Mass Spectrometry Techniques and Applications

AI Assisted Native Proteomics: Delineating Ribosomal Protein Conformations Pre- and Post-Assembly

This paper introduces an AI-assisted native proteomics method to identify protein conformations pre- and post-assembly, validated on ribosomal proteins and drug interactions.

Identifying Space-Resolved Proteins of the Murine Thymus, by Combining MALDI Mass Spectrometry Imaging and Proteomics

This paper combines MALDI-MSI and LC-MS/MS to map spatial protein changes in murine thymus during chemotherapy, identifying key proteins involved in regeneration and immune recovery.

Revealing Spatial Heterogeneity across the Gut Tissue-Lumen Interface through MALDI Mass Spectrometry Imaging

This study uses MALDI-MSI to reveal spatial metabolite heterogeneity at the gut tissue-lumen interface, highlighting molecular participants in host-microbe interactions.

Expanding the MR1 ligandome using chemical class-specific fragmentation and molecular networking

The paper reanalyzes mass spectrometry data to identify two new compound classes that bind to MR1, using fragmentation filtering, molecular networking, and spectral database searching.

Neural Spectral Prediction for Structure Elucidation with Tandem Mass Spectrometry

The paper introduces a deep learning model, ICEBERG, for structural elucidation using tandem mass spectrometry, achieving high accuracy in identifying molecular structures from complex mixtures.

Multiplexed Targeted Spatial Mass Spectrometry Imaging Assays to monitor lipids and NAD+ metabolites in CD38 knockout mice exhibiting improved metabolism.

The paper introduces a novel spatial mass spectrometry imaging method to analyze lipid and NAD+ metabolite distributions in CD38 knockout mice, revealing metabolic changes linked to CD38 deletion.

Trapped ion mobility spectrometry-guided molecular discrimination between plasmalogens and other ether lipids in lipidomics experiments

This paper demonstrates that ion mobility spectrometry can distinguish between plasmalogens and other ether lipids by analyzing their gas-phase geometries, improving lipid annotation accuracy.

Dual fragmentation via collision-induced and oxygen attachment dissociations using water and its radicals for C=C position-resolved lipidomics

This study introduces OAciD, a method combining OAD and CID in negative-ion mode for C=C position-resolved lipidomics, applied to marmoset brain regions.

HDgraphiX: A web-based tool for visualization of hydrogen deuterium exchange mass spectrometry data

HDgraphiX visualizes HDX-MS data using statistical analysis and generates publication-quality plots and structural maps.

Leveraging Pretrained Deep Protein Language Model to Predict Peptide Collision Cross Section

The paper introduces a pretrained deep protein language model for predicting peptide collision cross sections, reducing training time while maintaining or improving prediction performance.

Preserving Full Spectrum Information in ImagingMass Spectrometry Data Reduction

The paper introduces a data reduction method for imaging mass spectrometry that preserves full spectrum information while achieving size reduction comparable to traditional methods.

TEMI: Tissue Expansion Mass Spectrometry Imaging

TEMI maps biomolecule distributions in tissues at single-cell resolution, revealing metabolic heterogeneity in tumors.

Met-ID: An Open-Source Software for Comprehensive Annotation of Multiple On-Tissue Chemical Modifications in MALDI-MSI

Met-ID is an open-source software for annotating chemical modifications in MALDI-MSI data, combining MS1 and MS2 functionalities with a customizable database.

Improving MALDI Mass Spectrometry Imaging Performance: Low-Temperature Thermal Evaporation for Controlled Matrix Deposition and Improved Image Quality

This paper introduces low-temperature thermal evaporation (LTE) for matrix deposition in MALDI-MSI, showing improved image quality, purity, and stability compared to traditional methods.

Spatial proteomics with 100+ markers with Highly Multiplexed MALDI-IHC

This paper introduces a method for high-plex protein imaging using MALDI-IHC with PCMT-labeled antibodies and presents an open-source analysis pipeline called gutenTAG.

