Two elephants in the room: new hybrid nuclear magnetic resonance and mass spectrometry approaches for metabolomics

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Abstract

Purpose of review

This review describes some of the advances made over the past year in NMR-based metabolomics for the elucidation of known and unknown compounds, including new ways of how to combine this information with high-resolution mass spectrometry.

Recent findings

A new method allows the back-calculation of mass spectra from NMR spectra that have been queried against databases improving the accuracy of the identified compounds by validation and consistency analysis. For the de-novo characterization of unknown compounds, an algorithm has been introduced that predicts all viable NMR spectra from accurate masses allowing, by comparison with experimental NMR data, the determination of the structures of new metabolites in complex mixtures.

Summary

Recent advances in NMR and mass spectrometry-based metabolomics and their synergistic use promises to significantly improve metabolomics sample characterization both in terms of identification and quantitation, and accelerate metabolite discovery.

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Most cited references 30

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BioMagResBank

Eldon Ulrich, Hideo Akutsu, Jurgen F. Doreleijers … (2008)

The BioMagResBank (BMRB: www.bmrb.wisc.edu) is a repository for experimental and derived data gathered from nuclear magnetic resonance (NMR) spectroscopic studies of biological molecules. BMRB is a partner in the Worldwide Protein Data Bank (wwPDB). The BMRB archive consists of four main data depositories: (i) quantitative NMR spectral parameters for proteins, peptides, nucleic acids, carbohydrates and ligands or cofactors (assigned chemical shifts, coupling constants and peak lists) and derived data (relaxation parameters, residual dipolar couplings, hydrogen exchange rates, pKa values, etc.), (ii) databases for NMR restraints processed from original author depositions available from the Protein Data Bank, (iii) time-domain (raw) spectral data from NMR experiments used to assign spectral resonances and determine the structures of biological macromolecules and (iv) a database of one- and two-dimensional 1H and 13C one- and two-dimensional NMR spectra for over 250 metabolites. The BMRB website provides free access to all of these data. BMRB has tools for querying the archive and retrieving information and an ftp site (ftp.bmrb.wisc.edu) where data in the archive can be downloaded in bulk. Two BMRB mirror sites exist: one at the PDBj, Protein Research Institute, Osaka University, Osaka, Japan (bmrb.protein.osaka-u.ac.jp) and the other at CERM, University of Florence, Florence, Italy (bmrb.postgenomicnmr.net/). The site at Osaka also accepts and processes data depositions.

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Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database.

Jiang Zhu, Junhua Wang, W. Schultz … (2013)

Untargeted metabolomics provides a comprehensive platform for identifying metabolites whose levels are altered between two or more populations. By using liquid chromatography quadrupole time-of-flight mass spectrometry (LC-Q-TOF-MS), hundreds to thousands of peaks with a unique m/z ratio and retention time are routinely detected from most biological samples in an untargeted profiling experiment. Each peak, termed a metabolomic feature, can be characterized on the basis of its accurate mass, retention time and tandem mass spectral fragmentation pattern. Here a seven-step protocol is suggested for such a characterization by using the METLIN metabolite database. The protocol starts from untargeted metabolomic LC-Q-TOF-MS data that have been analyzed with the bioinformatics program XCMS, and it describes a strategy for selecting interesting features as well as performing subsequent targeted tandem MS. The seven steps described will require 2-4 h to complete per feature, depending on the compound.

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Current approaches and challenges for the metabolite profiling of complex natural extracts.

Jean-Luc Wolfender, Guillaume Marti, Aurélien Thomas … (2015)

Metabolite profiling is critical in many aspects of the life sciences, particularly natural product research. Obtaining precise information on the chemical composition of complex natural extracts (metabolomes) that are primarily obtained from plants or microorganisms is a challenging task that requires sophisticated, advanced analytical methods. In this respect, significant advances in hyphenated chromatographic techniques (LC-MS, GC-MS and LC-NMR in particular), as well as data mining and processing methods, have occurred over the last decade. Together, these tools, in combination with bioassay profiling methods, serve an important role in metabolomics for the purposes of both peak annotation and dereplication in natural product research. In this review, a survey of the techniques that are used for generic and comprehensive profiling of secondary metabolites in natural extracts is provided. The various approaches (chromatographic methods: LC-MS, GC-MS, and LC-NMR and direct spectroscopic methods: NMR and DIMS) are discussed with respect to their resolution and sensitivity for extract profiling. In addition the structural information that can be generated through these techniques or in combination, is compared in relation to the identification of metabolites in complex mixtures. Analytical strategies with applications to natural extracts and novel methods that have strong potential, regardless of how often they are used, are discussed with respect to their potential applications and future trends.

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Author and article information

Journal

Journal ID (nlm-ta): Curr Opin Clin Nutr Metab Care

Journal ID (iso-abbrev): Curr Opin Clin Nutr Metab Care

Journal ID (publisher-id): COCNM

Title: Current Opinion in Clinical Nutrition and Metabolic Care

Publisher: Lippincott Williams & Wilkins

ISSN (Print): 1363-1950

ISSN (Electronic): 1473-6519

Publication date (Print): September 2015

Publication date (Electronic): 10 August 2015

Volume: 18

Issue: 5

Pages: 471-477

Affiliations

[a ]Department of Chemistry and Biochemistry

[b ]Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio, USA

Author notes

Correspondence to Rafael Brüschweiler, PhD, Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA. E-mail: bruschweiler.1@ 123456osu.edu

Article

DOI: 10.1097/MCO.0000000000000206

PMC ID: 4533976

PubMed ID: 26154280

SO-VID: a0ac8272-2d9d-4a79-8973-9ea00b48d31c

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives License 4.0 (CCBY-NC-ND), where it is permissible to download and share the work provided it is properly cited. The work cannot be changed in any way or used commercially. http://creativecommons.org/licenses/by-nc-nd/4.0

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Keywords: combined nmr and ms hybrid approaches,complex mixture analysis,mass spectrometry,metabolomics,nuclear magnetic resonance spectroscopy

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Keywords: combined nmr and ms hybrid approaches, complex mixture analysis, mass spectrometry, metabolomics, nuclear magnetic resonance spectroscopy

Two elephants in the room: new hybrid nuclear magnetic resonance and mass spectrometry approaches for metabolomics

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Abstract

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Recent findings

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Most cited references 30

BioMagResBank

Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database.

Current approaches and challenges for the metabolite profiling of complex natural extracts.

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