Structure Elucidation of Unknown Metabolites in Metabolomics by Combined NMR and MS/MS Prediction

Boiteau, Rene; Hoyt, David; Nicora, Carrie; Kinmonth-Schultz, Hannah; Ward, Jodie; Bingol, Kerem

doi:10.3390/metabo8010008

Cited by 60 publications

(48 citation statements)

References 42 publications

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“…Next, all of the feasible candidate structures that are consisted with the chemical formula are generated by using a structure generator. MS/MS and NMR spectra of each candidate structures are predicted and compared with the experimental MS/MS and NMR spectra of the same sample, and finally ranked according to the level of agreement to determine the best matching candidate [ 66 ]. The authors first compared the performances of MS/MS and NMR predictions on a mixture of ten commonly known metabolites.…”

Section: Untargeted Metabolomicsmentioning

confidence: 99%

“…When multiple unknowns are present, the workflow is modified to consider all pairwise combinations; NMR predictions are generated for all of the structural isomers of each LC-MS feature (chemical formula), and they are all compared to every deconvoluted experimental NMR spectra of the mixture. Proof-of-principle was demonstrated on a ten-compound model mixture [ 66 ]. In 8 out of 10 cases, the rank orders of metabolite identifications did not increase from being the only metabolite in the NMR spectrum to being one of the ten metabolites in the mixture, which is a promising result for the identification of the real unknowns in mixtures.…”

Section: Untargeted Metabolomicsmentioning

confidence: 99%

“…MS/MS and NMR spectra of each candidate structures were predicted and compared with the experimental MS/MS and NMR spectra of the same sample and ranked according to the level of agreement to determine the best matching candidate. Adapted from reference [ 66 ].…”

Section: Figurementioning

confidence: 99%

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Recent Advances in Targeted and Untargeted Metabolomics by NMR and MS/NMR Methods

2018

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Metabolomics has made significant progress in multiple fronts in the last 18 months. This minireview aimed to give an overview of these advancements in the light of their contribution to targeted and untargeted metabolomics. New computational approaches have emerged to overcome the manual absolute quantitation step of metabolites in one-dimensional (1D) 1H nuclear magnetic resonance (NMR) spectra. This provides more consistency between inter-laboratory comparisons. Integration of two-dimensional (2D) NMR metabolomics databases under a unified web server allowed for very accurate identification of the metabolites that have been catalogued in these databases. For the remaining uncatalogued and unknown metabolites, new cheminformatics approaches have been developed by combining NMR and mass spectrometry (MS). These hybrid MS/NMR approaches accelerated the identification of unknowns in untargeted studies, and now they are allowing for profiling ever larger number of metabolites in application studies.

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Section: Untargeted Metabolomicsmentioning

confidence: 99%

Section: Untargeted Metabolomicsmentioning

confidence: 99%

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Recent Advances in Targeted and Untargeted Metabolomics by NMR and MS/NMR Methods

2018

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“…NMR-based metabolic profiling is quick, expedient, and efficient technology for the screening and identification of similar biological samples. It is non-destructive, selective, and very proficient at mapping metabolic pathways [27]. Moreover, its high reproducibility makes it a powerful tool in plant metabolomics research.…”

Section: Advanced Tools For Analytical Research In Plant Metabolomicsmentioning

confidence: 99%

Metabolomics: A Way Forward for Crop Improvement

et al. 2019

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Metabolomics is an emerging branch of “omics” and it involves identification and quantification of metabolites and chemical footprints of cellular regulatory processes in different biological species. The metabolome is the total metabolite pool in an organism, which can be measured to characterize genetic or environmental variations. Metabolomics plays a significant role in exploring environment–gene interactions, mutant characterization, phenotyping, identification of biomarkers, and drug discovery. Metabolomics is a promising approach to decipher various metabolic networks that are linked with biotic and abiotic stress tolerance in plants. In this context, metabolomics-assisted breeding enables efficient screening for yield and stress tolerance of crops at the metabolic level. Advanced metabolomics analytical tools, like non-destructive nuclear magnetic resonance spectroscopy (NMR), liquid chromatography mass-spectroscopy (LC-MS), gas chromatography-mass spectrometry (GC-MS), high performance liquid chromatography (HPLC), and direct flow injection (DFI) mass spectrometry, have sped up metabolic profiling. Presently, integrating metabolomics with post-genomics tools has enabled efficient dissection of genetic and phenotypic association in crop plants. This review provides insight into the state-of-the-art plant metabolomics tools for crop improvement. Here, we describe the workflow of plant metabolomics research focusing on the elucidation of biotic and abiotic stress tolerance mechanisms in plants. Furthermore, the potential of metabolomics-assisted breeding for crop improvement and its future applications in speed breeding are also discussed. Mention has also been made of possible bottlenecks and future prospects of plant metabolomics.

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“…Die Suche nach einem Werkzeug für eine vollständig automatische Zuordnung ist ein Gebiet aktiver Forschung mit vielversprechenden Ergebnissen (Abbildung , siehe auch Abschnitt 7) . Natürlich sind NMR und MS zwei komplementäre Techniken, die, wie in Tabelle dargestellt, zur korrekten Identifizierung zahlreicher Metabolite kombiniert werden können …”

Section: Analyse Der Spektrenunclassified

Hochdurchsatz‐Metabolomik mit 1D‐NMR

et al. 2018

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Metabolomik befasst sich mit der Gesamtheit aller Metabolite, dem Metabolom. Als eine der “Omics”‐Wissenschaften hat sie Querbeziehungen zur Biologie, Physiologie, Pathologie und Medizin; andererseits sind Metabolite chemische Verbindungen, kleine organische Moleküle oder anorganische Ionen. Ihre korrekte Identifizierung und Quantifizierung in komplexen biologischen Matrizen erfordert daher eine solide chemische Grundlage. Im Vergleich beispielsweise zu DNA unterliegen Metabolite sehr viel stärker der Oxidation oder dem enzymatischen Abbau: Wir können große Teile eines Mammut‐Genoms aus einer kleinen Probe rekonstruieren, sind aber nicht in der Lage, dasselbe mit seinem Metabolom zu tun, das innerhalb weniger Stunden nach dem Tod des Tieres wahrscheinlich weitgehend abgebaut war. Erforderlich sind daher Standardverfahren, gute chemische Fertigkeiten der Probenvorbereitung für die Lagerung und anschließende Analyse, genaue analytische Protokolle, eine umfangreiche Kenntnis der Chemometrie, erweiterte statistische Verfahren und fundiertes Wissen über mindestens eine der beiden Metabolomik‐typischen Verfahren, MS oder NMR. All diese Fertigkeiten besitzen traditionell die Chemiker. Entsprechend betrachten wir die Metabolomik aus chemischer Perspektive und beschränken uns auf NMR. Der Analytiker findet Argumente für und gegen NMR, jedoch bietet das Verfahren eine besondere ganzheitliche Perspektive, die für künftige Anwendungen als eine bevölkerungsweite Screeningtechnik für Reihenuntersuchungen sprechen.

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Structure Elucidation of Unknown Metabolites in Metabolomics by Combined NMR and MS/MS Prediction

Cited by 60 publications

References 42 publications

Recent Advances in Targeted and Untargeted Metabolomics by NMR and MS/NMR Methods

Recent Advances in Targeted and Untargeted Metabolomics by NMR and MS/NMR Methods

Metabolomics: A Way Forward for Crop Improvement

Hochdurchsatz‐Metabolomik mit 1D‐NMR

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