1
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Venetos M, Elkin M, Delaney C, Hartwig JF, Persson KA. Deconvolution and Analysis of the 1H NMR Spectra of Crude Reaction Mixtures. J Chem Inf Model 2024; 64:3008-3020. [PMID: 38573053 PMCID: PMC11040730 DOI: 10.1021/acs.jcim.3c01864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is an important analytical technique in synthetic organic chemistry, but its integration into high-throughput experimentation workflows has been limited by the necessity of manually analyzing the NMR spectra of new chemical entities. Current efforts to automate the analysis of NMR spectra rely on comparisons to databases of reported spectra for known compounds and, therefore, are incompatible with the exploration of new chemical space. By reframing the NMR spectrum of a reaction mixture as a joint probability distribution, we have used Hamiltonian Monte Carlo Markov Chain and density functional theory to fit the predicted NMR spectra to those of crude reaction mixtures. This approach enables the deconvolution and analysis of the spectra of mixtures of compounds without relying on reported spectra. The utility of our approach to analyze crude reaction mixtures is demonstrated with the experimental spectra of reactions that generate a mixture of isomers, such as Wittig olefination and C-H functionalization reactions. The correct identification of compounds in a reaction mixture and their relative concentrations is achieved with a mean absolute error as low as 1%.
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Affiliation(s)
- Maxwell
C. Venetos
- Department
of Materials Science and Engineering, University
of California, Berkeley, California 94720, United States
| | - Masha Elkin
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Connor Delaney
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - John F. Hartwig
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Kristin A. Persson
- Department
of Materials Science and Engineering, University
of California, Berkeley, California 94720, United States
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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2
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Wu Y, Sanati O, Uchimiya M, Krishnamurthy K, Wedell J, Hoch JC, Edison AS, Delaglio F. SAND: Automated Time-Domain Modeling of NMR Spectra Applied to Metabolite Quantification. Anal Chem 2024; 96:1843-1851. [PMID: 38273718 PMCID: PMC10896553 DOI: 10.1021/acs.analchem.3c03078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 01/27/2024]
Abstract
Developments in untargeted nuclear magnetic resonance (NMR) metabolomics enable the profiling of thousands of biological samples. The exploitation of this rich source of information requires a detailed quantification of spectral features. However, the development of a consistent and automatic workflow has been challenging because of extensive signal overlap. To address this challenge, we introduce the software Spectral Automated NMR Decomposition (SAND). SAND follows on from the previous success of time-domain modeling and automatically quantifies entire spectra without manual interaction. The SAND approach uses hybrid optimization with Markov chain Monte Carlo methods, employing subsampling in both time and frequency domains. In particular, SAND randomly divides the time-domain data into training and validation sets to help avoid overfitting. We demonstrate the accuracy of SAND, which provides a correlation of ∼0.9 with ground truth on cases including highly overlapped simulated data sets, a two-compound mixture, and a urine sample spiked with different amounts of a four-compound mixture. We further demonstrate an automated annotation using correlation networks derived from SAND decomposed peaks, and on average, 74% of peaks for each compound can be recovered in single clusters. SAND is available in NMRbox, the cloud computing environment for NMR software hosted by the Network for Advanced NMR (NAN). Since the SAND method uses time-domain subsampling (i.e., random subset of time-domain points), it has the potential to be extended to a higher dimensionality and nonuniformly sampled data.
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Affiliation(s)
- Yue Wu
- Institute
of Bioinformatics, University of Georgia, Athens, Georgia 30602, United States
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | - Omid Sanati
- School
of Electrical and Computer Engineering, University of Georgia, Athens, Georgia 30602, United States
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | - Mario Uchimiya
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | | | - Jonathan Wedell
- National
Magnetic Resonance Facility, University
of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Jeffrey C. Hoch
- Department
of Molecular Biology and Biophysics, University
of Connecticut, Farmington, Connecticut 06030-3305, United States
| | - Arthur S. Edison
- Institute
of Bioinformatics, University of Georgia, Athens, Georgia 30602, United States
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
- Department
of Biochemistry and Molecular Biology, University
of Georgia, Athens, Georgia 30602, United States
| | - Frank Delaglio
- Institute
for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University
of Maryland, Rockville, Maryland 20850, United States
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3
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Domżał B, Nawrocka EK, Gołowicz D, Ciach MA, Miasojedow B, Kazimierczuk K, Gambin A. Magnetstein: An Open-Source Tool for Quantitative NMR Mixture Analysis Robust to Low Resolution, Distorted Lineshapes, and Peak Shifts. Anal Chem 2024; 96:188-196. [PMID: 38117933 PMCID: PMC10782418 DOI: 10.1021/acs.analchem.3c03594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/22/2023]
Abstract
1H NMR spectroscopy is a powerful tool for analyzing mixtures including determining the concentrations of individual components. When signals from multiple compounds overlap, this task requires computational solutions. They are typically based on peak-picking and the comparison of obtained peak lists with libraries of individual components. This can fail if peaks are not sufficiently resolved or when peak positions differ between the library and the mixture. In this paper, we present Magnetstein, a quantification algorithm rooted in the optimal transport theory that makes it robust to unexpected frequency shifts and overlapping signals. Thanks to this, Magnetstein can quantitatively analyze difficult spectra with the estimation trueness an order of magnitude higher than that of commercial tools. Furthermore, the method is easier to use than other approaches, having only two parameters with default values applicable to a broad range of experiments and requiring little to no preprocessing of the spectra.
