Mass Spectrometry Techniques and Applications

Best practice mass photometry: A guide to optimal single molecule mass measurement

This paper provides guidelines for optimizing mass photometry to achieve high mass resolution and detection limits while maintaining simplicity.

Transforming Esogastric Cancer Surgery Integrating SpiderMass Mass Spectrometry with Clinical and Microbiome Data for Margin Delineation and Prognosis

The paper integrates SpiderMass mass spectrometry with clinical and microbiome data to improve intraoperative margin delineation and prognosis in esophageal-gastric cancers.

Simultaneous ligand binding to intact and partially formed ATP binding sites in the hexameric termination factor Rho

The paper uses native mass spectrometry to study ATP binding to Rho, revealing binding to hexameric and lower-order complexes and super-stoichiometric binding at partially formed sites.

Mass Spectrometric Profiling of Microbial Polysaccharides Using Laser Desorption/Ionization - Time-of-Flight (LDI-TOF) and Liquid Chromatography/Mass Spectrometry (LC/MS): A Novel Method for Structural Fingerprinting and Derivatization

This paper develops a method to detect microbial polysaccharides using derivatization and mass spectrometry without a MALDI matrix, validated with bacterial lipopolysaccharides and crude bacterial samples.

Next-Generation Protein Sequencing and individual ion mass spectrometry enable complementary analysis of interleukin-6

This study compares single-molecule protein sequencing and individual ion mass spectrometry to analyze IL-6 proteoforms, showing combined coverage of 52% of the sequence.

Computational method for mapping mass signatures along developmental gradients reveals a novel role for a monosaccharide tetrose in maize salt-stress response.

The paper develops DIMPLE, a computational method to analyze metabolite patterns along developmental gradients in maize roots, revealing D-erythrose's role in salt-stress response.

MassVision: An Open-Source End-to-End Platform for AI-Driven Mass Spectrometry Image Analysis

MassVision provides an end-to-end platform for analyzing mass spectrometry images, integrating visualization, preprocessing, and AI tools to streamline workflows and improve accessibility.

A Hit Prioritization Strategy for Compound Library Screening Using LiP-MS and Molecular Dynamics Simulations Applied to KRas G12D Inhibitors

This study combines LiP-MS and molecular dynamics simulations to prioritize KRas G12D inhibitors by analyzing cleavage site protection and binding affinity.

rtmsEcho: An Open-Source R Package for Automated Analysis of Acoustic Ejection Mass Spectrometry Data

rtmsEcho automates AEMS data processing tasks like peak detection and multimodal analysis, improving efficiency in high-throughput applications.

Analysis of Large Peptide Collisional Cross Section Dataset Reveals Structural Origin of Bimodal Behavior

The paper analyzes a large peptide collisional cross section dataset to identify structural determinants of bimodal CCS behavior in peptides.

MSI.EAGLE: An Open-Source GUI for Streamlined Mass Spectrometry Imaging Analysis

MSI.EAGLE provides an open-source GUI for MSI analysis, integrating advanced tools to simplify data processing and visualization for non-specialists.

Unified Mass Imaging Maps the Lipidome of Vertebrate Development

The paper maps lipid distribution across vertebrate development using mass spectrometry imaging and reveals spatially organized metabolic circuits.

MALDI-TIMS-MS2 Imaging and Annotation of Natural Products in Fungal-Bacterial Co-Culture

This paper demonstrates the use of MALDI iprm-PASEF to rapidly and accurately annotate coproporphyrin III in a fungal-bacterial co-culture.

Buffer-dependent conformational dynamics of α-synuclein revealed by nanopipette electrospray ionisation ion mobility mass spectrometry

This study uses nanopipette electrospray ionisation ion mobility mass spectrometry to investigate how buffer conditions affect α-synuclein conformational dynamics.

AlphaCross-XL: a seamless tool for automated and proteome-scale map-ping of crosslinked peptides onto three-dimensional protein structures

AlphaCross-XL automates mapping of crosslinked peptides to protein structures at proteome scale, enabling analysis of thousands of proteins.