Spatial differentiation of proteome in cervical cancer tissues using Imaging Mass Spectrometry

This study uses MALDI-IMS to profile protein spatial distribution in cervical cancer tissues, identifying overexpressed Keratin 5 and Prelamin A/C in cancerous regions.

Integrating Ambient Mass Spectrometry Imaging and Spatial Transcriptomics on the Same Cancer Tissues to Identify Gene-Metabolite Correlations

The paper integrates spatial metabolomics and spatial transcriptomics on cancer tissues to identify gene-metabolite correlations.

Resolving multi-image spatial lipidomic responses to inhaled toxicants by machine learning

The paper uses machine learning to analyze spatial lipidomic changes in mouse lungs exposed to allergens and ozone, revealing sex-specific lipid distribution differences.

Untargeted Pixel-by-Pixel Imaging of Metabolite Ratio Pairs as a Novel Tool for Biomedical Discovery in Mass Spectrometry Imaging

The paper develops an R package for pixel-by-pixel ratio imaging of metabolite pairs in mass spectrometry imaging, enhancing spatial contrast and revealing new tissue regions and biomarkers.

LC-MS analysis of RNA through hydrogen bonding of alkylamines

This study demonstrates that hydrogen bond donating alkylamines improve the purity analysis of oligonucleotides using LC-MS by reducing the need for fluoroalcohol reagents.

A framework for automated multimodal HDX-MS analysis

The paper introduces pyHXExpress, a tool for automated HDX-MS analysis, validated on synthetic data to detect multimodality and characterize protein dynamics.

Unveiling the Hidden: Dissecting Liraglutide Oligomerization Dual Pathways via Direct Mass Technology, Electron-Capture Dissociation, and Molecular Dynamics

This study uses mass spectrometry techniques to reveal dual oligomerization pathways of liraglutide, highlighting structural changes and interactions involved in aggregation.

Massively parallel assessment of designed protein solution properties using mass spectrometry and peptide barcoding

The paper develops a method to assess solution properties of designed proteins using mass spectrometry and peptide barcoding, enabling analysis of large protein libraries.

Fast-tracking native mass spectrometry: Skipping over buffer exchange

This paper introduces a fast-track affinity purification workflow that skips buffer exchange, enabling direct nMS analysis and improving protein recovery for challenging proteins.

Assessment of native mass spectrometry as a screening method to identify and characterize RNA-targeting small molecules

This study evaluates native mass spectrometry as a method to screen and characterize RNA-targeting small molecules using RNA aptamers as a model.

Spatial Proteomics By Parallel Accumulation-Serial Fragmentation Supported MALDI MS/MS Imaging: A First Glance Into Multiplexed and Spatial Peptide Identification

This paper introduces a novel MALDI imaging method combining TIMS-PASEF for multiplexed and spatial peptide identification in tissue samples.

Critical Evaluation of Sphingolipids Detection by MALDI-MSI

This study evaluates sphingolipid detection by MALDI-MSI, identifies optimal protocols, and reports artifacts from fragmentation in different ion modes.

Identification of a novel false-positive mechanism in RapidFire mass spectrometry and application in drug discovery

The paper identifies a novel false-positive mechanism in RapidFire mass spectrometry and develops a pipeline to detect and mitigate these false positives in drug discovery.

Optimized Time-segmented Acquisition Expands Peptide and Protein Identification in TIMS-TOF Pro Mass Spectrometry

The paper introduces a novel time-segmented acquisition method for TIMS-TOF mass spectrometry, improving peptide and protein identification by optimizing ion separation.

Recommendations for Automating Hydrogen/Deuterium Exchange Mass Spectrometry Measurements using Data-Independent Acquisition Methods

The paper demonstrates how data-independent acquisition methods can automate hydrogen/deuterium exchange mass spectrometry measurements with improved precision and throughput.