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Affiliation(s)
- Barbara Domżał
- Faculty
of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, Warsaw 02-097, Poland
| | - Ewa Klaudia Nawrocka
- Centre
of New Technologies, University of Warsaw, Banacha 2C, Warsaw 02-097, Poland
| | - Dariusz Gołowicz
- Institute
of Physical Chemistry, Polish Academy of
Sciences, Kasprzaka 44/52, Warsaw 01-224, Poland
| | - Michał Aleksander Ciach
- Faculty
of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, Warsaw 02-097, Poland
| | - Błażej Miasojedow
- Faculty
of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, Warsaw 02-097, Poland
| | | | - Anna Gambin
- Faculty
of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, Warsaw 02-097, Poland
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4
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Quantitative 1H NMR with global spectral deconvolution approach for the determination of gamma-aminobutyric acid in Chinese yam (Dioscorea polystachya Turczaninow). ANAL SCI 2023; 39:221-227. [PMID: 36427159 DOI: 10.1007/s44211-022-00221-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/14/2022] [Indexed: 11/27/2022]
Abstract
We developed a quantitative proton nuclear magnetic resonance (qNMR) with global spectral deconvolution (GSD) method to determine the gamma-aminobutyric acid content in Chinese yam with the proton signal at δH 2.30. Trimethylsilyl-2,2,3,3-tetradeuteropropionic acid sodium salt was set as the internal standard. The method was validated and showed admissible stability, repeatability, and precision. Compared to the traditional high-performance liquid chromatography method, this method did not involve tedious pre-treatment and expensive standard. Compared to ordinary qNMR, GSD algorithm could effectively remove the effect of noise, baseline distortions and signal overlapping. Overall, qNMR with GSD method is a rapid, simple and reliable method to quantitatively determine functional metabolites even overlapped with other compounds in herbs or foods.
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5
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Vu T, Xu Y, Qiu Y, Powers R. Shifting-corrected regularized regression for 1H NMR metabolomics identification and quantification. Biostatistics 2022; 24:140-160. [PMID: 36514939 PMCID: PMC9748598 DOI: 10.1093/biostatistics/kxac015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 04/11/2022] [Accepted: 04/24/2022] [Indexed: 12/15/2022] Open
Abstract
The process of identifying and quantifying metabolites in complex mixtures plays a critical role in metabolomics studies to obtain an informative interpretation of underlying biological processes. Manual approaches are time-consuming and heavily reliant on the knowledge and assessment of nuclear magnetic resonance (NMR) experts. We propose a shifting-corrected regularized regression method, which identifies and quantifies metabolites in a mixture automatically. A detailed algorithm is also proposed to implement the proposed method. Using a novel weight function, the proposed method is able to detect and correct peak shifting errors caused by fluctuations in experimental procedures. Simulation studies show that the proposed method performs better with regard to the identification and quantification of metabolites in a complex mixture. We also demonstrate real data applications of our method using experimental and biological NMR mixtures.
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Affiliation(s)
- Thao Vu
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Fitzsimons Building, 13001 East 17th Place, Aurora, CO 80045, USA
| | - Yuhang Xu
- Department of Applied Statistics and Operations Research, Bowling Green State University, Maurer Center, Ridge St, Bowling Green, OH 43403, USA
| | - Yumou Qiu
- Department of Statistics, Iowa State University, 3214 Snedecor, 2438 Osborn Dr Ames, IA 50011, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska - Lincoln, 639 N. 12th Street, Lincoln, NE 68588, USA
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6
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Wang X, Mickiewicz B, Thompson GC, Joffe AR, Blackwood J, Vogel HJ, Kopciuk KA. Comparison of Two Automated Targeted Metabolomics Programs to Manual Profiling by an Experienced Spectroscopist for 1H-NMR Spectra. Metabolites 2022; 12:metabo12030227. [PMID: 35323670 PMCID: PMC8949809 DOI: 10.3390/metabo12030227] [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: 12/16/2021] [Revised: 02/26/2022] [Accepted: 03/02/2022] [Indexed: 12/10/2022] Open
Abstract
Automated programs that carry out targeted metabolite identification and quantification using proton nuclear magnetic resonance spectra can overcome time and cost barriers that limit metabolomics use. However, their performance needs to be comparable to that of an experienced spectroscopist. A previously analyzed pediatric sepsis data set of serum samples was used to compare results generated by the automated programs rDolphin and BATMAN with the results obtained by manual profiling for 58 identified metabolites. Metabolites were selected using Student’s t-tests and evaluated with several performance metrics. The manual profiling results had the highest performance metrics values, especially for sensitivity (76.9%), area under the receiver operating characteristic curve (0.90), precision (62.5%), and testing accuracy based on a neural net (88.6%). All three approaches had high specificity values (77.7–86.7%). Manual profiling by an expert spectroscopist outperformed two open-source automated programs, indicating that further development is needed to achieve acceptable performance levels.
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Affiliation(s)
- Xiangyu Wang
- Department of Mathematics and Statistics, University of Calgary, Calgary, AB T2N 1N4, Canada;
| | - Beata Mickiewicz
- Department of Pediatrics, Cumming School of Medicine and Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada;
| | - Graham C. Thompson
- Departments of Pediatrics and Emergency Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada;
| | - Ari R. Joffe
- Department of Pediatrics, Division of Pediatric Critical Care, University of Alberta, Edmonton, AB T6G 1C9, Canada;
| | - Jaime Blackwood
- Department of PICU and Critical Care, Alberta Children’s Hospital, Alberta Health Services, Calgary, AB T3B 6A8, Canada;
| | - Hans J. Vogel
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB T2N 1N4, Canada
- Correspondence:
| | - Karen A. Kopciuk
- Departments of Community Health Sciences, Mathematics and Statistics, and Oncology, University of Calgary, Calgary, AB T2N 1N4, Canada;
- Cancer Epidemiology and Prevention Research, Alberta Health Sciences, Calgary, AB T2S 3C3, Canada
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7
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Soulsby D. Band-selective excitation NMR spectroscopy and quantitative time-domain analysis using Complete Reduction to Amplitude-Frequency Table (CRAFT) to determine distribution coefficients during drug development. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2019; 57:953-960. [PMID: 31070814 DOI: 10.1002/mrc.4888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 04/15/2019] [Accepted: 05/01/2019] [Indexed: 06/09/2023]
Abstract
A sensitive quantitative 1 H NMR method for determining distribution or partition coefficients has been developed that is applicable to early drug discovery. After partitioning and equilibration, aliquots from each layer are analyzed using band-selective excitation 1 H NMR spectroscopy in regions that are free of 1-octanol and water solvent signals. Signals are quantitated directly using CRAFT software, and their amplitudes are adjusted to correct for nonuniformity within the excitation band. Using this approach, the distribution coefficients for 20 drugs present at low concentrations were determined giving values that were in excellent agreement with literature values.
