Advances in the integration of metabolomics and metagenomics for human gut microbiome and their clinical applications

TrAC Trends in Analytical Chemistry, Journal Year: 2023, Volume and Issue: 167, P. 117248 - 117248

Published: Aug. 21, 2023

The human microbiome and its metabolic output play an important role in shaping health disease. host-microbe crosstalk is often characterised using metabolomics metagenomics, yet a large proportion of microbial metabolites the molecular functions gut microbes remain unknown. This review summarises strategies for annotation discovery novel from microbiome, either alone or combination with presents data analysis methods combining these two types to obtain biological insights. Applications research biomarker screening, precision medicine, drug are also discussed, along perspectives, challenges limitations this field.

Language: Английский

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Computational tools and algorithms for ion mobility spectrometry‐mass spectrometry

PROTEOMICS, Journal Year: 2024, Volume and Issue: 24(12-13)

Published: March 4, 2024

Abstract Ion mobility spectrometry‐mass spectrometry (IMS‐MS or IM‐MS) is a powerful analytical technique that combines the gas‐phase separation capabilities of IM with identification and quantification MS. IM‐MS can differentiate molecules indistinguishable masses but different structures (e.g., isomers, isobars, molecular classes, contaminant ions). The importance this reflected by staged increase in number applications for characterization across variety fields, from MS‐based omics (proteomics, metabolomics, lipidomics, etc.) to structural glycans, organic matter, proteins, macromolecular complexes. With increasing application there pressing need effective accessible computational tools. This article presents an overview most recent free open‐source software tools specifically tailored analysis interpretation data derived instrumentation. review enumerates these outlines their main algorithmic approaches, while highlighting representative fields. Finally, discussion current limitations expectable improvements presented.

Language: Английский

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Collision cross-section as a universal molecular descriptor in the analysis of PFAS and use of ion mobility spectrum filtering for improved analytical sensitivities

Analytica Chimica Acta, Journal Year: 2023, Volume and Issue: 1251, P. 341026 - 341026

Published: March 1, 2023

Language: Английский

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Collision Cross Section Prediction Based on Machine Learning

Molecules, Journal Year: 2023, Volume and Issue: 28(10), P. 4050 - 4050

Published: May 12, 2023

Ion mobility-mass spectrometry (IM-MS) is a powerful separation technique providing an additional dimension of to support the enhanced and characterization complex components from tissue metabolome medicinal herbs. The integration machine learning (ML) with IM-MS can overcome barrier lack reference standards, promoting creation large number proprietary collision cross section (CCS) databases, which help achieve rapid, comprehensive, accurate contained chemical components. In this review, advances in CCS prediction using ML past 2 decades are summarized. advantages ion spectrometers commercially available mobility technologies different principles (e.g., time dispersive, confinement selective release, space dispersive) introduced compared. general procedures involved based on (acquisition optimization independent dependent variables, model construction evaluation, etc.) highlighted. addition, quantum chemistry, molecular dynamics, theoretical calculations also described. Finally, applications metabolomics, natural products, foods, other research fields reflected.

Language: Английский

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Characterization of Electrospray Ionization Complexity in Untargeted Metabolomic Studies

Analytical Chemistry, Journal Year: 2024, Volume and Issue: 96(27), P. 10935 - 10942

Published: June 25, 2024

The annotation of metabolites detected in LC-MS-based untargeted metabolomics studies routinely applies accurate m/z the intact metabolite (MS1) as well chromatographic retention time and MS/MS data. Electrospray ionization transfer ions through mass spectrometer can result generation multiple "features" derived from same with different values but time. complexity charged neutral adducts, in-source fragments, charge states has not been previously deeply characterized. In this paper, we report first large-scale characterization using publicly available data sets research groups, instrument manufacturers, LC assays, sample types, ion modes. 271 differences relating to feature pairs were reported, 209 annotated. results show a wide range features being observed only core 32 reported >50% investigated. There no patterns reporting specific that relation mode, manufacturer, assay type, mammalian although some related study group (mammal, microbe, plant) mobile phase composition. provide community recommendations apply workflows.

Language: Английский

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A Fast-Pass, Desorption Electrospray Ionization Mass Spectrometry Strategy for Untargeted Metabolic Phenotyping

Journal of the American Society for Mass Spectrometry, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 27, 2025

Desorption electrospray ionization mass spectrometry imaging (DESI-MSI) provides direct analytical readouts of small molecules that can be used to characterize the metabolic phenotypes genetically engineered bacteria. In an effort accelerate time frame associated with screening mutant libraries, we have developed a high-throughput DESI-MSI workflow implementing single raster line-scan strategy facilitates collection location-resolved molecular information from strains on subminute scale. Evaluation this "Fast-Pass" phenotyping standards demonstrated capability acquiring full profiling throughput ∼40 s per sample. This Fast-Pass was implemented in analysis edited Escherichia coli been produce various free-fatty acids (FFAs) for applications relevant biofuels. Due untargeted nature DESI-MSI, investigation these yielded both global metabolites and targeted detection accumulated bioproducts, allowing simultaneous strain-specific chemical profiles comparative measurements FFA production levels.

