A. Nagana Gowda
- Department of Anethesiology and Pain Medicine, Northwest Metabolomics Research Center, University of Washington, 850 Republican St., Seattle, WA 98109 USA
| | - Daniel Raftery
- Department of Anethesiology and Pain Medicine, Northwest Metabolomics Research Center, University of Washington, 850 Republican St., Seattle, WA 98109 USA
| | - Yulan Wang
- Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Beijing, China
| | - Lorraine Brennan
- Institute of Food and Health and Conway Institute, School of Agriculture & Food Science, Dublin 4, Ireland
| | - David S. Wishart
- Department of Computing Science, University of Alberta, Edmonton, Alberta Canada
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23
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Öman T, Tessem MB, Bathen TF, Bertilsson H, Angelsen A, Hedenström M, Andreassen T. Identification of metabolites from 2D (1)H-(13)C HSQC NMR using peak correlation plots. BMC Bioinformatics 2014; 15:413. [PMID: 25511422 PMCID: PMC4274720 DOI: 10.1186/s12859-014-0413-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 12/08/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Identification of individual components in complex mixtures is an important and sometimes daunting task in several research areas like metabolomics and natural product studies. NMR spectroscopy is an excellent technique for analysis of mixtures of organic compounds and gives a detailed chemical fingerprint of most individual components above the detection limit. For the identification of individual metabolites in metabolomics, correlation or covariance between peaks in (1)H NMR spectra has previously been successfully employed. Similar correlation of 2D (1)H-(13)C Heteronuclear Single Quantum Correlation spectra was recently applied to investigate the structure of heparine. In this paper, we demonstrate how a similar approach can be used to identify metabolites in human biofluids (post-prostatic palpation urine). RESULTS From 50 (1)H-(13)C Heteronuclear Single Quantum Correlation spectra, 23 correlation plots resembling pure metabolites were constructed. The identities of these metabolites were confirmed by comparing the correlation plots with reported NMR data, mostly from the Human Metabolome Database. CONCLUSIONS Correlation plots prepared by statistically correlating (1)H-(13)C Heteronuclear Single Quantum Correlation spectra from human biofluids provide unambiguous identification of metabolites. The correlation plots highlight cross-peaks belonging to each individual compound, not limited by long-range magnetization transfer as conventional NMR experiments.
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Affiliation(s)
- Tommy Öman
- Department of Chemistry, Umeå University, Umeå, Sweden.
| | - May-Britt Tessem
- MI Lab, Department of Circulation and Medical Imaging, Norwegian University of Science and Technology (NTNU), Trondheim, Norway. .,St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway.
| | - Tone F Bathen
- MI Lab, Department of Circulation and Medical Imaging, Norwegian University of Science and Technology (NTNU), Trondheim, Norway. .,St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway.
| | - Helena Bertilsson
- Department of Urology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway. .,Department of Cancer Research and Molecular Medicine, NTNU, Trondheim, Norway.
| | - Anders Angelsen
- Department of Urology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway. .,Department of Cancer Research and Molecular Medicine, NTNU, Trondheim, Norway.
| | | | - Trygve Andreassen
- MR Core Facility, Department of Circulation and Medical Imaging, NTNU, Trondheim, Norway.