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Affiliation(s)
- David Soulsby
- Chemistry Department, University of Redlands, Redlands, California
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8
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Matviychuk Y, Bostock MJ, Nietlispach D, Holland DJ. Time-domain signal modelling in multidimensional NMR experiments for estimation of relaxation parameters. JOURNAL OF BIOMOLECULAR NMR 2019; 73:93-104. [PMID: 31055682 DOI: 10.1007/s10858-018-00224-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 12/29/2018] [Indexed: 06/09/2023]
Abstract
We present a model-based method for estimation of relaxation parameters from time-domain NMR data specifically suitable for processing data in popular 2D phase-sensitive experiments. Our model is formulated in terms of commutative bicomplex algebra, which allows us to use the complete information available in an NMR signal acquired with principles of quadrature detection without disregarding any of its dimensions. Compared to the traditional intensity-analysis method, our model-based approach offers an important advantage for the analysis of overlapping peaks and is robust over a wide range of signal-to-noise ratios. We assess its performance with simulated experiments and then apply it for determination of [Formula: see text], [Formula: see text], and [Formula: see text] relaxation rates in datasets of a protein with more than 100 cross peaks.
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Affiliation(s)
- Yevgen Matviychuk
- Department of Chemical and Process Engineering, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand.
| | - Mark J Bostock
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Daniel J Holland
- Department of Chemical and Process Engineering, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
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9
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Padayachee T, Khamiakova T, Louis E, Adriaensens P, Burzykowski T. The impact of the method of extracting metabolic signal from 1H-NMR data on the classification of samples: A case study of binning and BATMAN in lung cancer. PLoS One 2019; 14:e0211854. [PMID: 30726273 PMCID: PMC6364941 DOI: 10.1371/journal.pone.0211854] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 01/23/2019] [Indexed: 11/23/2022] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a principal analytical technique in metabolomics. Extracting metabolic information from NMR spectra is complex due to the fact that an immense amount of detail on the chemical composition of a biological sample is expressed through a single spectrum. The simplest approach to quantify the signal is through spectral binning which involves subdividing the spectra into regions along the chemical shift axis and integrating the peaks within each region. However, due to overlapping resonance signals, the integration values do not always correspond to the concentrations of specific metabolites. An alternate, more advanced statistical approach is spectral deconvolution. BATMAN (Bayesian AuTomated Metabolite Analyser for NMR data) performs spectral deconvolution using prior information on the spectral signatures of metabolites. In this way, BATMAN estimates relative metabolic concentrations. In this study, both spectral binning and spectral deconvolution using BATMAN were applied to 400 MHz and 900 MHz NMR spectra of blood plasma samples from lung cancer patients and control subjects. The relative concentrations estimated by BATMAN were compared with the binning integration values in terms of their ability to discriminate between lung cancer patients and controls. For the 400 MHz data, the spectral binning approach provided greater discriminatory power. However, for the 900 MHz data, the relative metabolic concentrations obtained by using BATMAN provided greater predictive power. While spectral binning is computationally advantageous and less laborious, complementary models developed using BATMAN-estimated features can add complementary information regarding the biological interpretation of the data and therefore are clinically useful.
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Affiliation(s)
| | | | - Evelyne Louis
- Faculty of Medicine and Life Sciences, Hasselt University, Diepenbeek, Belgium
| | - Peter Adriaensens
- Applied and Analytical Chemistry, Institute for Materials Research, Hasselt University, Diepenbeek, Belgium
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10
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De Francesco A, Scaccia L, Maccarini M, Formisano F, Zhang Y, Gang O, Nykypanchuk D, Said AH, Leu BM, Alatas A, Cai YQ, Cunsolo A. Damping Off Terahertz Sound Modes of a Liquid upon Immersion of Nanoparticles. ACS NANO 2018; 12:8867-8874. [PMID: 30052427 DOI: 10.1021/acsnano.8b03101] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The control of phonon propagation in nanoparticle arrays is one of the frontiers of nanotechnology, potentially enabling the discovery of materials with unknown functionalities for potential innovative applications. The exploration of the terahertz window appears quite promising as phonons in this range are the leading carriers of heat transport in insulators and their control is the key to implement devices for heat flow management. Unfortunately, this scientific field is still in its infancy, and even a basic topic such as the influence of floating nanoparticles on the terahertz phonon propagation of a colloidal suspension still eludes a firm answer. Shedding some light on this topic is the main motivation of the present work, which focuses an inelastic X-ray scattering (IXS) measurements on a dilute suspension of Au nanospheres in water. Measured spectra showed a nontrivial shape displaying multiple inelastic features that, based on a Bayesian inference analysis, we assign to phonon modes propagating throughout the nanoparticle interior. Surprisingly, the spectra bear no evidence of propagating modes, which are known to dominate the spectrum of pure water, owing to the scattering that these modes suffer from the sparse nanoparticles in suspension. In perspective, this finding may inspire simple routes to manipulate high-frequency acoustic propagation in hybrid-liquid and solid-materials.