Single-cell mass spectrometry imaging combined with immunofluorescence reveals neutrophil heterogeneity in inflammation

The paper combines single-cell mass spectrometry imaging and immunofluorescence to identify pathogenic neutrophils in liver cirrhosis patients.

An automated software-assisted approach for exploring metabolic susceptibility and degradation products in macromolecules using High-Resolution Mass Spectrometry

The paper introduces automated algorithms for LC-HRMS data analysis of small and macromolecules, reducing processing time and improving metabolite identification and visualization.

Increased EThcD efficiency on the hybrid Orbitrap Excedion Pro Mass Analyzer extends the depth in identification and sequence coverage of HLA class I immunopeptidomes

This study shows that using EThcD on a new mass spectrometer improves the identification and sequence coverage of HLA class I immunopeptidomes by filling gaps in fragmentation data.

Reference Library for Suspect Non-targeted Screening of Environmental Toxicants Using Ion Mobility Spectrometry-Mass Spectrometry

The paper creates a database of IMS-MS data for 4,685 xenobiotic chemicals to enable rapid suspect screening of environmental contaminants.

Nova: A library for rapid development of mass spectrometry software applications

Nova is a C# library for handling mass spectrometry data, offering native support and extensibility for real-time analysis and instrument control applications.

Breaking barriers in the sensitive and accurate mass determination of large DNA plasmids by mass photometry

This paper develops a protocol to accurately measure the mass of large DNA plasmids using mass photometry by converting dsDNA to ssDNA-like particles, achieving mass accuracy within 1-3%.

Collisional cross-section prediction for multiconformational peptide ions with IM2Deep

The paper improves IM2Deep to predict collisional cross-sections for peptides with multiple conformations, using a comprehensive dataset and tailored architecture.

In-vitro Metabolite Identification for MEDI7219, an Oral GLP-1 Peptide, using LC-MS/MS with CID and EAD Fragmentation

This study identifies 13 metabolites of the orally-bioavailable GLP-1 peptide MEDI7219 using in vitro pancreatin assays with CID and EAD fragmentation, revealing cleavage sites and enzyme-specific degradation patterns.

Enhancing tandem MS sensitivity and peptide identification via ion pre-accumulation in an Orbitrap mass spectrometer

This paper introduces a new scanning strategy called pre-accumulation to enhance ion utilization and sensitivity in Orbitrap mass spectrometers, improving peptide and protein identification in high-throughput proteomics.

Rational design of a foldon-derived heterotrimer guided by quantitative native mass spectrometry

This study designs a stable heterotrimeric protein complex using rational design and native mass spectrometry, validated by X-ray crystallography.

A journey towards developing a new cleavable crosslinker reagent for in-cell crosslinking

This paper introduces a new cleavable crosslinker, DiSPASO, for in-cell crosslinking and evaluates its performance in different model systems.

Predicting High-Resolution Spatial and Spectral Features in Mass Spectrometry Imaging with Machine Learning and Multimodal Data Fusion

This paper develops a multimodal data fusion approach to enhance spatial and spectral resolution in mass spectrometry imaging using machine learning and physical constraints.

A multimodal imaging approach for imaging the metabolic changes resulting from bronchopulmonary dysplasia

This paper presents a multimodal imaging approach to characterize metabolic changes in bronchopulmonary dysplasia, revealing altered lipid distributions and collagen remodeling in affected tissues.

Structure guided significance testing correction for hydrogen deuterium exchange mass spectrometry

The paper introduces a structural false discovery rate (sFDR) method to improve statistical power in HDX-MS by accounting for structural dependencies in peptide comparisons.

Deepening imaging-based spatial proteomics at high spatial resolution through controlled tissue resizing and in-situ bottom-up mass spectrometry

The paper introduces IMPACT, a method to enhance spatial proteomics resolution and sensitivity through tissue compression and optimized digestion, demonstrating improved protein detection and anatomical resolution.