Metabolomics and Mass Spectrometry Studies

Genetic architecture of the murine serum metabolome reveals carboxyl esterases as master regulators of circulating fatty acid metabolism

The paper identifies genetic regulators of the murine serum metabolome, highlighting carboxyl esterases as key controllers of fatty acid metabolism.

Agentic AI for Structural Elucidation and Discovery of Drug Metabolites from Mass Spectrometry Data

The paper develops an agentic AI system using LLMs and domain tools to hypothesize and validate structures of unknown drug metabolites from mass spectrometry data.

Metabolic analysis in intact human-derived cerebral organoids by high-resolution magic-angle spinning NMR spectroscopy

This study uses HR-MAS NMR to analyze metabolism in human-derived cerebral organoids at different developmental stages, finding a metabolic profile similar to the human brain with some differences.

Reducing background ion burden in tributylamine ion-pairing LC-MS improves signal intensity and feature coverage in metabolomics

This study improves LC-MS metabolomics by reducing background ion burden from tributylamine, enhancing signal intensity and feature coverage across multiple biological samples.

Learning interpretable structural similarity from tandem mass spectra for small molecule analog discovery

This paper introduces SIMBA, a transformer-based model that learns interpretable structural similarity from tandem mass spectra to improve small molecule analog discovery.

Complementary Single-Cell Microflow HILIC and Ion Pair LC-MS Reveal Bystander Metabolic Effects in a Macrophage Model of Tuberculosis

The paper develops and applies complementary microflow HILIC and ion pair LC-MS methods to analyze single-cell metabolomics in a tuberculosis macrophage model, revealing infection-associated metabolic changes and a distinct bystander phenotype.

First characterization of metabolomic and lipidomic exchange over the healthy human brain

The paper characterizes metabolomic and lipidomic exchanges in the healthy human brain, finding net release of acylcarnitine and variability in respiratory quotient linked to purine salvage pathway activity.

FeatureMSEA: Metabolic Feature-based Metabolite Set Enrichment Analysis

FeatureMSEA enables metabolite set enrichment analysis from ambiguous LC-MS metabolomics features, identifying dysregulated pathways in Huntington's disease.

A protocol for lab-scale production of 13C yeast extract as internal standard for metabolomics and quantification of intracellular metabolites

The paper describes a protocol for producing 13C-labelled yeast extract as an internal standard for metabolomics and quantifying intracellular metabolites.

Host, diet, microbiome, and xenobiotic plasma metabolites associate with kidney cell-type transcriptional programs in CKD

The paper identifies plasma metabotypes linked to kidney cell-type transcriptional programs in CKD, showing associations between metabolites of different origins and specific injury pathways.

Unlocking Precision Diagnostics: A Multimodal Framework Integrating Metabolomics with Advanced Machine Learning Techniques

This paper integrates metabolomics data with machine learning techniques to improve cancer detection and biomarker discovery by comparing multiple integration strategies.

Robust metabolomics data normalization across scales and experimental designs

This paper introduces robust normalization methods for metabolomics data to reduce technical variance and improve downstream analysis.

Robust analytical methods for bis(monoacylglycero)phosphate profiling in health and disease

This study develops LC/MS methods for accurate BMP profiling, using CLN5 knockout cells to distinguish BMP from PG and introduce BMPII and BMPES metrics.

Nanoflow ion-pairing LC-MS for ultra-low-input polar metabolomics and isotope tracing

This paper introduces a nanoflow ion-pairing LC-MS method for ultra-low-input polar metabolomics and isotope tracing, showing improved sensitivity and retention for metabolites.

RISOP, a Reference-Assisted Approach for Enhanced Identification of Oxidized Phospholipids

RISOP improves identification of oxidized phospholipids using reference pools, increasing detected species in stressed cells.

LipidCruncher: An open-source platform for processing, visualizing, and analyzing lipidomic data

LipidCruncher processes, visualizes, and analyzes lipidomic data with quality controls, enabling efficient and rigorous analysis of lipid profiles.

Ordering molecular diversity in untargeted metabolomics via molecular community networking

This paper introduces molecular community networking to organize metabolite data, revealing hidden connections and discovering novel dipeptide-conjugated bile acids.

Low-temperature HILIC provides enhanced separations and stability for LC-MS-based metabolomics

The paper introduces a low-temperature zwitterionic HILIC method for LC-MS metabolomics, showing improved peak shapes, resolution, and retention time stability compared to standard methods.

TIMS-Bench: Towards community standards for benchmarking untargeted trapped ion mobility metabolomics tools and datasets

TIMS-Bench evaluates three TIMS feature-finding tools using public and benchmark datasets, identifying strengths and weaknesses in feature detection and annotation.

Magnetic Levitation Derived Metabolomic Fingerprinting Enables Exploratory Discrimination of Breast Cancer Subtypes

This study uses magnetic levitation and metabolomics to distinguish breast cancer subtypes by their unique metabolic fingerprints.

maxiM/Ze: An Image Recognition Approach for Visualizing and Processing Mass Spectrometry Based Metabolomics Data

maxiM/Ze processes LC-HRMS metabolomics data using image recognition to automate feature detection, annotation, and alignment with minimal user input.

MSLipidMapper: a pathway-centered lipidome analysis environment linking lipid class, acyl-chain subsets, and multi-omics data

MSLipidMapper provides a pathway-centered lipidomics analysis tool that integrates lipid structure, subclass annotations, and multi-omics data for structured exploration.

OAC-PCA: orthogonal adjustment of confounding effects in principal component analysis for metabolomics data mining

OAC-PCA improves PCA for metabolomics by ensuring orthogonal components and correlation-based loadings, enabling better statistical analysis of metabolite associations with confounding factors.

Assessing the metabolomics "dark matter" by a detectable khipu model

The paper analyzes metabolomics 'dark matter' using a detectable khipu model, showing most abundant features have identifiable ion patterns, while many remain unknown.

An atlas of the human metabolome

The paper presents the Human Metabolome Atlas, a comprehensive resource with metabolomic profiles of 70 human cell lines across 22 tissues, offering expanded coverage and detailed metabolic pathway insights.

Systemic metabolic correlates of environmental sensitivity in group-housed mice

This study identifies systemic metabolic differences between mice with high and low responsiveness to environmental changes, linking behavior to metabolic signatures.

Nutritional-Metabolic Lipid Profiling with LipidOne for plasma lipidomics interpretation in metabolic health

The paper introduces NMLP, a module within LipidOne that translates plasma lipidomics data into interpretable nutritional-metabolic indices, revealing metabolic shifts and phenotypes across different dietary and health conditions.

Alkamines reveal a hidden layer of steroid and drug metabolism

The paper identifies alkamines as a previously hidden class of metabolites formed via reductive amination, revealing significant gaps in metabolomics and drug metabolism understanding.

Predicting Discrete Structural Transformations in Small Molecules from Tandem Mass Spectrometry

This paper introduces MT-GEM and STEP to predict discrete structural transformations in metabolites from MS/MS spectra, achieving significant improvements over existing methods.

Metabolic Coherence of the Mouse Brain

The paper maps spatial metabolome coherence across mouse brain regions using MALDI imaging and optimal transport, showing preserved coherence in Alzheimer's model despite metabolic changes and demonstrating intervention effects.