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Affiliation(s)
- Alessio De Francesco
- Consiglio Nazionale delle Ricerche , Istituto Officina dei Materiali c/o OGG Grenoble 38043 , France
| | - Luisa Scaccia
- Dipartimento di Economia e Diritto , Universita' di Macerata , Via Crescimbeni 20 , 62100 Macerata , Italy
| | - Marco Maccarini
- Laboratoire TIMC/IMAG UMR CNRS 5525 , Université Grenoble-Alpes , Grenoble 38042 , France
| | - Ferdinando Formisano
- Consiglio Nazionale delle Ricerche , Istituto Officina dei Materiali c/o OGG Grenoble 38043 , France
| | | | - Oleg Gang
- Department of Chemical Engineering and Department of Applied Physics and Applied Mathematics , Columbia University , New York , New York 10027 , United States
| | | | - Ayman H Said
- Advanced Photon Source , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - Bogdan M Leu
- Advanced Photon Source , Argonne National Laboratory , Argonne , Illinois 60439 , United States
- Department of Physics , Miami University , Oxford , Ohio 45056 , United States
| | - Ahmet Alatas
- Advanced Photon Source , Argonne National Laboratory , Argonne , Illinois 60439 , United States
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11
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Ebbels TMD, Rodriguez-Martinez A, Dumas ME, Keun HC. Advances in Computational Analysis of Metabolomic NMR Data. NMR-BASED METABOLOMICS 2018. [DOI: 10.1039/9781782627937-00310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In this chapter we discuss some of the more recent developments in preprocessing and statistical analysis of NMR spectra in metabolomics. Bayesian methods for analyzing NMR spectra are summarized and we describe one particular approach, BATMAN, in more detail. We consider techniques based on statistical associations, such as correlation spectroscopy (e.g. STOCSY and recent variants), as well as approaches that model the associations as a network and how these change under different biological conditions. The link between metabolism and genotype is explored by looking at metabolic GWAS and related techniques. Finally, we describe the relevance and current status of data standards for NMR metabolomics.
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Affiliation(s)
- Timothy M. D. Ebbels
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London London SW7 2AZ UK
| | - Andrea Rodriguez-Martinez
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London London SW7 2AZ UK
| | - Marc-Emmanuel Dumas
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London London SW7 2AZ UK
| | - Hector C. Keun
- Division of Cancer, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London London W12 0NN UK
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12
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Abstract
Fecal analysis can generate data that is relevant for the exploration of gut microbiota and their relationship with the host. Nuclear magnetic resonance (NMR) spectroscopy is an excellent tool for the profiling of fecal extracts as it enables the simultaneous detection of various metabolites from a broad range of chemical classes including, among others, short-chain fatty acids, organic acids, amino acids, bile acids, carbohydrates, amines, and alcohols. Compounds present at low μM concentrations can be detected and quantified with a single measurement. Moreover, NMR-based profiling requires a relatively simple sample preparation. Here we describe the three main steps of the general workflow for the NMR-based profiling of feces: sample preparation, NMR data acquisition, and data analysis.
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Affiliation(s)
- Hye Kyong Kim
- Natural Product Laboratory, Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Sarantos Kostidis
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Young Hae Choi
- Natural Product Laboratory, Institute of Biology, Leiden University, Leiden, The Netherlands.
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13
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Matviychuk Y, von Harbou E, Holland DJ. An experimental validation of a Bayesian model for quantification in NMR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 285:86-100. [PMID: 29127944 DOI: 10.1016/j.jmr.2017.10.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/20/2017] [Accepted: 10/21/2017] [Indexed: 06/07/2023]
Abstract
The traditional peak integration method for quantitative analysis in nuclear magnetic resonance (NMR) spectroscopy is inherently limited by its ability to resolve overlapping peaks and is susceptible to noise. The alternative model-based approaches not only extend quantification capabilities to these challenging examples but also provide a means for automation of the entire process of NMR data analysis. In this paper, we present a general model for an NMR signal that, in a principled way, takes into account the effects of chemical shifts, relaxation, lineshape imperfections, phasing, and baseline distortions. We test the model using both simulations and experiments, concentrating on simple spectra with well-resolved peaks where we expect conventional analysis to be effective. Our results of quantifying mixture compositions compare favorably with the established methods. At high SNR (>40dB), all approaches usually achieve for these test systems an absolute accuracy of at least 0.01mol/mol for the concentrations of all species. Our model-based approach is successful even for SNR<20dB; it achieves 0.05-0.1mol/mol accuracy in cases where precise phasing is practically impossible due to high levels of noise in the data.
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Affiliation(s)
- Yevgen Matviychuk
- University of Canterbury, Private Bag 4800, Cristchurch 8140, New Zealand.
| | - Erik von Harbou
- Technische Universität Kaiserslautern, Erwin-Schrödinger-Straße 44, 67663 Kaiserslautern, Germany
| | - Daniel J Holland
- University of Canterbury, Private Bag 4800, Cristchurch 8140, New Zealand
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14
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Deborde C, Moing A, Roch L, Jacob D, Rolin D, Giraudeau P. Plant metabolism as studied by NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 102-103:61-97. [PMID: 29157494 DOI: 10.1016/j.pnmrs.2017.05.001] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 05/19/2017] [Accepted: 05/22/2017] [Indexed: 05/07/2023]
Abstract
The study of plant metabolism impacts a broad range of domains such as plant cultural practices, plant breeding, human or animal nutrition, phytochemistry and green biotechnologies. Plant metabolites are extremely diverse in terms of structure or compound families as well as concentrations. This review attempts to illustrate how NMR spectroscopy, with its broad variety of experimental approaches, has contributed widely to the study of plant primary or specialized metabolism in very diverse ways. The review presents recent developments of one-dimensional and multi-dimensional NMR methods to study various aspects of plant metabolism. Through recent examples, it highlights how NMR has proved to be an invaluable tool for the global characterization of sample composition within metabolomic studies, and shows some examples of use for targeted phytochemistry, with a special focus on compound identification and quantitation. In such cases, NMR approaches are often used to provide snapshots of the plant sample composition. The review also covers dynamic aspects of metabolism, with a description of NMR techniques to measure metabolic fluxes - in most cases after stable isotope labelling. It is mainly intended for NMR specialists who would be interested to learn more about the potential of their favourite technique in plant sciences and about specific details of NMR approaches in this field. Therefore, as a practical guide, a paragraph on the specific precautions that should be taken for sample preparation is also included. In addition, since the quality of NMR metabolic studies is highly dependent on approaches to data processing and data sharing, a specific part is dedicated to these aspects. The review concludes with perspectives on the emerging methods that could change significantly the role of NMR in the field of plant metabolism by boosting its sensitivity. The review is illustrated throughout with examples of studies selected to represent diverse applications of liquid-state or HR-MAS NMR.
