Metabolomics and Mass Spectrometry Studies

A Python Dash App and cPanel workflow to automate metabolomics data analyses and visualisation

The paper presents a Python Dash App and cPanel workflow to automate metabolomics data analysis and visualization, enabling interactive statistical analysis and result sharing.

Feasibility of multimodal metabolic analysis for detecting early changes in acute neuroinflammation

This study uses multimodal metabolic analysis to detect early metabolic changes in acute neuroinflammation, showing reduced pyruvate metabolism and ongoing inflammation without structural MRI changes.

SMEW: An interactive multi-scale toolkit for cross-condition and network-based analysis of spatial metabolomics data

SMEW provides a code-free, interactive platform for analyzing spatial metabolomics data across multiple scales and conditions to identify metabolic patterns and biological pathways.

Navigating the Lipid Universe with LipidLibrarian: A Cross-Linked Database for Lipidomics Data Integration

LipidLibrarian integrates lipidomics data from multiple databases to provide a unified search interface for lipid information.

MSAgent: An Evidence Grounded Agentic Framework for LLM-driven Scientific Exploration in Mass Spectrometry-based Metabolomics

MSAgent improves molecular identification from mass spectrometry data by integrating LLMs with domain tools, achieving higher accuracy and reliability than existing methods.

Metabolic fingerprinting of 17 Brassicaceae species across three tissues

The paper collects and standardizes metabolic fingerprints of 17 Brassicaceae species across three tissues using LC-MS/MS, enabling integration with genomic and transcriptomic data for natural product discovery.

SIMO - Single Section Integrative Multi-Omics - spatial mapping of metabolites and lipids combined with region-specific proteomics in a single tissue slice

SIMO integrates spatial metabolomics, lipidomics, and proteomics from a single tissue section to enable comprehensive multi-omics analysis across spatial regions.

The CcpNmr Analysis Simulated Metabolomics Database (CASMDB): An Open-Source Collection of Metabolite Annotation Data for 1D 1H NMR-Based Metabolomics

The paper describes the creation of CASMDB, a database of metabolite annotations for 1D 1H NMR-based metabolomics, enabling accurate simulation and visualization of spectra.

A Multimodal Workflow for Spatial Metabolic Neighborhood Mapping in Neural Rosette Cultures

The paper develops a workflow to map metabolic neighborhoods in neural rosettes using MALDI imaging and single-cell analysis, enabling spatial and metabolic characterization of differentiating stem cells.

Saliva Metabolomics Reveals Distinct Metabolic Signatures in Patients with Chronic Obstructive Pulmonary Disease: A GC-MS-based approach.

This study identifies metabolic signatures in COPD patients using saliva metabolomics, revealing distinct patterns in smokers and ex-smokers compared to healthy controls.

Isotopic tracing of scyllo-inositol uncovers its incorporation into phosphatidylinositols in mammalian cells

This paper develops [13C6]scyllo-inositol as an isotopic tracer to study its metabolism and shows its incorporation into phosphatidylinositols in mammalian cells.

Lipidomic and metabolomic profiling on low count human spermatozoa: A robust and reproducible method for untargeted HPLC-ESI-MS/MS-based approach

This paper develops a sensitive untargeted HPLC-ESI-MS/MS workflow for lipidomic and metabolomic profiling of human spermatozoa using only 1.25 million cells, revealing interconnected lipid and metabolic pathways.

Information-Content-Informed Kendall-tau Correlation Methodology: Interpreting Missing Values in Metabolomics as Potentially Useful Information

The paper introduces ICI-Kt, a method to interpret left-censored missing values in metabolomics as informative, improving outlier detection and network construction.

New insights into the metabolomic signatures of spontaneously hypertensive rats

This study identifies metabolomic signatures in spontaneously hypertensive rats, revealing altered steroid hormone, bile acid, purine, and microbiota-derived metabolite profiles associated with hypertension.