Language: Английский

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Noncovalent Host–Guest Complexes of Artemisinin with α-, β-, and γ- Cyclodextrin Examined by Structural Mass Spectrometry Strategies

Analytical Chemistry, Journal Year: 2023, Volume and Issue: 95(21), P. 8180 - 8188

Published: May 15, 2023

Cyclodextrins (CDs) are a family of macrocyclic oligosaccharides with amphiphilic properties, which can improve the stability, solubility, and bioavailability therapeutic compounds. There has been growing interest in advancement efficient reliable analytical methods that assist elucidating CD host–guest drug complexation. In this study, we investigate noncovalent ion complexes formed between naturally occurring dextrins (αCD, βCD, γCD, maltohexaose) poorly water-soluble antimalarial drug, artemisinin, using combination mobility-mass spectrometry (IM-MS), tandem MS/MS, theoretical modeling approaches. This study aims to determine if complex within core dextrin cavity forming an inclusion or nonspecifically bind periphery dextrins. We explore use group I alkali earth metal additives promote formation various gas-phase different drug/dextrin stoichiometries (1:1, 1:2, 1:3, 1:4, 2:1). Broad IM-MS collision cross section (CCS) mapping (n > 300) power-law regression analysis were used confirm stoichiometric assignments. The 1:1 drug:αCD drug:βCD exhibited strong preferences for Li+ Na+ charge carriers, whereas drug:γCD preferred adducts larger metals, K+, Rb+, Cs+. Although ion-measured CCS increased cation size unbound artemisinin CDs, drug:dextrin exhibit near-identical values regardless cation, suggesting these complexes. Tandem MS/MS survival yield curves [artemisinin:βCD + X]+ (X = H, Li, Na, K) showed decreased stability increasing size. Empirical measurements Li]+ correlated predicted from low-energy structures incorporated βCD cavity, providing further evidence experiments. Taken together, work demonstrates utility combining information IM-MS, computational approaches interpreting presence phenomena.

Language: Английский

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Solvent Composition Can Have a Measurable Influence on the Ion Mobility-Derived Collision Cross Section of Small Molecules

Journal of the American Society for Mass Spectrometry, Journal Year: 2023, Volume and Issue: 35(2), P. 234 - 243

Published: Dec. 12, 2023

Ion mobility (IM) is an important analytical technique for increasing identification coverage of metabolites in untargeted studies, especially when integrated into traditional liquid chromatography–mass spectrometry workflows. While there has been extensive work surrounding best practices to obtain and standardize collision cross section (CCS) measurements necessary comparing across different IM techniques laboratories, little investigation experimental factors beyond the separation region that could potentially influence CCS measurements. The first-principles derived 15 chemical standards were evaluated 27 aqueous:organic solvent compositions using a high-precision drift tube instrument. A small but measurable dependency on composition was observed, with larger analytes from this study (m/z > 400) exhibiting characteristic increase at intermediate (40–60%) compositions. Parallels behavior viscosity protonation site tautomers (protomers) noted, although origin these solvent-dependent trends as yet unclear. Taken together, findings document CCS, which, while minor (<0.5%), identifies need reporting system utilizing comparative ion studies.

Language: Английский

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Direct Enantiomer Differentiation of Drugs and Drug-Like Compounds via Noncovalent Copper–Amino Acid Complexation and Ion Mobility-Mass Spectrometry

Analytical Chemistry, Journal Year: 2024, Volume and Issue: 96(31), P. 12892 - 12900

Published: July 25, 2024

Drug enantiomers can possess vastly different pharmacological properties, yet they are identical in their chemical composition and structural connectivity. Thus, resolving poses a great challenge the field of separation science. Enantiomer separations necessitate interaction analyte with chiral environment─in mass spectrometry-based analysis, common approach is through three-point selector commonly introduced during sample preparation. In select cases, difference imparted noncovalent complexation results enantiomer-specific differences, facilitating measurement using structurally selective analytical technique such as ion mobility-mass spectrometry (IM-MS). this work, we investigate direct IM-MS differentiation drug compounds mononuclear copper complexes incorporating an amino acid selector. A panel 20 drugs drug-like were investigated for separation, four l-amino acids (l-histidine, l-tryptophan, l-proline, l-tyrosine) evaluated selectors (CS) to provide environment necessary differentiation. was achieved molecule pairs (

Language: Английский

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An Untargeted Lipidomics Workflow Incorporating High-Resolution Demultiplexing (HRdm) Drift Tube Ion Mobility-Mass Spectrometry

Journal of the American Society for Mass Spectrometry, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 14, 2024

Global discovery lipidomics can provide comprehensive chemical information toward understanding the intricacies of metabolic lipid disorders such as dyslipidemia; however, isomeric complexity species remains an analytical challenge. Orthogonal separation strategies, ion mobility (IM), be inserted into liquid chromatography-mass spectrometry (LC-MS) untargeted lipidomic workflows for additional isomer and high-confidence annotation, emergence high-resolution (HRIM) strategies provides marked improvements to resolving power (

Language: Английский

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