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NMR-Based Chromatography Readouts: Indispensable Tools to Translate Analytical Features into Molecular Structures

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Automated Annotation of Untargeted All-Ion Fragmentation LC-MS Metabolomics Data with MetaboAnnotatoR

Goncalo Graca et al.

Summary: This paper proposes a novel approach for automated annotation of isotopologues, adducts, and in-source fragments from untargeted metabolomics and lipidomics LC-MS datasets. The method combines correlation-based parent-fragment linking with molecular fragment matching. The workflow demonstrates high precision and recall values and outperforms current state-of-the-art software for AIF data annotation.

ANALYTICAL CHEMISTRY (2022)

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Article Chemistry, Analytical

Modular Pulse Program Generation for NMR Supersequences

Jonathan R. J. Yong et al.

Summary: NMR supersequences allow for faster experiments by tailoring the detection of NMR responses. The online tool GENESIS generates pulse programs for NOAH supersequences compatible with Bruker spectrometers. It provides customized supersequences, related scripts, and detailed instructions, while also facilitating the dissemination of new developments in NOAH sequences.

ANALYTICAL CHEMISTRY (2022)

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Editorial Material Clinical Neurology

Philosophy of science and black swan

Tayfun Hakan

CHILDS NERVOUS SYSTEM (2022)

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Review Endocrinology & Metabolism

The health effects of vitamin D supplementation: evidence from human studies

Roger Bouillon et al.

Summary: The review highlights that vitamin D supplementation in vitamin D-replete adults does not provide significant health benefits, but vitamin D deficiency should be corrected. The vitamin D supplementation can prevent and cure nutritional rickets in infants and children.

NATURE REVIEWS ENDOCRINOLOGY (2022)

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Article Chemistry, Applied

Analysis of individual anthocyanins, flavanols, flavonols and other polyphenols in Pistacia lentiscus L. fruits during ripening

Aghiles Karim Aissat et al.

Summary: This study investigated the phenolic composition of Pistacia lentiscus L. fruits at different physiological stages. The results revealed significant variation in the qualitative and quantitative content of phenolic compounds during fruit ripening, suggesting potential applications as nutraceuticals and food colorants.

JOURNAL OF FOOD COMPOSITION AND ANALYSIS (2022)

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Article Biology

The LOTUS initiative for open knowledge management in natural products research

Adriano Rutz et al.

Summary: Contemporary bioinformatic and chemoinformatic capabilities have the potential to reshape knowledge management, analysis, and interpretation in natural products research. However, the reliance on disparate and specialized databases poses challenges for data access and integration. The LOTUS initiative aims to address these challenges by consolidating and sharing referenced structure-organism pairs on an open platform, promoting collaboration and transformative research.

ELIFE (2022)

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Review Food Science & Technology

Miniaturized NIR Spectroscopy in Food Analysis and Quality Control: Promises, Challenges, and Perspectives

Krzysztof B. Bec et al.

Summary: The ongoing miniaturization of NIR spectrometers provides significant benefits in the field of food analysis. Various factors affect the performance of these devices in different analytical scenarios. Systematic evaluation studies are being conducted to assess the accuracy and reliability of miniaturized spectrometers based on different technologies. Advanced calibration methods and quantum-mechanical simulation improve the performance and information gathered from NIR spectra. A data-fusion framework enables intelligent design of future NIR analyses using miniaturized instruments in the complex matrix of food samples.

FOODS (2022)

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Editorial Material Medicine, General & Internal

VITAL Findings - A Decisive Verdict on Vitamin D Supplementation

Steven R. Cummings et al.

Summary: This study analyzed the results of an ancillary study of the Vitamin D and Omega-3 Trial (VITAL) and found that vitamin D supplements do not have important health benefits in the general population of older adults, even in those with low 25-hydroxyvitamin D levels.

NEW ENGLAND JOURNAL OF MEDICINE (2022)

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Article Virology

HYGIEIA: HYpothesizing the Genesis of Infectious Diseases and Epidemics through an Integrated Systems Biology Approach

Bradley Ward et al.

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VIRUSES-BASEL (2022)

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Review Endocrinology & Metabolism

An evaluation of the National Institutes of Health grants portfolio: identifying opportunities and challenges for multi-omics research that leverage metabolomics data

Catherine T. Yu et al.

