Unlabelled: Metabolomics extensively utilizes Nuclear Magnetic Resonance (NMR) spectroscopy due to its excellent reproducibility and high throughput. Both one-dimensional (1D) and two-dimensional (2D) NMR spectra provide crucial information for metabolite annotation and quantification, yet present complex overlapping patterns which may require sophisticated machine learning algorithms to decipher. Unfortunately, the limited availability of labeled spectra can hamper application of machine learning, especially deep learning algorithms which require large amounts of labelled data. In this context, simulation of spectral data becomes a tractable solution for algorithm development.Here, we introduce MetAssimulo 2.0, a comprehensive upgrade of the MetAssimulo 1.0 metabolomic 1H NMR simulation tool, reimplemented as a Python-based web application. Where MetAssimulo 1.0 only simulated 1D 1H spectra of human urine, MetAssimulo 2.0 expands functionality to urine, blood, and cerebral spinal fluid (CSF), enhancing the realism of blood spectra by incorporating a broad protein background. This enhancement enables a closer approximation to real blood spectra, achieving a Pearson correlation of approximately 0.82. Moreover, this tool now includes simulation capabilities for 2D J-resolved (J-Res) and Correlation Spectroscopy (COSY) spectra, significantly broadening its utility in complex mixture analysis. MetAssimulo 2.0 simulates both single, and groups, of spectra with both discrete (case-control, e.g. heart transplant vs healthy) and continuous (e.g. BMI) outcomes and includes inter-metabolite correlations. It thus supports a range of experimental designs and demonstrating associations between metabolite profiles and biomedical responses.By enhancing NMR spectral simulations, MetAssimulo 2.0 is well positioned to support and enhance research at the intersection of deep learning and metabolomics.
Availability And Implementation: The code and the detailed instruction/tutorial for MetAssimulo 2.0 is available at https://github.com/yanyan5420/MetAssimulo_2.git The relevant NMR spectra for metabolites are deposited in MetaboLights with accession number MTBLS12081.
Supplementary Information: Supplementary data are available at Bioinformatics online.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1093/bioinformatics/btaf045 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Structural features of dioxane lignin: A comparative study with milled wood and formaldehyde-stabilized lignins.
Int J Biol Macromol
January 2025
Core Facility Center "Arktika", Northern (Arctic) Federal University named after M.V. Lomonosov, Northern Dvina Emb., 17, Arkhangelsk 163002, Russian Federation. Electronic address:
Dioxane lignin (DL) is isolated from plant material under mild acidolysis conditions and is widely used in many studies as a representative sample of protolignin, an alternative to milled wood lignin (MWL). However, the structural changes caused by hydrolytic degradation reactions during DL extraction are still poorly understood. In this work, an integrated approach based on 2D NMR and high-resolution mass spectrometry was used to establish the features of the lignin structure on the example of pine lignin isolated using dioxane under various conditions: MWL, DL and "formaldehyde stabilized" lignin (LSF).
View Article and Find Full Text PDFMetAssimulo 2.0: a web app for simulating realistic 1D & 2D Metabolomic 1H NMR spectra.
Bioinformatics
January 2025
Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, W12 0NN, United Kingdom.
Unlabelled: Metabolomics extensively utilizes Nuclear Magnetic Resonance (NMR) spectroscopy due to its excellent reproducibility and high throughput. Both one-dimensional (1D) and two-dimensional (2D) NMR spectra provide crucial information for metabolite annotation and quantification, yet present complex overlapping patterns which may require sophisticated machine learning algorithms to decipher. Unfortunately, the limited availability of labeled spectra can hamper application of machine learning, especially deep learning algorithms which require large amounts of labelled data.
View Article and Find Full Text PDF2,4-Dichlorophenoxyacetic Acid in the Gas and Crystal Phases and Its Intercalation in Montmorillonite-An Experimental and Theoretical Study.
Molecules
January 2025
Instituto Andaluz de Ciencias de la Tierra (IACT-CSIC), Consejo Superior de Investigaciones Científicas, Av. de las Palmeras 4, 18100 Armilla, Granada, Spain.
Many properties of 2,4-dichlorophenoxyacetic acid (2,4-D) depend on its molecular environment, such as whether it is an isolated molecule, a dimer, or in a crystalline state. The molecular geometry, conformational analysis, and vibrational spectrum of 2,4-D were theoretically calculated using Density Functional Theory (DFT) methods. A new slightly more stable conformer was found, which is different to those previously reported.
View Article and Find Full Text PDFHydrogen-Bonded Di(hydroperoxy)alkane Adducts of the Type CyP=O·(HOO)CHR (R = Alkyl).
Molecules
January 2025
Department of Chemistry, Texas A&M University, College Station, TX 77842-3012, USA.
Five representatives of a novel type of di(hydroperoxy)alkane adducts of phosphine oxides have been synthesized and fully characterized, including their solubility in organic solvents. The phosphine oxide CyPO () has been used in combination with the corresponding aldehydes to create the adducts CyPO·(HOO)CHCH (), CyPO·(HOO)CHCHCH (), CyPO·(HOO)CH(CH)CH (), CyPO·(HOO)CH(CH)CH (), and CyPO·(HOO)CH(CH)CH (). All adducts crystallize easily and contain the peroxide and phosphine oxide hydrogen-bonded in 1:1 ratios.
View Article and Find Full Text PDFA Photocontrolled Molecular Rotor Based on Azobenzene-Strapped Mixed (Phthalocyaninato)(Porphyrinato) Rare Earth Triple-Decker.
Molecules
January 2025
Beijing Key Laboratory for Science and Application of Functional Molecular and Crystalline Materials, Department of Chemistry and Chemical Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China.
Effectively regulating the rotary motions of molecular rotors through external stimuli poses a tremendous challenge. Herein, a new type of molecular rotor based on azobenzene-strapped mixed (phthalocyaninato)(porphyrinato) rare earth triple-decker complex is reported. Electronic absorption and H NMR spectra manifested the reversible isomerization of the rotor between the configuration and the configuration.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!