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Affiliation(s)
- Catherine Deborde
- INRA, UMR 1332 Biologie du Fruit et Pathologie, Centre INRA Bordeaux, F-33140 Villenave d'Ornon, France; Plateforme Métabolome Bordeaux - MetaboHUB, Centre de Génomique Fonctionnelle Bordeaux, IBVM, Centre INRA Bordeaux, F-33140 Villenave d'Ornon, France
| | - Annick Moing
- INRA, UMR 1332 Biologie du Fruit et Pathologie, Centre INRA Bordeaux, F-33140 Villenave d'Ornon, France; Plateforme Métabolome Bordeaux - MetaboHUB, Centre de Génomique Fonctionnelle Bordeaux, IBVM, Centre INRA Bordeaux, F-33140 Villenave d'Ornon, France
| | - Léa Roch
- INRA, UMR 1332 Biologie du Fruit et Pathologie, Centre INRA Bordeaux, F-33140 Villenave d'Ornon, France; Plateforme Métabolome Bordeaux - MetaboHUB, Centre de Génomique Fonctionnelle Bordeaux, IBVM, Centre INRA Bordeaux, F-33140 Villenave d'Ornon, France
| | - Daniel Jacob
- INRA, UMR 1332 Biologie du Fruit et Pathologie, Centre INRA Bordeaux, F-33140 Villenave d'Ornon, France; Plateforme Métabolome Bordeaux - MetaboHUB, Centre de Génomique Fonctionnelle Bordeaux, IBVM, Centre INRA Bordeaux, F-33140 Villenave d'Ornon, France
| | - Dominique Rolin
- Plateforme Métabolome Bordeaux - MetaboHUB, Centre de Génomique Fonctionnelle Bordeaux, IBVM, Centre INRA Bordeaux, F-33140 Villenave d'Ornon, France; Univ. Bordeaux, UMR1332, Biologie du Fruit et Pathologie, 71 av Edouard Bourlaux, 33140 Villenave d'Ornon, France
| | - Patrick Giraudeau
- Chimie et Interdisciplinarité: Synthèse, Analyse, Modélisation (CEISAM), UMR 6230, CNRS, Université de Nantes, Faculté des Sciences, BP 92208, 2 rue de la Houssinière, F-44322 Nantes Cedex 03, France; Institut Universitaire de France, 1 rue Descartes, 75005 Paris, France.
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15
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Kostidis S, Addie RD, Morreau H, Mayboroda OA, Giera M. Quantitative NMR analysis of intra- and extracellular metabolism of mammalian cells: A tutorial. Anal Chim Acta 2017. [PMID: 28622799 DOI: 10.1016/j.aca.2017.05.011] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Metabolomics analysis of body fluids as well as cells is depended on many factors. While several well-accepted standard operating procedures for the analysis of body fluids are available, the NMR based quantitative analysis of cellular metabolites is less well standardized. Experimental designs depend on the cell type, the quenching protocol and the applied post-acquisition workflow. Here, we provide a tutorial for the quantitative description of the metabolic phenotype of mammalian cells using NMR spectroscopy. We discuss all key steps of the process, starting from the selection of the appropriate culture medium, quenching techniques to arrest metabolism in a reproducible manner, the extraction of the intracellular components and the profiling of the culture medium. NMR data acquisition and methods for both qualitative and quantitative analysis are also provided. The suggested methods cover experiments for adherent cells and cells in suspension. We ultimately describe the application of the discussed workflow to a thyroid cancer cell line. Although this tutorial focuses on mammalian cells, the given guidelines and procedures may be adjusted for the analysis of other cell types.
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Affiliation(s)
- Sarantos Kostidis
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2300RC, Leiden, The Netherlands.
| | - Ruben D Addie
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2300RC, Leiden, The Netherlands; Department of Pathology, Leiden University Medical Center, Albinusdreef 2, 2300RC, Leiden, The Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Albinusdreef 2, 2300RC, Leiden, The Netherlands
| | - Oleg A Mayboroda
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2300RC, Leiden, The Netherlands
| | - Martin Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2300RC, Leiden, The Netherlands
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16
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Verhoeven A, Slagboom E, Wuhrer M, Giera M, Mayboroda OA. Automated quantification of metabolites in blood-derived samples by NMR. Anal Chim Acta 2017; 976:52-62. [PMID: 28576318 DOI: 10.1016/j.aca.2017.04.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/30/2017] [Accepted: 04/03/2017] [Indexed: 12/20/2022]
Abstract
NMR is widely applied in the field of metabolomics due to the quantitative nature of the technology and the reproducible data generated. However, because of severe spectral crowding, quantifying individual metabolites in body fluids such as serum and plasma remains a challenge. In this study, a method to automatically annotate and quantify a number of small metabolites in human serum and EDTA plasma is introduced. It combines the superior signal-to-noise ratio of the commonly applied CPMG and NOESY1D pulse sequences with the superior resolution of the 2D JRES experiment to construct a model that extracts the metabolite concentrations directly from the 1D spectra without tedious deconvolution. The performance of the method was assessed by comparing the calculated areas of the various glucose peaks with known clinical values, by comparing several peaks of the same metabolite (extracted versus non-extracted), and by comparing areas obtained from various NMR pulse sequences. Additionally, the models were tested on independent datasets. It was found that for many metabolites peaks could be assigned that show a consistent behavior, indicating a precise quantification. The same method should be applicable to other biofluids with a stable composition and pH, such as CSF fluid, cell extracts, and cell media.