Summary: Metabolomics is an important field of research that can contribute to biomarker discovery and improving disease monitoring, diagnosis, prognosis, and treatment response. Integrating metabolomics data with other -omics data can further enhance understanding of human disease development and treatment. However, the current level of integration of metabolomics data needs improvement.

METABOLOMICS (2022)

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Article Chemistry, Multidisciplinary

Minimizing the risk of deducing wrong natural product structures from NMR data

Darcy C. Burns et al.

Summary: There is a concerning number of inaccuracies in the structural elucidation of natural products due to limited nuclear magnetic resonance training among natural product chemists. This tutorial aims to address these issues, highlight common errors, and provide guidance on avoiding such mistakes to minimize the risk of reporting incorrect structures.

MAGNETIC RESONANCE IN CHEMISTRY (2021)

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Review Chemistry, Analytical

Multi-omics integration in biomedical research - A metabolomics-centric review

Maria A. Woerheide et al.

Summary: Recent advances in high-throughput technologies have enabled the profiling of multiple layers of a biological system, generating vast amounts of data that can be integrated in multi-omics studies. Integrative analysis of such datasets is complicated by the high dimensionality, heterogeneity, and lack of universal protocols. While previous reviews focused on integrating two omics layers with a phenotype, this review highlights methods to combine metabolomics data with two or more omics layers without focusing on a specific phenotype.

ANALYTICA CHIMICA ACTA (2021)

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Review Chemistry, Multidisciplinary

Computer Assisted Structure Elucidation (CASE): Current and future perspectives

Mikhail Elyashberg et al.

Summary: The development of Computer-Assisted Structure Elucidation methods, based on NMR data, has a history of more than 50 years. Expert systems using 1D and 2D NMR data have matured considerably, and will likely be influenced by new NMR experiments, computational chemistry methods, and emerging technologies in the future.

MAGNETIC RESONANCE IN CHEMISTRY (2021)

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Article Biochemistry & Molecular Biology

Combination of Pseudo-LC-NMR and HRMS/MS-Based Molecular Networking for the Rapid Identification of Antimicrobial Metabolites From Fusarium petroliphilum

Abdulelah Alfattani et al.

Summary: An endophytic fungal strain isolated from a seagrass endemic to the Mediterranean Sea was studied for its antimicrobial constituents and metabolome composition, revealing its ability to inhibit quorum sensing of Staphylococcus aureus. An innovative one-step strategy was devised to analyze the extract, leading to the characterization of major specialized metabolites and bioactive compounds. This approach identified new natural products and inhibitors of quorum sensing, demonstrating its potential for generic applications in natural extracts.

FRONTIERS IN MOLECULAR BIOSCIENCES (2021)

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Article Chemistry, Multidisciplinary

NMReDATA: Tools and applications

Stefan Kuhn et al.

Summary: The NMReDATA format is proposed as a standardized way to store and exchange NMR data and metadata of chemical compounds. This paper discusses analytical workflows utilizing the NMReDATA format and provides a repository of sample data for validating software packages.

MAGNETIC RESONANCE IN CHEMISTRY (2021)

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Article Chemistry, Analytical

Tandem of Countercurrent Separation and qHNMR Enables Gravimetric Analyses: Absolute Quantitation of the Rhodiola rosea Metabolome

Yu Tang et al.

Summary: The off-line combination of CCS and qHNMR allows for the systematic dissection and gravimetric quantification of a chemically complex Rhodiola rosea crude extract, providing accurate discrimination of various metabolite classes. This approach resolves challenges with baselines in NMR and UHPLC analyses, allowing for precise quantitation of metabolites. The use of single, nonidentical internal calibrant in qHNMR enables unambiguous identification of metabolites and absolute quantification, realizing the first chemical standardization of a botanical material capturing a comprehensive metabolome.

ANALYTICAL CHEMISTRY (2021)

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Article Plant Sciences

Dual High-Resolution α-Glucosidase and PTP1B Inhibition Profiling Combined with HPLC-PDA-HRMS-SPE-NMR Analysis for the Identification of Potentially Antidiabetic Chromene Meroterpenoids from Rhododendron capitatum

Chao Liang et al.

Summary: Thirteen new chromene meroterpenoids were identified from ethyl acetate extract of Rhododendron capitatum, along with one known compound and other compounds. The structures of the new compounds were elucidated through NMR analysis and their absolute configurations were determined through ECD spectroscopy analysis. Some of the compounds exhibited inhibitory activity against α-glucosidase and PTP1B.

