Metabolomics and Mass Spectrometry Studies

Optimized Lipid Extraction and Hybrid Annotation Pipeline for Individual Chitinous Mesozooplankton Using UPLC-HRMS

The paper develops an optimized lipid extraction protocol and hybrid annotation pipeline for individual chitinous mesozooplankton, improving lipid recovery and annotation accuracy.

The Neurolipid Atlas: a lipidomics resource for neurodegenerative diseases uncovers cholesterol as a regulator of astrocyte reactivity impaired by ApoE4

The paper introduces the Neurolipid Atlas, a lipidomics resource for neurodegenerative diseases, revealing that ApoE4 impairs astrocyte reactivity by promoting cholesterol ester accumulation.

UCL-MetIsoLib: A Public High-Resolution Tandem Mass Spectrometry Library for HILIC-Based Isomer-Resolved Profiling of Glycolysis, Central Carbon Metabolism, and Beyond in Urine, Plasma, Tissues, Cells, and Patient-Derived Organoids

The paper introduces UCL-MetIsoLib, a high-resolution metabolomics library for isomer-resolved profiling, validated across multiple biological matrices and applied to colorectal cancer organoids.

Hyperspherical geometry positions the lipidome as a partly independent axis of human brain organization

The paper maps lipidomic and transcriptomic profiles in human brain regions, revealing distinct spatial patterns and three classes of lipid-gene relationships.

Optimization of 13C stable isotope labeling for the study of tricarboxylic cycle intermediates in mouse models

This study optimizes bolus-based 13C stable isotope labeling in mouse models to achieve maximum TCA cycle labeling across multiple organs.

HT SpaceM: A High-Throughput and Reproducible Method for Small-Molecule Single-Cell Metabolomics

HT SpaceM is a high-throughput single-cell metabolomics method that detects small molecules with high reproducibility and identifies cell-type markers and metabolic pathways in diverse cell lines.

QC4Metabolomics: Real-time and Retrospective Quality Control of Metabolomics Data

QC4Metabolomics provides real-time and retrospective quality control for untargeted metabolomics data by monitoring compound-specific features and contaminants.

MultiNMRFit: A software to fit 1D and pseudo-2D NMR spectra

MultiNMRFit is a software tool for analyzing NMR spectra to extract signal parameters, offering flexibility and robustness in metabolomics and isotope labeling studies.

A dual-dimensional deconvolution environment for ZT Scan DIA in metabolomics

The paper introduces ZT Scan DIA, a metabolomics method improving annotation rates and isomer quantification in complex mixtures, with results validated in human plasma and mouse liver tissues.

Metabolomics of a Cysteinyl Leukotriene Receptor 1 (CysLTR1) Knockout Mouse Model by Analysis of Bronchoalveolar Lavage Fluid Using Gas Chromatography-time of Flight Mass Spectrometry.

This study examines the metabolic changes in CysLTR1 knockout mice using metabolomics of BALF, revealing disruptions in glucose, lipid, and microbial metabolism.

Rapid Liquid Chromatography-Mass Spectrometry (rLC-MS) for Deep Metabolomics Analysis of Population Scale Studies

The paper introduces a high-throughput rLC-MS system for metabolomics analysis, demonstrating its ability to capture metabolic variation in large human populations and predict metabolic aging.

Spatial quantitative metabolomics enables identification of remote and sustained ipsilateral cortical metabolic reprogramming after stroke

This paper introduces a quantitative MSI workflow using 13C-labeled yeast extract to enable reliable spatial metabolomics, revealing metabolic changes in the ipsilateral cortex after stroke.

mzrtsim: Raw Data Simulation for Reproducible Gas/Liquid Chromatography Mass Spectrometry Based Non-targeted Metabolomics Data Analysis

The paper introduces mzrtsim, an R package that simulates raw metabolomics data for comparing software tools against a ground truth.