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Affiliation(s)
- Aswin Verhoeven
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333ZA Leiden, The Netherlands.
| | - Eline Slagboom
- Department of Molecular Epidemiology, Leiden University Medical Center, Albinusdreef 2, 2333ZA Leiden, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333ZA Leiden, The Netherlands
| | - Martin Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333ZA Leiden, The Netherlands
| | - Oleg A Mayboroda
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333ZA Leiden, The Netherlands
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17
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Wallmeier J, Samol C, Ellmann L, Zacharias HU, Vogl FC, Garcia M, Dettmer K, Oefner PJ, Gronwald W. Quantification of Metabolites by NMR Spectroscopy in the Presence of Protein. J Proteome Res 2017; 16:1784-1796. [PMID: 28294621 DOI: 10.1021/acs.jproteome.7b00057] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The high reliability of NMR spectroscopy makes it an ideal tool for large-scale metabolomic studies. However, the complexity of biofluids and, in particular, the presence of macromolecules poses a significant challenge. Ultrafiltration and protein precipitation are established means of deproteinization and recovery of free or total metabolite content, but neither is ever complete. In addition, aside from cost and labor, all deproteinization methods constitute an additional source of experimental variation. The Carr-Purcell-Meiboom-Gill (CPMG) echo-train acquisition of NMR spectra obviates the need for prior deproteinization by attenuating signals from macromolecules, but concentration values of metabolites measured in blood plasma will not necessarily reflect total or free metabolite content. Here, in contrast to approaches that propose the determination of individual T1 and T2 relaxation times for the computation of correction factors, we demonstrate their determination by spike-in experiments with known amounts of metabolites in pooled samples of the matrix of interest to facilitate the measurement of total metabolite content. Provided that the protein content does not vary too much among individual samples, accurate quantitation of metabolites is feasible. Moreover, samples with significantly deviating protein content may be readily recognized by inclusion of a standard that shows moderate protein binding. It is also shown that urinary proteins when present in high concentrations may effect detection of common urinary metabolites prone to strong protein binding such as tryptophan.
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Affiliation(s)
- Jens Wallmeier
- Institute of Functional Genomics, University of Regensburg , Am Biopark 9, 93053 Regensburg, Germany
| | - Claudia Samol
- Institute of Functional Genomics, University of Regensburg , Am Biopark 9, 93053 Regensburg, Germany
| | - Lisa Ellmann
- Institute of Functional Genomics, University of Regensburg , Am Biopark 9, 93053 Regensburg, Germany
| | - Helena U Zacharias
- Institute of Functional Genomics, University of Regensburg , Am Biopark 9, 93053 Regensburg, Germany
| | - Franziska C Vogl
- Institute of Functional Genomics, University of Regensburg , Am Biopark 9, 93053 Regensburg, Germany
| | - Muriel Garcia
- Institute of Functional Genomics, University of Regensburg , Am Biopark 9, 93053 Regensburg, Germany
| | - Katja Dettmer
- 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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18
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Phansalkar RS, Simmler C, Bisson J, Chen SN, Lankin DC, McAlpine JB, Niemitz M, Pauli GF. Evolution of Quantitative Measures in NMR: Quantum Mechanical qHNMR Advances Chemical Standardization of a Red Clover (Trifolium pratense) Extract. JOURNAL OF NATURAL PRODUCTS 2017; 80:634-647. [PMID: 28067513 PMCID: PMC5368683 DOI: 10.1021/acs.jnatprod.6b00923] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Indexed: 05/09/2023]
Abstract
Chemical standardization, along with morphological and DNA analysis ensures the authenticity and advances the integrity evaluation of botanical preparations. Achievement of a more comprehensive, metabolomic standardization requires simultaneous quantitation of multiple marker compounds. Employing quantitative 1H NMR (qHNMR), this study determined the total isoflavone content (TIfCo; 34.5-36.5% w/w) via multimarker standardization and assessed the stability of a 10-year-old isoflavone-enriched red clover extract (RCE). Eleven markers (nine isoflavones, two flavonols) were targeted simultaneously, and outcomes were compared with LC-based standardization. Two advanced quantitative measures in qHNMR were applied to derive quantities from complex and/or overlapping resonances: a quantum mechanical (QM) method (QM-qHNMR) that employs 1H iterative full spin analysis, and a non-QM method that uses linear peak fitting algorithms (PF-qHNMR). A 10 min UHPLC-UV method provided auxiliary orthogonal quantitation. This is the first systematic evaluation of QM and non-QM deconvolution as qHNMR quantitation measures. It demonstrates that QM-qHNMR can account successfully for the complexity of 1H NMR spectra of individual analytes and how QM-qHNMR can be built for mixtures such as botanical extracts. The contents of the main bioactive markers were in good agreement with earlier HPLC-UV results, demonstrating the chemical stability of the RCE. QM-qHNMR advances chemical standardization by its inherent QM accuracy and the use of universal calibrants, avoiding the impractical need for identical reference materials.