JOURNAL OF NATURAL PRODUCTS (2021)

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The Advantage of Automatic Peer-Reviewing of C-13-NMR Reference Data Using the CSEARCH-Protocol

Wolfgang Robien

Summary: This study systematically investigates the quality of experimental C-13-NMR spectra published in the journal Molecules from 1996 to 2015 using CSEARCH technology. The results show that using the CSEARCH-Robot-Referee during peer review can prevent trivial assignment errors and wrong structure proposals. Comparison of key numbers with other journals in natural product chemistry indicates a similar level of quality among publishers.

MOLECULES (2021)

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Article Biochemical Research Methods

Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices

Saleh Alseekh et al.

Summary: Compound identification and reliable quantification in metabolomics are complicated by the chemical complexity and dynamic range of the metabolome, while quantification in complex mixtures can be further complicated by ion suppression and the presence of isomers.

NATURE METHODS (2021)

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Ion identity molecular networking for mass spectrometry-based metabolomics in the GNPS environment

Robin Schmid et al.

Summary: The authors develop a new Ion Identity Molecular Networking (IIMN) approach that integrates chromatographic peak shape correlation analysis to connect and collapse different ion species of the same molecule, improving network connectivity for structurally related molecules.

NATURE COMMUNICATIONS (2021)

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Article Biochemistry & Molecular Biology

Recent Developments Toward Integrated Metabolomics Technologies (UHPLC-MS-SPE-NMR and MicroED) for Higher-Throughput Confident Metabolite Identifications

Rajarshi Ghosh et al.

Summary: Metabolomics relies on accurate annotations of spectral features from MS and/or NMR, with less than 20% of features confidently identified in most experiments. Integration of multiple analytical instruments, such as UHPLC-MS/MS-SPE-NMR and MicroED, enables large-scale and confident metabolite identifications. The combination of MicroED with UHPLC-MS/MS-SPE-NMR accelerates and enhances metabolite identification rates.

FRONTIERS IN MOLECULAR BIOSCIENCES (2021)

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Article Biochemistry & Molecular Biology

Combining HPLC-DAD-QTOF-MS and HPLC-SPE-NMR to Monitor In Vitro Vitetrifolin D Phase I and II Metabolism

Sonja Sturm et al.

Summary: The study investigated the in vitro metabolism of vitetrifolin D using HPLC-DAD-QTOF-MS and HPLC-SPE-NMR, identifying 27 phase I and phase II metabolites, with structural characterization of nine phase I metabolites. By avoiding preparative isolation of metabolites, the study demonstrated the successful performance of in vitro metabolism studies using hyphenated instrumental analysis methodologies even with limited substance availability.

METABOLITES (2021)

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Article Multidisciplinary Sciences

The Brazilian octocoral Phyllogorgia dilatata as a source of cytotoxic compounds

Thayssa S. F. Fagundes et al.

Summary: The study demonstrated the biomedical potential of the Brazilian octocoral Phyllogorgia dilatata, highlighting its antiproliferative effect against tumor cell lines. A subfraction obtained from chemical fractionation showed enhanced cytotoxic activity, suggesting a potentiated effect of the diastereoisomeric mixture, encouraging further bioactivity studies with stereoisomer mixtures.

ANAIS DA ACADEMIA BRASILEIRA DE CIENCIAS (2021)

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Review Biochemistry & Molecular Biology

Advances in decomposing complex metabolite mixtures using substructure- and network-based computational metabolomics approaches

Mehdi A. Beniddir et al.

Summary: This review highlights the impact of computational metabolome mining tools on untargeted metabolomics analyses, providing a pathway to decompose complex metabolite mixtures into substructures and chemical class information. The tools discussed aim at processing liquid chromatography coupled to mass spectrometry fragmentation data, with a focus on substructure identification and chemical compound annotation. The technical advances outlined in this review have the potential to transform spectral data into knowledge that can address biological questions in various metabolomics disciplines.

NATURAL PRODUCT REPORTS (2021)

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Review Multidisciplinary Sciences

Parallel nuclear magnetic resonance spectroscopy

Eriks Kupce et al.

