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- Publication date: Available online 7 November 2025Source: Journal of Mass Spectrometry and Advances in the Clinical LabAuthor(s): J. Brandsma, J.W. Thompson, K.L. Schully, J.G. Chenoweth, P. Genzor, S. Krishnan, D.A. Striegel, L.St. John-Williams, A. Moseley, G. Oduro, N. Adams, T. Vantha, E.L. Tsalik, C.W. Woods, D.V. Clark
- Formalin-fixed paraffin-embedded (FFPE) samples are essential for clinical research and spatial proteomics (SP) but are technically challenging to analyze by liquid-chromatography coupled mass-spectrometry (LC-MS) due to losses during protein extraction, evaporation during decrosslinking and low-throughput sample preparation methods. Here, we present a streamlined micro-FFPE proteomics sample preparation protocol for laser-capture micro-dissection (LMD) that enables scalable and high-throughput processing in 96-well format, completing the entire process from tissue lysis to tryptic peptide mixtures on LC-MS-ready Evotips in just 2-hours. Our method […]
- Objective: Primary liver cancer is a leading cause of cancer-related mortality and harbors recurrent mutations in chromatin regulators such as BRCA1-associated protein 1 (BAP1), yet their functional impact remains unclear. We investigated how BAP1 deficiency affects liver homeostasis and tumorigenesis to clarify its functional role. Design: We employed inducible, liver-specific BAP1 knockdown in mice subjected to diet-induced metabolic stress (including rescue experiments), alongside autochthonous hydrodynamic CRISPR models, and profiled livers by RNA-seq, immunohistochemistry, and mass spectrometry-based lipidomics. Complementary mechanistic assays […]
- Publication date: Available online 7 November 2025Source: TrAC Trends in Analytical ChemistryAuthor(s): David Fabregat-Safont, Francisco Madrid-Gambin, Alex Gomez-Gomez, Élida Alechaga, Gabriel Gil-Gómez, Óscar J. Pozo
- Analytical ChemistryDOI: 10.1021/acs.analchem.5c04075
- Analytical ChemistryDOI: 10.1021/acs.analchem.5c05632
- Analytical ChemistryDOI: 10.1021/acs.analchem.5c05341
- Publication date: Available online 6 November 2025Source: Journal of Chromatography AAuthor(s): Hannah Schanzmann, Veronika Ruzsanyi, Parviz Ahmad-Nejad, Ursula Telgheder, Stefanie Sielemann
- Suitability of prolonged meloxicam treatment in mice seems limited due to unfavorable pharmacokinetics, side effects, and impact on home-cage behaviors
- Publication date: Available online 6 November 2025Source: International Journal of Mass SpectrometryAuthor(s): Kenzo Hiraoka, Stephanie Rankin-Turner, Dilshadbek T. Usmanov, Satoshi Ninomiya
- Untargeted tandem mass spectrometry (MS/MS)-based metabolomics enables broad characterization of small molecules in complex samples, yet the majority of spectra in a typical experiment remain unannotated, limiting biological interpretation. Reference data-driven (RDD) metabolomics addresses this gap by contextualizing spectra through comparison to curated, metadata-annotated reference datasets, allowing inference of spectrum origins without requiring exact structural identification. Here, we present an open-source RDD metabolomics platform comprising a user-friendly web application and a Python software package that perform RDD analyses directly from […]
- Mass spectrometry imaging (MSI) is emerging as a powerful tool for uncovering the distribution of metabolites in the tumor microenvironment and studying tumor metabolism in vivo. However, to date, MSI of primary patient biobanked tissues contextualized by patient data has been limited to peptides, proteins, and glycans – with few examples for metabolites. This is because most biobanked fresh-frozen tissue required for spatial metabolomics is embedded in optimal cutting temperature compound (OCT), which introduces high-abundance polymeric interferents. Herein, we use […]
- Refining EI-MS library search results through atomic-level insights
- Click-linking: a cell-compatible protein crosslinking method based on click chemistry
- Exosomes are extracellular vesicles (EVs) that carry bioactive molecules from a cell of origin and may alter gene expression of the acceptor cell via binding to cell surface receptors and/or delivering their cargo into the cell. Tumor-associated macrophages (TAMs) can increase or decrease tumor growth through various mechanisms, but the impact of TAM-EVs on tumors has been difficult to elucidate due to challenges in isolating and culturing TAMs for EV purification. In this study, we set out to uncover the […]
- Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00256
- Analytical ChemistryDOI: 10.1021/acs.analchem.5c05564
- Analytical ChemistryDOI: 10.1021/acs.analchem.5c05114
- Analytical ChemistryDOI: 10.1021/acs.analchem.5c03549
- NOS1AP (CAPON) is an adaptor protein of neuronal nitric oxide synthase (nNOS) correlated with Alzheimers disease progression, making it an attractive yet unexplored therapeutic target. To assess its chemical tractability, we employed affinity selection-mass spectrometry (AS-MS) to screen approximately 10,000 small molecules for CAPON binding, identifying 52 initial hits. These compounds were further evaluated for true binding interactions and potential autofluorescence or quenching effects using the Dianthus platform. Five compounds were selected for quantitative affinity determination by microscale thermophoresis (MST). […]
- Publication date: Available online 6 November 2025Source: Journal of Chromatography AAuthor(s): Guangyu Dong, Linchun Nie, Jiawei Liao, Dejing Meng, Wenjing Liu, Rui Yang, Haobo Yang, Qingxiang Zhou
- Publication date: January 2026Source: International Journal of Mass Spectrometry, Volume 519Author(s): Matjaž Finšgar, Katja Andrina Varda
- The advent of wearable biosensors is empowering clinical and lifestyle decision making. Nicotine is a drug of significant negative impact on public health given the prevalence of smoking and vaping. Yet noninvasive, continuous monitoring of nicotine is challenging due to lack of specific and sensitive biosensing elements. Here, we report a wearable highly sensitive nicotine biosensor and demonstrate on-body deployment of the sensor in a first-in-human study. The biosensor comprises nicotine oxidoreductase (NicA2) with its natural cytochrome c electron acceptor […]
- Bacteria produce high-affinity iron-chelating secondary metabolites called siderophores to access insoluble Fe(III) in their environments. Genome mining has revealed many predicted siderophore biosynthetic gene clusters (BGCs) in bacterial genomes, however the structures of their siderophore products remain mostly undetermined. This limits our molecular-level understanding of how bacteria acquire iron, as well as how they interact with other taxa that may use the same siderophores within bacterial communities. Here, we apply inverse stable isotope labeling (InverSIL) to rapidly connect predicted siderophore […]
- High-throughput peptide-centric local stability assay extends protein–ligand identification to membrane proteins, tissues and bacteria