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Affiliation(s)
- Rasika S. Phansalkar
- UIC/NIH Center for
Botanical Dietary Supplements Research and Center for Natural Product Technologies, Department of Medicinal Chemistry
and Pharmacognosy, University of Illinois
at Chicago, College of Pharmacy, 833 S. Wood Street, Chicago, Illinois 60612, United
States
| | - Charlotte Simmler
- UIC/NIH Center for
Botanical Dietary Supplements Research and Center for Natural Product Technologies, Department of Medicinal Chemistry
and Pharmacognosy, University of Illinois
at Chicago, College of Pharmacy, 833 S. Wood Street, Chicago, Illinois 60612, United
States
| | - Jonathan Bisson
- UIC/NIH Center for
Botanical Dietary Supplements Research and Center for Natural Product Technologies, Department of Medicinal Chemistry
and Pharmacognosy, University of Illinois
at Chicago, College of Pharmacy, 833 S. Wood Street, Chicago, Illinois 60612, United
States
| | - Shao-Nong Chen
- UIC/NIH Center for
Botanical Dietary Supplements Research and Center for Natural Product Technologies, Department of Medicinal Chemistry
and Pharmacognosy, University of Illinois
at Chicago, College of Pharmacy, 833 S. Wood Street, Chicago, Illinois 60612, United
States
| | - David C. Lankin
- UIC/NIH Center for
Botanical Dietary Supplements Research and Center for Natural Product Technologies, Department of Medicinal Chemistry
and Pharmacognosy, University of Illinois
at Chicago, College of Pharmacy, 833 S. Wood Street, Chicago, Illinois 60612, United
States
| | - James B. McAlpine
- UIC/NIH Center for
Botanical Dietary Supplements Research and Center for Natural Product Technologies, Department of Medicinal Chemistry
and Pharmacognosy, University of Illinois
at Chicago, College of Pharmacy, 833 S. Wood Street, Chicago, Illinois 60612, United
States
| | | | - Guido F. Pauli
- UIC/NIH Center for
Botanical Dietary Supplements Research and Center for Natural Product Technologies, Department of Medicinal Chemistry
and Pharmacognosy, University of Illinois
at Chicago, College of Pharmacy, 833 S. Wood Street, Chicago, Illinois 60612, United
States
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19
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De Francesco A, Guarini E, Bafile U, Formisano F, Scaccia L. Bayesian approach to the analysis of neutron Brillouin scattering data on liquid metals. Phys Rev E 2016; 94:023305. [PMID: 27627410 DOI: 10.1103/physreve.94.023305] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Indexed: 11/07/2022]
Abstract
When the dynamics of liquids and disordered systems at mesoscopic level is investigated by means of inelastic scattering (e.g., neutron or x ray), spectra are often characterized by a poor definition of the excitation lines and spectroscopic features in general and one important issue is to establish how many of these lines need to be included in the modeling function and to estimate their parameters. Furthermore, when strongly damped excitations are present, commonly used and widespread fitting algorithms are particularly affected by the choice of initial values of the parameters. An inadequate choice may lead to an inefficient exploration of the parameter space, resulting in the algorithm getting stuck in a local minimum. In this paper, we present a Bayesian approach to the analysis of neutron Brillouin scattering data in which the number of excitation lines is treated as unknown and estimated along with the other model parameters. We propose a joint estimation procedure based on a reversible-jump Markov chain Monte Carlo algorithm, which efficiently explores the parameter space, producing a probabilistic measure to quantify the uncertainty on the number of excitation lines as well as reliable parameter estimates. The method proposed could turn out of great importance in extracting physical information from experimental data, especially when the detection of spectral features is complicated not only because of the properties of the sample, but also because of the limited instrumental resolution and count statistics. The approach is tested on generated data set and then applied to real experimental spectra of neutron Brillouin scattering from a liquid metal, previously analyzed in a more traditional way.
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Affiliation(s)
- A De Francesco
- Consiglio Nazionale delle Ricerche, Istituto Officina dei Materiali, Operative Group in Grenoble (OGG), c/o Institut Laue Langevin, 71 Ave des Martyrs, BP 156 F-38042 Grenoble Cedex, France
| | - E Guarini
- Dipartimento di Fisica e Astronomia, Università di Firenze, via G. Sansone 1, I-50019 Sesto Fiorentino, Italy
| | - U Bafile
- Consiglio Nazionale delle Ricerche, Istituto dei Sistemi Complessi, via Madonna del Piano 10, I-50019 Sesto Fiorentino, Italy
| | - F Formisano
- Consiglio Nazionale delle Ricerche, Istituto Officina dei Materiali, Operative Group in Grenoble (OGG), c/o Institut Laue Langevin, 71 Ave des Martyrs, BP 156 F-38042 Grenoble Cedex, France
| | - L Scaccia
- Dipartimento di Economia e Diritto, Università di Macerata, Via Crescimbeni 20, 62100 Macerata, Italy
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20
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Simmler C, Kulakowski D, Lankin DC, McAlpine JB, Chen SN, Pauli GF. Holistic Analysis Enhances the Description of Metabolic Complexity in Dietary Natural Products. Adv Nutr 2016; 7:179-89. [PMID: 27180381 PMCID: PMC4717887 DOI: 10.3945/an.115.009928] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In the field of food and nutrition, complex natural products (NPs) are typically obtained from cells/tissues of diverse organisms such as plants, mushrooms, and animals. Among them, edible fruits, grains, and vegetables represent most of the human diet. Because of an important dietary dependence, the comprehensive metabolomic analysis of dietary NPs, performed holistically via the assessment of as many metabolites as possible, constitutes a fundamental building block for understanding the human diet. Both mass spectrometry (MS) and nuclear magnetic resonance (NMR) are important complementary analytic techniques, covering a wide range of metabolites at different concentrations. Particularly, 1-dimensional 1H-NMR offers an unbiased overview of all metabolites present in a sample without prior knowledge of its composition, thereby leading to an untargeted analysis. In the past decade, NMR-based metabolomics in plant and food analyses has evolved considerably. The scope of the present review, covering literature of the past 5 y, is to address the relevance of 1H-NMR–based metabolomics in food plant studies, including a comparison with MS-based techniques. Major applications of NMR-based metabolomics for the quality control of dietary NPs and assessment of their nutritional values are presented.
