Mass Spectrometry Techniques and Applications

A framework for testing structural hypotheses of protein dynamics against experimental HDX-MS data

The paper introduces ValDX, a framework to validate and quantify uncertainty in HDX-MS data integration with protein structural ensembles, showing it outperforms conventional metrics in distinguishing correct from incorrect models.

Mass-spectrometry imaging-based explainable machine learning reveals biochemical landscapes of the brain

This paper uses mass-spectrometry imaging and explainable machine learning to create a high-resolution brain lipid and metabolite atlas, revealing novel lipid patterns, anatomical connections, and disease-related signatures.

Bead-Ejection Scenario in Electrospray Ionization of Multi-Domain Nucleic Acids

This study investigates how multi-domain nucleic acids charge and retain structure during electrospray ionization, revealing multiple conformational states and ionization mechanisms.

A Machine Learning and Benchmarking Approach for Molecular Formula Assignment of Ultra High-Resolution Mass Spectrometry Data from Complex Mixtures

This paper applies machine learning to improve molecular formula assignment in UHRMS data, achieving higher annotation rates and accuracy compared to traditional methods.

Intrinsic Hydrogen Deuterium Exchange Rates in H2O/D2O Mixtures

The paper presents a method to predict intrinsic forward and reverse amide exchange rates in H2O/D2O mixtures, accounting for solvent composition and acidity.

Sodium ion-assisted structural lipidomics for sphingolipid profiling

This study develops a sodium ion-assisted structural lipidomics method to improve ceramide annotation by stabilizing ions and enabling structural determination of hydrophobic moieties.

MolSpecFlow: Mass-Constrained Hybrid Flow Matching for Joint Molecular-Spectral Analysis

MolSpecFlow bridges the gap between molecules and mass spectra using a hybrid flow matching model, achieving state-of-the-art results in de novo generation and spectral simulation.

Localisation of corticosteroids in male mouse kidney by mass spectrometry imaging

This study uses mass spectrometry imaging to map corticosteroid distribution in mouse kidneys, revealing regional localization patterns and dietary salt effects on corticosterone levels.

Ion Mobility Separation of Isomeric Acyl-lysine Marks in Peptides

This paper evaluates ion mobility spectrometry for resolving isomeric acyl-lysine modifications on histone peptides, showing improved separation with cyclic IMS and revealing structure-mobility relationships.

In Situ, Antibody-Independent, and Multiplexed Characterization of Amyloid Plaques by MALDI MS/MS Imaging Using iprm-PASEF

This study demonstrates the use of iprm-PASEF for in situ, antibody-independent, and multiplexed characterization of amyloid plaques in tissue samples.

Enhancing Lipid Detection and Spatial Accuracy in Carotid Plaques Using Mass Spectrometry Imaging Techniques

This study improves MALDI-MSI sample preparation for carotid plaque lipid analysis by comparing methods, finding Cryofilm with sublimation best balances tissue preservation and lipid detection.

Membrane proteins retain native architecture through native ESI and soft-landing

This study shows that native electrospray ion beam deposition preserves membrane protein structure, enabling high-resolution cryo-EM analysis of complexes like AmtB.

A computational workflow for microscopy-guided ion identification in clinical mass spectrometry imaging datasets

This paper presents a computational workflow to identify TBI-specific ions in MALDI-MSI datasets using microscopy-guided analysis and validation with a synthetic dataset.

Regarding Emitter Positioning for Nanoflow Electrospray Ionization

The paper investigates how emitter positioning affects peptide signal intensity in nanoflow electrospray ionization for proteomics, finding consistent signal behavior across m/z range.

Enantioselective Protein Affinity Selection Mass Spectrometry (E-ASMS)

This study introduces E-ASMS, a method to detect weak binders and assess enantioselectivity, identifying 16 binders across 12 human protein targets with confirmed binding mechanisms.

De novo sequencing of complex glycans by ion mobility-mass spectrometry using a self-expanding reference database

This paper introduces a de novo sequencing method using ion mobility-mass spectrometry to identify isomeric glycans by building a self-expanding reference database from biological samples.

FIDDLE: a deep learning method for chemical formulas prediction from tandem mass spectra

FIDDLE is a deep learning method that predicts chemical formulas from tandem mass spectra, achieving high accuracy and speed compared to existing methods.

MS4MS: LLMs-driven Multi-agent System for Small-molecule Identification via LC-MS/MS

MS4MS is a multi-agent system using large language models to automate small molecule identification from LC-MS/MS data, achieving state-of-the-art performance and improved interpretability.

IsoSpace: Chemistry-Informed Dimensionality Reduction and Automated Isotope Candidate Detection in Imaging Mass Spectrometry

IsoSpace provides a chemistry-informed dimensionality reduction method for imaging mass spectrometry that identifies isotopic patterns without prior assumptions.

Mass Spectrometry Imaging of Caenorhabditis elegans with Fluorescence Microscopy of Tissue-Specific Reporters and Oriented Cryo-Sectioning

This paper develops a sample preparation workflow for high-resolution mass spectrometry imaging of C. elegans using fluorescence microscopy of tissue-specific reporters and cryo-sectioning.

Spatially Resolved Determination of Small Molecule Protein Affinities by Hydrogen Deuterium Exchange Mass Spectrometry

This paper introduces an HDX-MS workflow to estimate dissociation constants for ligand-protein interactions at peptide and amino acid resolution, enabling spatially resolved affinity mapping.

Breaking Barriers in Crosslinking Mass Spectrometry: Enhanced Throughput and Sensitivity with the Orbitrap Astral Mass Analyzer

This study compares the performance of Orbitrap Astral and Eclipse mass spectrometers in CLMS, finding the Astral provides higher sensitivity and more unique residue pairs.

High-throughput peptide-centric local stability assay extends protein-ligand identification to membrane proteins, tissues, and bacteria

This paper introduces HT-PELSA, a high-throughput adaptation of a peptide-centric local stability assay, enabling sensitive protein-ligand profiling in diverse biological samples.

Ambient mass spectrometry imaging enables spatial metabolomics of optimal cutting temperature compound (OCT)-embedded tumors

This paper demonstrates ambient mass spectrometry imaging of metabolites in OCT-embedded tumors, revealing spatial metabolic changes in a preclinical model.

Unmixing of Imaging Mass Spectrometry Measurements Using Microscopy-Informed Constraints

This paper introduces TULIP, a method to unmix IMS data using microscopy constraints, improving analysis of tissue structures in synthetic and kidney datasets.

A prototype timsOmni platform enables confident annotation of key hypervariable regions of IgG immunoglobulins using low- and high-energy electron-based fragmentation.

Aird-MSI: a high compression rate and decompression speed format for mass spectrometry imaging data

This paper introduces Aird-MSI, a new format for mass spectrometry imaging data that reduces storage size and improves decompression speed while maintaining high data precision.

Subcellular mass spectrometry imaging of lipids and nucleotides using transmission geometry ambient laser desorption and plasma ionisation

This paper introduces a subcellular mass spectrometry imaging technique that enhances lipid and nucleotide detection using transmission geometry ambient laser desorption and plasma ionisation.

LipidQMap - An Open-Source Tool for Quantitative Mass Spectrometry Imaging of Lipids

LipidQMap is an open-source tool for processing quantitative mass spectrometry imaging lipidomics data, enabling accurate and reproducible spatial lipid quantification across MSI platforms.

Histology-Guided Single-Cell Mass Spectrometry Imaging using Integrated Bright-field and Fluorescence Microscopy

This paper integrates MALDI-MSI with bright-field and fluorescence microscopy to correlate lipid profiles with morphological and protein features at the single-cell level.