1
|
Serrano-Contreras JI, Lindon JC, Frost G, Holmes E, Nicholson JK, Garcia-Perez I. Implementation of pure shift 1 H NMR in metabolic phenotyping for structural information recovery of biofluid metabolites with complex spin systems. NMR IN BIOMEDICINE 2024; 37:e5060. [PMID: 37937465 DOI: 10.1002/nbm.5060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 11/09/2023]
Abstract
NMR spectroscopy is a mainstay of metabolic profiling approaches to investigation of physiological and pathological processes. The one-dimensional proton pulse sequences typically used in phenotyping large numbers of samples generate spectra that are rich in information but where metabolite identification is often compromised by peak overlap. Recently developed pure shift (PS) NMR spectroscopy, where all J-coupling multiplicities are removed from the spectra, has the potential to simplify the complex proton NMR spectra that arise from biosamples and hence to aid metabolite identification. Here we have evaluated two complementary approaches to spectral simplification: the HOBS (band-selective with real-time acquisition) and the PSYCHE (broadband with pseudo-2D interferogram acquisition) pulse sequences. We compare their relative sensitivities and robustness for deconvolving both urine and serum matrices. Both methods improve resolution of resonances ranging from doublets, triplets and quartets to more complex signals such as doublets of doublets and multiplets in highly overcrowded spectral regions. HOBS is the more sensitive method and takes less time to acquire in comparison with PSYCHE, but can introduce unavoidable artefacts from metabolites with strong couplings, whereas PSYCHE is more adaptable to these types of spin system, although at the expense of sensitivity. Both methods are robust and easy to implement. We also demonstrate that strong coupling artefacts contain latent connectivity information that can be used to enhance metabolite identification. Metabolite identification is a bottleneck in metabolic profiling studies. In the case of NMR, PS experiments can be included in metabolite identification workflows, providing additional capability for biomarker discovery.
Collapse
Affiliation(s)
- Jose Ivan Serrano-Contreras
- Department of Metabolism, Digestion and Reproduction, Division of Digestive Diseases, Section of Nutrition, Faculty of Medicine, Imperial College London, London, UK
| | - John C Lindon
- Department of Metabolism, Digestion and Reproduction, Division of Systems Medicine, Imperial College London, London, UK
| | - Gary Frost
- Department of Metabolism, Digestion and Reproduction, Division of Digestive Diseases, Section of Nutrition, Faculty of Medicine, Imperial College London, London, UK
| | - Elaine Holmes
- Department of Metabolism, Digestion and Reproduction, Division of Digestive Diseases, Section of Nutrition, Faculty of Medicine, Imperial College London, London, UK
- Australian National Phenome Centre, Computational and Systems Medicine, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia
- Center for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia
| | - Jeremy K Nicholson
- Australian National Phenome Centre, Computational and Systems Medicine, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia
- Center for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia
- Imperial College London, Institute of Global Health Innovation, London, UK
| | - Isabel Garcia-Perez
- Department of Metabolism, Digestion and Reproduction, Division of Digestive Diseases, Section of Nutrition, Faculty of Medicine, Imperial College London, London, UK
| |
Collapse
|
2
|
Hulse SG, Foroozandeh M. Newton meets Ockham: Parameter estimation and model selection of NMR data with NMR-EsPy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 338:107173. [PMID: 35366620 DOI: 10.1016/j.jmr.2022.107173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
We present NMR-EsPy (NMR Estimation in Python), a versatile, simple-to-use Python package for estimating the signal parameters that describe one-dimensional time-domain NMR data. The software is fully integrated into Topspin, a widely used NMR platform, and comes with a Graphical User Interface, allowing users unfamiliar with the underlying theory and/or Python programming to access the full functionality of the software package. NMR-EsPy utilises Newton's method, an iterative non-linear programming technique. By including the variance of oscillator phases in the optimization, NMR-EsPy can generate parsimonious parameter estimates, giving NMR users access to meaningful quantitative information. This principle is easily extendable to study specific regions of an NMR spectrum to reduce computational cost. The complete mathematical treatment along with examples of the implementation of the estimation routine are presented.
Collapse
Affiliation(s)
- Simon G Hulse
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, UK
| | | |
Collapse
|
3
|
Ilgen J, Nowag J, Kaltschnee L, Schmidts V, Thiele CM. Gradient selected pure shift EASY-ROESY techniques facilitate the quantitative measurement of 1H, 1H-distance restraints in congested spectral regions. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 324:106900. [PMID: 33503522 DOI: 10.1016/j.jmr.2020.106900] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
For elucidating molecular structure and dynamics in solution, NMR experiments such as NOESY, ROESY and EXSY have been used excessively over the past decades, to provide interatomic distance restraints or rates for chemical exchange. The extraction of such information, however, is often prohibited by signal overlap in these spectra. To reduce this problem, pure shift methods for improving the spectral resolution have become popular. We report on pure shift EASY-ROESY experiments and their application to extract cross-relaxation rates, proton-proton distances and exchange rates. Homonuclear decoupling (pure shift) is applied in the indirect dimension using the PSYCHE or the perfectBASH technique, to enhance the spectral resolution of severely overcrowded spectral regions. The spectral quality is further improved by using a gradient selected F1-PSYCHE-EASY-ROESY, which produces significantly less t1-noise than the experiment used previously, as also demonstrated by employing the recently introduced SAN (signal-artefact-noise) plots. Applications include the quantification of distance restraints in a peptide organocatalyst and the extraction of a number of distance restraints in cyclosporine A, which were previously not available for analysis, because they were either located in overcrowded spectral regions or hidden under t1-noise. Distances extracted and exchange rates obtained are accurate. Also, the 2D gradient-selected F1-perfectBASH-EASY-ROESY with the additional gradient selection proposed herein, which is superior in terms of sensitivity, can be used to accurately quantify cross-relaxation.