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Affiliation(s)
- Charlotte Simmler
- UIC/NIH Center for Botanical Dietary Supplements Research; and
- Center for Natural Product Technologies, Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL
| | | | - David C Lankin
- UIC/NIH Center for Botanical Dietary Supplements Research; and
| | - James B McAlpine
- UIC/NIH Center for Botanical Dietary Supplements Research; and
- Center for Natural Product Technologies, Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL
| | - Shao-Nong Chen
- UIC/NIH Center for Botanical Dietary Supplements Research; and
- Center for Natural Product Technologies, Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL
| | - Guido F Pauli
- UIC/NIH Center for Botanical Dietary Supplements Research; and
- Center for Natural Product Technologies, Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, IL
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21
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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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22
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An interval estimator for the unmixing of mixtures with set-based source descriptions. Int J Approx Reason 2015. [DOI: 10.1016/j.ijar.2015.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Hao J, Liebeke M, Astle W, De Iorio M, Bundy JG, Ebbels TMD. Bayesian deconvolution and quantification of metabolites in complex 1D NMR spectra using BATMAN. Nat Protoc 2014; 9:1416-27. [PMID: 24853927 DOI: 10.1038/nprot.2014.090] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Data processing for 1D NMR spectra is a key bottleneck for metabolomic and other complex-mixture studies, particularly where quantitative data on individual metabolites are required. We present a protocol for automated metabolite deconvolution and quantification from complex NMR spectra by using the Bayesian automated metabolite analyzer for NMR (BATMAN) R package. BATMAN models resonances on the basis of a user-controllable set of templates, each of which specifies the chemical shifts, J-couplings and relative peak intensities for a single metabolite. Peaks are allowed to shift position slightly between spectra, and peak widths are allowed to vary by user-specified amounts. NMR signals not captured by the templates are modeled non-parametrically by using wavelets. The protocol covers setting up user template libraries, optimizing algorithmic input parameters, improving prior information on peak positions, quality control and evaluation of outputs. The outputs include relative concentration estimates for named metabolites together with associated Bayesian uncertainty estimates, as well as the fit of the remainder of the spectrum using wavelets. Graphical diagnostics allow the user to examine the quality of the fit for multiple spectra simultaneously. This approach offers a workflow to analyze large numbers of spectra and is expected to be useful in a wide range of metabolomics studies.
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Affiliation(s)
- Jie Hao
- Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Manuel Liebeke
- 1] Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, UK. [2] Present address: Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - William Astle
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Maria De Iorio
- Department of Statistical Science, University College London, London, UK
| | - Jacob G Bundy
- Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Timothy M D Ebbels
- Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, UK
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24
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Behrends V, Bell TJ, Liebeke M, Cordes-Blauert A, Ashraf SN, Nair C, Zlosnik JEA, Williams HD, Bundy JG. Metabolite profiling to characterize disease-related bacteria: gluconate excretion by Pseudomonas aeruginosa mutants and clinical isolates from cystic fibrosis patients. J Biol Chem 2013; 288:15098-109. [PMID: 23572517 PMCID: PMC3663530 DOI: 10.1074/jbc.m112.442814] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Metabolic footprinting of supernatants has been proposed as a tool for assigning gene function. We used NMR spectroscopy to measure the exometabolome of 86 single-gene transposon insertion mutant strains (mutants from central carbon metabolism and regulatory mutants) of the opportunistic pathogen Pseudomonas aeruginosa, grown on a medium designed to represent the nutritional content of cystic fibrosis sputum. Functionally related genes had similar metabolic profiles. E.g. for two-component system mutants, the cognate response regulator and sensor kinase genes clustered tightly together. Some strains had metabolic phenotypes (metabotypes) that could be related to the known gene function. E.g. pyruvate dehydrogenase mutants accumulated large amounts of pyruvate in the medium. In other cases, the metabolic phenotypes were not easily interpretable. The rpoN mutant, which lacks the alternative σ factor RpoN (σ54), accumulated high levels of gluconate in the medium. In addition, endometabolome profiling of intracellular metabolites identified a number of systemic metabolic changes. We linked this to indirect regulation of the catabolite repression protein Crc via the non-coding RNA crcZ and found that a crcZ (but not crc) mutant also shared the high-gluconate phenotype. We profiled an additional set of relevant metabolic enzymes and transporters, including Crc targets, and showed that the Crc-regulated edd mutant (gluconate-6-phosphate dehydratase) had similar gluconate levels as the rpoN mutant. Finally, a set of clinical isolates showed patient- and random amplification of polymorphic DNA (RAPD) type-specific differences in gluconate production, which were associated significantly with resistance across four antibiotics (tobramycin, ciprofloxacin, aztreonam, and imipenem), indicating that this has potential clinical relevance.
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Affiliation(s)
- Volker Behrends
- Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, United Kingdom
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25
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Liebeke M, Hao J, Ebbels TMD, Bundy JG. Combining Spectral Ordering with Peak Fitting for One-Dimensional NMR Quantitative Metabolomics. Anal Chem 2013; 85:4605-12. [DOI: 10.1021/ac400237w] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Manuel Liebeke
- Department of Surgery and Cancer, Imperial College London, Sir Alexander Fleming Building, London
SW7 2AZ, U.K
| | - Jie Hao
- Department of Surgery and Cancer, Imperial College London, Sir Alexander Fleming Building, London
SW7 2AZ, U.K
| | - Timothy M. D. Ebbels
- Department of Surgery and Cancer, Imperial College London, Sir Alexander Fleming Building, London
SW7 2AZ, U.K
| | - Jacob G. Bundy
- Department of Surgery and Cancer, Imperial College London, Sir Alexander Fleming Building, London
SW7 2AZ, U.K
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26
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An efficient spectra processing method for metabolite identification from 1H-NMR metabolomics data. Anal Bioanal Chem 2013; 405:5049-61. [PMID: 23525538 DOI: 10.1007/s00216-013-6852-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Revised: 02/08/2013] [Accepted: 02/19/2013] [Indexed: 12/17/2022]
Abstract
The spectra processing step is crucial in metabolomics approaches, especially for proton NMR metabolomics profiling. During this step, noise reduction, baseline correction, peak alignment and reduction of the 1D (1)H-NMR spectral data are required in order to allow biological information to be highlighted through further statistical analyses. Above all, data reduction (binning or bucketing) strongly impacts subsequent statistical data analysis and potential biomarker discovery. Here, we propose an efficient spectra processing method which also provides helpful support for compound identification using a new data reduction algorithm that produces relevant variables, called buckets. These buckets are the result of the extraction of all relevant peaks contained in the complex mixture spectra, rid of any non-significant signal. Taking advantage of the concentration variability of each compound in a series of samples and based on significant correlations that link these buckets together into clusters, the method further proposes automatic assignment of metabolites by matching these clusters with the spectra of reference compounds from the Human Metabolome Database or a home-made database. This new method is applied to a set of simulated (1)H-NMR spectra to determine the effect of some processing parameters and, as a proof of concept, to a tomato (1)H-NMR dataset to test its ability to recover the fruit extract compositions. The implementation code for both clustering and matching steps is available upon request to the corresponding author.
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