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24
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Larive CK, Barding GA, Dinges MM. NMR spectroscopy for metabolomics and metabolic profiling. Anal Chem 2014; 87:133-46. [PMID: 25375201 DOI: 10.1021/ac504075g] [Citation(s) in RCA: 170] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Cynthia K Larive
- Department of Chemistry, University of California-Riverside , Riverside, California 92521, United States
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25
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Guennec AL, Giraudeau P, Caldarelli S. Evaluation of Fast 2D NMR for Metabolomics. Anal Chem 2014; 86:5946-54. [DOI: 10.1021/ac500966e] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Adrien Le Guennec
- Centre de Recherche CNRS de Gif-sur-Yvette, Institut
de Chimie des Substances Naturelles, Laboratoire de Chimie et Biologie
Structurales, UPR 2301,
1, avenue de la Terrasse, 91198 Gif-sur-Yvette, France
- Université de Nantes, CNRS, CEISAM UMR 6230, BP 92208, 2 rue de la Houssinière, F-44322 Nantes Cedex 03, France
| | - Patrick Giraudeau
- Université de Nantes, CNRS, CEISAM UMR 6230, BP 92208, 2 rue de la Houssinière, F-44322 Nantes Cedex 03, France
| | - Stefano Caldarelli
- Centre de Recherche CNRS de Gif-sur-Yvette, Institut
de Chimie des Substances Naturelles, Laboratoire de Chimie et Biologie
Structurales, UPR 2301,
1, avenue de la Terrasse, 91198 Gif-sur-Yvette, France
- Aix Marseille Université, Centrale Marseille,
CNRS, iSm2 UMR 7313, 13397, Marseille, France
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26
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Bingol K, Bruschweiler-Li L, Li DW, Brüschweiler R. Customized metabolomics database for the analysis of NMR ¹H-¹H TOCSY and ¹³C-¹H HSQC-TOCSY spectra of complex mixtures. Anal Chem 2014; 86:5494-501. [PMID: 24773139 PMCID: PMC4051244 DOI: 10.1021/ac500979g] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
![]()
A customized metabolomics NMR database,
termed 1H(13C)-TOCCATA, is introduced, which
contains complete 1H and 13C chemical shift
information on individual spin
systems and isomeric states of common metabolites. Since this information
directly corresponds to cross sections of 2D 1H–1H TOCSY and 2D 13C–1H HSQC-TOCSY
spectra, it allows the straightforward and unambiguous identification
of metabolites of complex metabolic mixtures at 13C natural
abundance from these types of experiments. The 1H(13C)-TOCCATA database, which is complementary to the previously
introduced TOCCATA database for the analysis of uniformly 13C-labeled compounds, currently contains 455 metabolites, and it can
be used through a publicly accessible web portal. We demonstrate its
performance by applying it to 2D 1H–1H TOCSY and 2D 13C–1H HSQC-TOCSY spectra
of a cell lysate from E. coli, which
yields a substantial improvement over other databases, as well as
1D NMR-based approaches, in the number of compounds that can be correctly
identified with high confidence.
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Affiliation(s)
- Kerem Bingol
- Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States
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27
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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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28
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Bingol K, Brüschweiler R. Multidimensional approaches to NMR-based metabolomics. Anal Chem 2013; 86:47-57. [PMID: 24195689 DOI: 10.1021/ac403520j] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Kerem Bingol
- Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210
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29
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Mavel S, Nadal-Desbarats L, Blasco H, Bonnet-Brilhault F, Barthélémy C, Montigny F, Sarda P, Laumonnier F, Vourc′h P, Andres CR, Emond P. 1H–13C NMR-based urine metabolic profiling in autism spectrum disorders. Talanta 2013; 114:95-102. [DOI: 10.1016/j.talanta.2013.03.064] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 03/16/2013] [Accepted: 03/25/2013] [Indexed: 01/04/2023]
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30
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Bingol K, Zhang F, Bruschweiler-Li L, Brüschweiler R. Quantitative analysis of metabolic mixtures by two-dimensional 13C constant-time TOCSY NMR spectroscopy. Anal Chem 2013; 85:6414-20. [PMID: 23773204 PMCID: PMC4447502 DOI: 10.1021/ac400913m] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An increasing number of organisms can be fully (13)C-labeled, which has the advantage that their metabolomes can be studied by high-resolution two-dimensional (2D) NMR (13)C-(13)C constant-time (CT) total correlation spectroscopy (TOCSY) experiments. Individual metabolites can be identified via database searching or, in the case of novel compounds, through the reconstruction of their backbone-carbon topology. Determination of quantitative metabolite concentrations is another key task. Because strong peak overlaps in one-dimensional (1D) NMR spectra prevent straightforward quantification through 1D peak integrals, we demonstrate here the direct use of (13)C-(13)C CT-TOCSY spectra for metabolite quantification. This is accomplished through the quantum mechanical treatment of the TOCSY magnetization transfer at short and long-mixing times or by the use of analytical approximations, which are solely based on the knowledge of the carbon-backbone topologies. The methods are demonstrated for carbohydrate and amino acid mixtures.
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Affiliation(s)
- Kerem Bingol
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310
| | - Fengli Zhang
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310
| | - Lei Bruschweiler-Li
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306
| | - Rafael Brüschweiler
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306
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