Collapse
Affiliation(s)
- Julian Ilgen
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 16, D-64287 Darmstadt, Germany
| | - Jens Nowag
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 16, D-64287 Darmstadt, Germany
| | - Lukas Kaltschnee
- Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen, Germany; Center for Biostructural Imaging of Neurodegeneration (BIN), Von-Siebold-Str. 3a, 37075 Göttingen, Germany
| | - Volker Schmidts
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 16, D-64287 Darmstadt, Germany
| | - Christina M Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 16, D-64287 Darmstadt, Germany.
| |
Collapse
|
4
|
Howe PWA. Is perfection ever attainable? Strong coupling effects in the Perfect Echo. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:77-83. [PMID: 31348542 DOI: 10.1002/mrc.4927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 06/10/2023]
Abstract
The Perfect Echo sequence, originally proposed in the late 1980s, has recently been popularised with many applications in the field of small-molecule proton NMR spectroscopy. The Perfect Echo refocuses all homonuclear J-couplings for AX spin systems and refocuses magnetization in-phase for more complex weakly coupled spin systems, albeit with some intensity reduction. In contrast to suggestions in previous publications, spectra acquired in our laboratory showed that the Perfect Echo caused intensity distortions in strongly coupled systems where the chemical shift difference between the coupled spins was not large compared to the J-coupling. This paper reports experimental observations and theoretical analysis of strongly coupled spins to confirm the distortions are real and that they originate principally from transfer of magnetization caused by the final inversion pulse of the Perfect Echo. The intensity changes are not large, but because of them, identifications of coupling partners based on resonance intensities ("roofing") can no longer be relied on when the Perfect Echo is used. However, theory and experiment confirm that adding an orthogonal excitation pulse at the end of the Perfect Echo greatly reduces the distortions.
Collapse
|
5
|
Zhan C, Zeng Q, Chen J, Lin Y, Chen Z. PE-SERF: A sensitivity-improved experiment to measure J HH in crowded spectra. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 308:106590. [PMID: 31513964 DOI: 10.1016/j.jmr.2019.106590] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/22/2019] [Accepted: 09/02/2019] [Indexed: 06/10/2023]
Abstract
Aiming at facilitating the analysis of molecular structure, the gradient-encoded selective refocusing methods (G-SERF) and a great number of its variants for measuring proton-proton coupling constants have been proposed. However, the sensitivity is an issue in the 2D gradient-encoded experiments, because the signal intensity is determined by the slice thickness of the sample that depends on encoding gradient and the bandwidth of selective pulses which is limited by the smallest chemical shift difference of any two coupled protons. Here, we present a method dubbed PE-SERF (perfect echo selective refocusing) which can determine all JHH values involving a selected proton with improved sensitivity compared to original G-SERF experiment. The modules of perfect echo involving selective pulses and gradient-encoded selective refocusing are combined in the method, so that the unwanted J couplings arising from coupled spin pairs in the same sample slice would be nullified. In this way, instead of single proton, a pair of coupled protons is allowed to share a sample slice, and thus the slice thickness can be increased and the spectral sensitivity can be improved. The performance of the method is demonstrated by experiments on quinine and strychnine.
Collapse
Affiliation(s)
- Chaoqun Zhan
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Qing Zeng
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Jinyong Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| | - Yanqin Lin
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China; Shenzhen Research Institute of Xiamen University, Shenzhen 518057, China.
| | - Zhong Chen
- Department of Electronic Science, Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, State Key Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China
| |
Collapse
|
6
|
Parella T. Towards perfect NMR: Spin-echo versus perfect-echo building blocks. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2019; 57:13-29. [PMID: 29927497 DOI: 10.1002/mrc.4776] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/10/2018] [Accepted: 06/12/2018] [Indexed: 06/08/2023]
Abstract
The development of new tools to improve the quality of nuclear magnetic resonance (NMR) spectra is a challenging task. The concept of "perfect NMR" includes the design of robust pulse sequences that allow an investigator to obtain undistorted pure in-phase signals, with pure absorption lineshapes that are free of phase anomalies derived from undesired J modulations. Here, alternative NMR building blocks to the spin-echo that are based on a general double SE module, known as a perfect-echo, are reviewed. Several implementations to minimize/remove unwanted dispersive contributions in homonuclear and heteronuclear NMR experiments are described and illustrated with some examples of broad interest for small molecules.
Collapse
Affiliation(s)
- Teodor Parella
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
| |
Collapse
|
7
|
Ilgen J, Kaltschnee L, Thiele CM. perfectBASH: Band-selective homonuclear decoupling in peptides and peptidomimetics. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:918-933. [PMID: 29885093 DOI: 10.1002/mrc.4757] [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: 03/27/2018] [Revised: 05/14/2018] [Accepted: 05/29/2018] [Indexed: 06/08/2023]
Abstract
Band selective techniques offer the highest sensitivity of all pure shift approaches and thus are the best choice for decoupling well-separated 1 H-frequency regions, such as the amide- or the α-proton region of α-peptides. They are inept to fully decouple the amide- and the α-proton region simultaneously, though. Herein, we present a new homonuclear decoupling technique, which extends the capabilities of band selective decoupling using the perfect echo principle. This modification allows a complete backbone decoupling (amide- and α-protons) in peptides and opens band selective homonuclear decoupling to substances with two mutually coupled protons in the spectral range of interest.
Collapse
Affiliation(s)
- Julian Ilgen
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Darmstadt, Germany
| | - Lukas Kaltschnee
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Darmstadt, Germany
| | - Christina M Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Darmstadt, Germany
| |
Collapse
|