Summary: This article discusses different approaches to accelerate data acquisition and increase sensitivity of NMR measurements through parallelization, enabled by hardware design and/or pulse sequence development. By coupling multiple detectors to samples and using magnetic field gradients and frequency-selective manipulations, parallelization can compress multidimensional acquisition and yield new pulse schemes. The promising future developments are expected through combining these discussed techniques for maximum gains.

NATURE REVIEWS METHODS PRIMERS (2021)

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Review Plant Sciences

Modeling Plant Metabolism: From Network Reconstruction to Mechanistic Models

Teresa J. Clark et al.

ANNUAL REVIEW OF PLANT BIOLOGY, VOL 71, 2020 (2020)

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Efficient identification of Acetylcholinesterase and Hyaluronidase inhibitors from Paeonia parnassica extracts through a HeteroCovariance Approach

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Diastereomeric identification of neolignan rhamnosides from Trochodendron aralioides leaves by LC-SPE-NMR and circular dichroism

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FITOTERAPIA (2020)

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HPLC-DAD-SPE-NMR isolation of tetracyclic spiro-alkaloids with antiplasmodial activity from the seeds of Erythrina latissima

Yancho Zarev et al.

NATURAL PRODUCT RESEARCH (2020)

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Review Chemistry, Multidisciplinary

NMR signal processing, prediction, and structure verification with machine learning techniques

Carlos Cobas

MAGNETIC RESONANCE IN CHEMISTRY (2020)

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Quantum Mechanics-Based Structure Analysis of Cyclic Monoterpene Glycosides from Rhodiola rosea

Yu Tang et al.

JOURNAL OF NATURAL PRODUCTS (2020)

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Structure Elucidation and Absolute Configuration Determination of Nortriterpenoids from Picramnia glazioviana

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JOURNAL OF NATURAL PRODUCTS (2020)

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Review Biochemistry & Molecular Biology

The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research

James B. McAlpine et al.

NATURAL PRODUCT REPORTS (2019)

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Autonomous METLIN-Guided In-source Fragment Annotation for Untargeted Metabolomics

Xavier Domingo-Almenara et al.

ANALYTICAL CHEMISTRY (2019)

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Identification of bioactive metabolites using activity metabolomics

Markus M. Rinschen et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2019)

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Triplet NOAH supersequences optimised for small molecule structure characterisation

Tim D. W. Claridge et al.

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Nils Eling et al.

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Lijuan Ma et al.

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Accelerating Metabolite Identification in Natural Product Research: Toward an Ideal Combination of Liquid Chromatography-High-Resolution Tandem Mass Spectrometry and NMR Profiling, in Silico Databases, and Chemometrics

Jean-Luc Wolfender et al.

ANALYTICAL CHEMISTRY (2019)

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Review Biochemistry & Molecular Biology

Innovative omics-based approaches for prioritisation and targeted isolation of natural products - new strategies for drug discovery

Jean-Luc Wolfender et al.

NATURAL PRODUCT REPORTS (2019)

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Review Biochemistry & Molecular Biology

The role of computer-assisted structure elucidation (CASE) programs in the structure elucidation of complex natural products

Darcy C. Burns et al.

NATURAL PRODUCT REPORTS (2019)

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Article Biochemical Research Methods

Quadruple high-resolution α-glucosidase/α-amylase/PTP1B/radical scavenging profiling combined with high-performance liquid chromatography-high-resolution mass spectrometry-solid-phase extraction-nuclear magnetic resonance spectroscopy for identification of antidiabetic constituents in crude root bark of Morus alba L.

Yong Zhao et al.

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Targeted isolation and identification of bioactive compounds lowering cholesterol in the crude extracts of crabapples using UPLC-DAD-MS-SPE/NMR based on pharmacology-guided PLS-DA

Chao Wen et al.

JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS (2018)

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NMReDATA, a standard to report the NMR assignment and parameters of organic compounds

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MAGNETIC RESONANCE IN CHEMISTRY (2018)

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Absolute Configuration Determination of Retroflexanone Using the Advanced Mosher Method and Application of HPLC-NMR

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Athenolide A, a New Steroidal Lactone from the Leaves of Athenaea martiana (Solanaceae) Determined by Means of HPLC-HR-MS-SPE-NMR Analysis

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New oleanane saponins from the roots of Dendrobangia boliviana identified by LC-SPE-NMR

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MAGNETIC RESONANCE IN CHEMISTRY (2017)

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PHYTOCHEMISTRY (2017)

