Mass Spectrometry Techniques and Applications

Thyra: Bridging Mass Spectrometry Imaging and SpatialData for Unified Multi-Modal Analysis

Thyra converts Mass Spectrometry Imaging data into the SpatialData format to improve interoperability and enable multi-modal spatial analysis.

Metabolic niches: MALDI imaging reveals lipidomic heterogeneity in the human heart

This paper uses MALDI-MSI to create the first spatially resolved lipidomic atlas of the human heart, identifying region-specific lipid differences.

Integrating UHPLC-MS and MALDI-MSI for Spatial Nucleoside Profiling in FFPE Breast Cancer: A Multimodal Molecular Pathology Framework

This paper develops a workflow integrating UHPLC-MS and MALDI-MSI to spatially map nucleosides in FFPE breast cancer tissues, revealing metabolic changes across tumor stages and validating findings in patient samples.

Enzymatic Ligation Strategy to Enhance Electrospray Ionization Efficiency and Liquid Chromatography-Mass Spectrometry of DNA and RNA Oligonucleotides

This paper introduces an enzymatic ligation strategy to enhance MS detection of RNA oligonucleotides by attaching signal enhancers, improving sensitivity and LC retention.

Advances in the Design and Functionality of a Compact Multi-Reflecting Time-of-Flight Mass Spectrometer

This paper describes improvements in a compact multi-reflecting time-of-flight mass spectrometer, showing it maintains high resolving power and accuracy at high acquisition rates.

Solid Ionic Matrices applied via Low-Temperature Evaporation enable High-Resolution and Sensitive MALDI Imaging of Metabolites

This paper introduces a method using solid ionic matrices with low-temperature evaporation to improve MALDI-MSI sensitivity and resolution for small metabolites, achieving detection of 73 metabolites in mouse brain.

A machine learning method for calculating highly localized protein stabilities

PFNet calculates residue-level free energy of opening from HX/MS data, enabling scalable and accessible protein stability analysis.

Truthful visualizations for mass spectrometry imaging enable high spatial resolution interactive m/z mapping and exploration

MSI-VISUAL provides interactive tools for MSI analysis, improving visualization and detection of tissue differences in mouse brain and kidney data.

Ten-Fold Expansion MALDI Mass Spectrometry Imaging of Tissues and Cells at 500 nm Resolution

This paper introduces a novel MALDI-MSI method achieving 500 nm resolution for subcellular imaging in mouse brain tissues and cultured cells.

Evaluating the performance of photon- and electron-based fragmentation methods in Omnitrap-LCMS analysis of N-glycopeptides

The paper evaluates photon- and electron-based fragmentation methods for glycopeptide analysis using Omnitrap-LCMS, finding UVPD and EID provide detailed structural information comparable to traditional methods.

Activation of oligonucleotide polyanions using collisions, electrons and photons in a timsOmni platform

The paper evaluates different ion activation methods on a timsOmni mass spectrometer for analyzing oligonucleotides, showing that EDD combined with other techniques improves fragmentation analysis.

Bimodal peptide collision cross section distribution reflects two stable conformations in the gas phase

The paper identifies a bimodal distribution of peptide collision cross sections, showing two stable conformations, and proposes a two-valued predictor to improve peptide identification in proteomics.

Curation of mass spectrometry reference data for improved identification and dereplication of cyanobacterial specialized metabolites

The paper curates HRMS/MS reference spectra for cyanobacterial specialized metabolites, expanding existing libraries and demonstrating improved annotation success.

Single-Cell Metabolic Profiling in a Glioblastoma Co-culture Model Using AP-MALDI-based Mass Spectrometry Imaging

This paper introduces a single-cell mass spectrometry imaging platform to profile metabolites in glioblastoma co-cultures, revealing cell-type-specific metabolic signatures and interactions.

Next-level high-precision spatial omics enabled through parallel image acquisition and spatial similarity networking

This paper introduces a platform combining parallel image acquisition and spatial similarity networking to improve molecular annotation in mass spectrometry imaging, achieving high-precision annotation of phospholipids and oxysterols in mouse and human tissues.

Low-resolution FAIMS for increased peptide coverage in low-load and single-cell proteomics

This paper shows that lowering FAIMS resolution improves peptide identification in low-load and single-cell proteomics by increasing ion transmission and sensitivity.

A Nature-Inspired Ion Trap for Parallel Manipulation of Ions on a Massive Scale

This paper introduces a nature-inspired ion trap that enables massively parallel mass spectrometry, improving signal-to-noise ratios and detection sensitivity through parallel ion manipulation.

A universal buffer system for native LC-MS analysis of antibody-based therapeutics

This paper introduces a universal volatile buffer system using fluorinated ethylamines for native LC-MS analysis of antibody-based therapeutics, enabling broad pH range buffering and compatibility with mass spectrometry.

HXMS: a standardized file format for HX-MS data

The paper introduces HXMS, a standardized file format for HX-MS data, and provides PFLink to convert existing data to this format, enhancing data processing and sharing.

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.

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.

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.

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.

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.