A benchmarking workflow for assessing the reliability of batch correction methods

This paper introduces a benchmarking framework to evaluate batch correction methods in metabolomics using statistical and visualization tools.

Biochemical signatures from dried blood spots in untargeted metabolics are influenced by matrix effects

The paper investigates matrix effects on metabolite recovery from dried blood spots (DBS) and shows that despite these effects, DBS can be used for diagnostics with proper validation.

Urinary Signatures Predict Calorie Restriction-Mediated Weight Loss in Obese Diversity Outbred Mice

The paper identifies urinary metabolite signatures predictive of calorie restriction-mediated weight loss in obese mice, with sex-specific differences observed.

SMART: an approach for accurate formula assignment in spatially-resolved metabolomics

SMART improves formula assignment in spatial metabolomics by using a database and regression model, achieving 92.4% accuracy in mouse embryo imaging.

A Large Language Model-Powered Map of Metabolomics Research

PubMedBERT embeddings of 80,656 metabolomics abstracts, projected with t-SNE and grouped into 20 GPT-4o mini-labelled topics, map the field's domains and trends (1998 to early 2024), browsable online.

SingleFrag: A deep learning tool for MS/MS fragment and spectral prediction and metabolite annotation

SingleFrag predicts MS/MS fragments and annotates metabolites using deep learning, outperforming existing tools and identifying three unknown compounds in human samples.

Systemic metabolic changes in acute and chronic lymphocytic choriomeningitis virus infection

This study compares metabolic changes in acute and chronic LCMV infection using metabolomics and isotope tracing, finding more dramatic changes in chronic infection and altered thymidine metabolism as a marker.

Untargeted and Semi-Targeted Metabolomics Approach for Profiling Small Intestinal and Fecal Metabolome Using High-Resolution Mass Spectrometry

The paper develops a combined untargeted and semi-targeted metabolomics approach to profile small intestinal and fecal metabolomes, revealing distinct metabolomes and potential new bile acids.

Longitudinal analysis of genetic and environmental interplay in human metabolic profiles and the implication for metabolic health

The paper analyzes how genetics and environmental factors influence metabolic profiles over two years in 101 healthy individuals, identifying 22 genetically determined metabolites and 87 causal metabolite-protein associations.

High energy charge, antioxidant capacity, and amino acid contents are conserved features of T cell metabolism

The paper quantifies T cell metabolomes across subtypes and individuals, revealing conserved features that support immune response readiness.

DuReS: An R package for denoising experimental tandem mass spectrometry-based metabolomics data

DuReS improves metabolomics data by removing noise while preserving significant peaks, enhancing spectral matching and reducing false positives.

DoliClock: A Lipid-Based Aging Clock Reveals Accelerated Aging in Neurological Disorders

This study introduces DoliClock, a lipid-based aging clock that identifies accelerated aging in neurological disorders like autism and schizophrenia.

Dried Blood Spot Lipidomics in Diabetes

This study demonstrates that dried blood spot lipidomics can capture biologically meaningful lipid changes in diabetes, supporting its use in remote and personalized monitoring.

Complete360: A Multi-Omics Liquid Biopsy Platform with Attomole Sensitivity and High Reproducibility

Complete360 is a liquid biopsy platform that detects and quantifies proteins, metabolites, and lipids with high sensitivity, specificity, and reproducibility, revealing novel disease mechanisms in human plasma.

Eclipse: A Python package for alignment of two or more nontargeted LC-MS metabolomics datasets

Eclipse aligns multiple nontargeted LC-MS metabolomics datasets using a graph-based subalignment approach.

LC-MS system for automatically collecting time-resolved metabolomics data of cultured cells

The paper develops TUNA, an LC-MS system for time-resolved metabolomics of cultured cells, and uses it to identify novel metabolic phenotypes in uropathogens.

Constructing a consensus serum metabolome

The paper constructs a consensus serum metabolome from over 100,000 mass spectrometry acquisitions, revealing gaps in current databases and improving LC-MS metabolomics annotation.