Knowns and unknowns in metabolomics identified by multidimensional NMR and hybrid MS/NMR methods

Bingol, Kerem; Brüschweiler, Rafael

doi:10.1016/j.copbio.2016.07.006

Cited by 57 publications

(54 citation statements)

References 53 publications

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“…Bundy and co-workers [31] applied three different platforms to analyse C. elegans , including 1D 1 H NMR spectroscopy, GC/MS and UPLC-MS. The deeper integration of NMR and MS data in automated metabolite identification pipelines is an emerging topic [32]. An even broader range of metabolites were measured in 31 varieties of rice using HS SPME GC-MS, primary polar metabolites by GC-ToF-MS, both polar and semi-polar compounds by 1 H NMR and direct infusion MS, and multi-elemental analysis using ICP-MS [33].…”

Section: Introductionmentioning

confidence: 99%

How close are we to complete annotation of metabolomes?

Viant

Kurland

Jones

et al. 2017

Current Opinion in Chemical Biology

230

211

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The metabolome describes the full complement of the tens to hundreds of thousands of low molecular weight metabolites present within a biological system. Identification of the metabolome is critical for discovering the maximum amount of biochemical knowledge from metabolomics datasets. Yet no exhaustive experimental characterisation of any organismal metabolome has been reported to date, dramatically contrasting with the genome sequencing of thousands of plants, animals and microbes. Here we review the status of metabolome annotation and describe advances in the analytical methodologies being applied. In part through new international coordination, we conclude that we are now entering a new era of metabolome annotation.

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Section: Introductionmentioning

confidence: 99%

How close are we to complete annotation of metabolomes?

Viant

Kurland

Jones

et al. 2017

Current Opinion in Chemical Biology

230

211

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“…There is much room for improvement, and each predicted epimetabolite must still be validated by confirmation using an authentic, synthesized chemical standard. Other approaches include using nuclear magnetic resonance (NMR) which can provide additional insight into unknown structure identification [47]. …”

Section: From Elemental Formulas To Correct Epimetabolite Structure Amentioning

confidence: 99%

Epimetabolites: discovering metabolism beyond building and burning

Showalter

Čajka

Fiehn

2017

Current Opinion in Chemical Biology

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Enzymatic transformations of primary, canonical metabolites generate active biomolecules that regulate important cellular and physiological processes. Roles include regulation of histone demethylation in epigenetics, inflammation in tissue injury, insulin sensitivity, cancer cell invasion, stem cell pluripotency status, inhibition of nitric oxide signaling and others. Such modified compounds, defined as epimetabolites, have functions distinct from classic hormones as well as removed from generic anabolism and catabolism. Epimetabolites are discovered by untargeted metabolomics using liquid- or gas chromatography–high resolution mass spectrometry and structurally annotated by in-silico fragmentation prediction tools. Their specific biological functions are subsequently investigated by targeted metabolomics methods.

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“…1234 In 2D NMR experiments, where pairs of spins (e.g. two 1 H spins or a 1 H spin and a 13 C spin) are physically correlated with each other leading to the appearance of cross-peaks in the resulting 2D NMR spectrum, peak overlap is greatly diminished when compared with the corresponding 1D NMR spectrum.…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Metabolite Identification Strategy Using Multiple Two-Dimensional NMR Spectra of a Complex Mixture Implemented in the COLMARm Web Server

Bingol

Li²,

Zhang³

et al. 2016

Anal. Chem.

Self Cite

102

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Identification of metabolites in complex mixtures represents a key step in metabolomics. A new strategy is introduced, which is implemented in a new public web server, COLMARm, that permits the co-analysis of up to three 2D NMR spectra, namely 13C-1H HSQC, 1H-1H TOCSY, and 13C-1H HSQC-TOCSY for the comprehensive, accurate, and efficient performance of this task. The highly versatile and interactive nature of COLMARm permits its application to a wide range of metabolomics samples independent of the magnetic field. Database query is performed using the HSQC spectrum and the top metabolite hits are then validated against the TOCSY-type experiment(s) by superimposing the expected cross-peaks on the mixture spectrum. In this way the user can directly accept or reject candidate metabolites by taking advantage of the complementary spectral information offered by these experiments and their different sensitivities. The power of COLMARm is demonstrated for a human serum sample uncovering the existence of 14 metabolites that hitherto were not identified by NMR.

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Knowns and unknowns in metabolomics identified by multidimensional NMR and hybrid MS/NMR methods

Cited by 57 publications

References 53 publications

How close are we to complete annotation of metabolomes?

How close are we to complete annotation of metabolomes?

Epimetabolites: discovering metabolism beyond building and burning

Comprehensive Metabolite Identification Strategy Using Multiple Two-Dimensional NMR Spectra of a Complex Mixture Implemented in the COLMARm Web Server

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