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Comprehensive comparison of in silico MS/MS fragmentation tools of the CASMI contest: database boosting is needed to achieve 93% accuracy

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NOAH: NMR Supersequences for Small Molecule Analysis and Structure Elucidation

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ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2017)

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CURRENT OPINION IN CHEMICAL BIOLOGY (2017)

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Identification of Two New Phosphorylated Polyketides from a Brazilian Streptomyces sp Through the Use of LC-SPE/NMR

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Statistical Correlations between HPLC Activity-Based Profiling Results and NMR/MS Microfraction Data to Deconvolute Bioactive Compounds in Mixtures

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Heterocovariance Based Metabolomics as a Powerful Tool Accelerating Bioactive Natural Product Identification

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Flavonol profiles in berries of wild Vitis accessions using liquid chromatography coupled to mass spectrometry and nuclear magnetic resonance spectrometry

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Improving Natural Products Identification through Targeted LC-MS/MS in an Untargeted Secondary Metabolomics Workflow

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Nuclear Magnetic Resonance at the Picomole Level of a DNA Adduct

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Detection and identification of hydrolysis products of sulfur mustards at trace levels in environmental samples using liquid chromatography solid phase extraction combined with off-line nuclear magnetic resonance analysis

Urs C. Meier

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Molecular Networking as a Dereplication Strategy

Jane Y. Yang et al.

JOURNAL OF NATURAL PRODUCTS (2013)

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Mass spectrometry and NMR spectroscopy: modern high-end detectors for high resolution separation techniques - state of the art in natural product HPLC-MS, HPLC-NMR, and CE-MS hyphenations

Christoph Seger et al.

NATURAL PRODUCT REPORTS (2013)

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Review Biochemistry & Molecular Biology

Using NMR to identify and characterize natural products

Rosemary C. Breton et al.

NATURAL PRODUCT REPORTS (2013)

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From single to multiple microcoil flow probe NMR and related capillary techniques: a review

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Identification of Three Novel Polyphenolic Compounds, Origanine A-C, with Unique Skeleton from Origanum vulgare L. Using the Hyphenated LC-DAD-SPE-NMR/MS Methods

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Liquid chromatography-nuclear magnetic resonance coupling as alternative to liquid chromatography-mass spectrometry hyphenations: Curious option or powerful and complementary routine tool?

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Article Biochemical Research Methods

Alkaloid analysis by high-performance liquid chromatography-solid phase extraction-nuclear magnetic resonance: New strategies going beyond the standard

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Diarylheptanoids from Dioscorea villosa (Wild Yam)

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Rapid isolation and identification of minor natural products by LC-MS, LC-SPE-NMR and ECD: Isoflavanones, biflavanones and bisdihydrocoumarins from Ormocarpum kirkii

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Herbal Medicines and Infectious Diseases: Characterization by LC-SPE-NMR of Some Medicinal Plant Extracts Used against Malaria

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LC-MS-SPE-NMR for the Isolation and Characterization of neo-Clerodane Diterpenoids from Teucrium luteum subsp flavovirens

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Optimized liquid chromatography-mass spectrometry approach for the isolation of minor stress biomarkers in plant extracts and their identification by capillary nuclear magnetic resonance

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Characterization of bixin by LC-MS and LC-NMR

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Evaluation of on-line solid-phase extraction parameters for hyphenated, high-performance liquid chromatography-solid-phase extraction-nuclear magnetic resonance applications

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Conventional sample enrichment strategies combined with high-performance liquid chromatography-solid phase extraction-nuclear magnetic resonance analysis allows analyte identification from a single minuscule Corydalis solida plant tuber

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Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry

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Reaction product analysis by high-performance liquid chromatography-solid-phase extraction-nuclear magnetic resonance - Application to the absolute configuration determination of naturally occurring polyyne alcohols

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Hyphenation of capillary HPLC to microcoil 1H NMR spectroscopy for the determination of tocopherol homologues

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ent-Labdane glycosides from the aquatic plant Potamogeton lucens and analytical evaluation of the lipophilic extract constituents of various Potamogeton species

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Solid-phase extraction NMR studies of chromatographic fractions of saponins from Quillaja saponaria

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A photometric screening method for dimeric naphthylisoquinoline alkaloids and complete on-line structural elucidation of a dimer in crude plant extracts, by the LC-MS/LC-NMR/LC-CD triad

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