Mapping the mammalian dark metabolome by in vivo isotope tracing

The paper uses in vivo isotope tracing and AI to identify biosynthetic origins of unknown metabolites, revealing new metabolic pathways and age-related changes.

A high-resolution mass spectrometry-based method for quantifying insulin-stimulated glucose uptake in mice following an intraperitoneal injection of tracer

This paper develops and validates a mass spectrometry-based method to measure insulin-stimulated tissue-specific glucose clearance in mice without radiolabels or catheters.

Serum metabolic signatures of cognitive resilience in a longitudinal aging cohort

The paper identifies serum metabolic signatures associated with cognitive resilience in a longitudinal aging cohort using untargeted LC-MS/MS profiling.

Pan-Metabolomics Repository Mapping of the Carnitine Landscape

The paper systematically extracts and catalogs acylcarnitine metabolites from multiple repositories, identifying previously unknown carnitines and providing a resource for further metabolic research.

Single-Injection Multi-Omics Analysis by Direct Infusion Mass Spectrometry (SMAD-MS)

SMAD-MS enables rapid single-injection multi-omics analysis of proteomics, metabolomics, and lipidomics without liquid chromatography, achieving high throughput and efficiency.

METABOLOMIC SIGNATURES OF EXTREME OLD AGE: FINDINGS FROM THE NEW ENGLAND CENTENARIAN STUDY

The paper identifies metabolomic signatures associated with extreme old age using data from the New England Centenarian Study and links them to biological age and mortality risk.

Cell-specific isotope labeling identifies myo-inositol transfer between neurons and oligodendroglia to support myelin repair

The paper uses cell-specific isotope labeling to identify myo-inositol transfer from neurons to oligodendrocyte progenitor cells, promoting myelin repair and revealing a metabolic target for neurodegenerative disease therapy.

BertMS-enabled molecular networking for unknown compounds dereplication

This paper introduces BertMS, a transformer-based spectral similarity framework that improves compound identification in metabolomics by better capturing structural relationships in MS/MS data.

Tracing the origins of molecular signals in food through integrative metabolomics and chemical databases

The paper analyzes food metabolomics data to trace molecular signals from agricultural practices and environmental exposures, revealing contamination pathways and natural products.

Quantification and Localisation of New Brain Lipid Synthesis Using Deuterium Oxide and High Resolution Mass Spectrometry

This study quantifies and localizes new myelin lipid synthesis in mice using deuterium oxide and mass spectrometry during remyelination.

A Rapid Reversed-Phase LC-MS Method for Polar Metabolite Profiling

The paper develops a rapid reversed-phase LC-MS method for profiling polar metabolites, achieving high coverage and stability for 123 compounds in E. coli extracts.

Clinical Metabolomics studies in diagnosing Prediabetes and Type 2 Diabetes: Unveiling Trends through Bibliometric Analysis

This study uses bibliometric analysis to identify trends in metabolomics research related to prediabetes and type 2 diabetes, highlighting key topics and influential journals.

Functional Lipid Analysis via Index-Based Lipidomics Profile: A New Computational Module in LipidOne

The paper introduces a new computational module, Functional Lipid Analysis (FLA), to assess lipid function through 42 indices, linking lipidomic data to biological pathways and enabling systems-level insights.

Learning from All Views: A Multiview Contrastive Framework for Metabolite Annotation

This paper introduces MVP, a multiview contrastive framework for metabolite annotation that improves molecular candidate ranking using multiple data views.

Comprehensive Lipidomic Characterization of Human Blood by High-Throughput UHPSFC/MS using Bioinert Column and Modified MTBE Extraction

This paper introduces a novel UHPSFC/MS method for comprehensive lipidomic analysis of human blood, achieving high-throughput and accurate identification of 657 lipid species.

An open-source platform for reference data-driven analysis of untargeted metabolomics

The paper introduces an open-source platform for reference data-driven metabolomics analysis, demonstrating its ability to extract dietary patterns from stool metabolomics data.