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- Stressful events are a leading factor in development of depression. The medial prefrontal cortex (mPFC) is strongly associated with depression etiology and exposure to uncontrollable stressors results in synaptic dysfunction and loss. Learned helplessness is a behavioral paradigm that measures effects of repeated exposure to uncontrollable, inescapable stress on later responses to escapable stress. We therefore performed a proteomic analysis of mPFC synaptosomes in a mouse learned helplessness model to identify molecular changes that could contribute to functional consequences of […]
- The RNA exosome is an essential and ubiquitous RNase with exonucleolytic activity, involved in ribosome biogenesis and RNA quality control in eukaryotes. It is present both in nucleus and cytoplasm, and interacts with specific cofactors in each cell compartment, which are essential for recruitment and activity control of the exosome. Posttranslational modifications are known to regulate enzyme activity and protein interaction, although their precise roles are individually specific. In this study, we investigated the phosphorylation status of proteins associated with […]
- Reactive oxygen species (ROS) are central regulators of plant growth and stress responses. Cellular ROS levels are tightly controlled by antioxidant systems, including the evolutionarily conserved catalases that detoxify hydrogen peroxide (H2O2) predominantly within peroxisomes. Despite their importance, substantial gaps remain in our understanding of catalase biogenesis, regulation, subcellular targeting, and potential extra-peroxisomal functions. Using affinity purification of the UV-B photoreceptor UVR8 coupled with mass spectrometry, we identified a REGULATOR OF CHROMATIN CONDENSATION 1–like protein in Arabidopsis, which we named […]
- Publication date: Available online 29 January 2026Source: Journal of Chromatography BAuthor(s): Christof Manuel SchĂśnenberger, Aurelie Berthet, Matthias Briel, Alain Amstutz, Matthias Cavassini, LoĂŻc Sartori, Camille Rime, Davide Staedler, Fiorella Lucarini
- Chemistry â A European Journal, EarlyView.
- As part of the US HUPO sponsored "Pony Express" series highlighting speakers at the upcoming 2026 US HUPO meeting in St. Louis, Ben and Ben sit down to talk with Dr. William Noble, University of Washington, recipient of the 2026 Gilbert S. Omenn Computational Proteomics Award.keywords: genomics; machine learning; AI; computational; Bridgerton; cocaine monkeys; birding
- Journal of Mass Spectrometry, Volume 61, Issue 2, February 2026.
- Journal of Mass Spectrometry, Volume 61, Issue 2, February 2026.
- Polygenic scores (PGS) summarize the combined effects of common single-nucleotide polymorphisms and contribute to predictions of disease severity, but biological consequences linked to these common variants remain poorly defined. Here, we focused on polygenic liability for a measurable electrophysiologic trait (the QT interval). Prolonged QT interval, measured on patient electrocardiograms, is associated with an increased risk for cardiac arrhythmia. We investigated human induced pluripotent stem cell cardiomyocytes (hiPSC-CMs) from donors with extreme PGS (i.e., high and low) related to QT […]
-  Are you ready for deep visual lipidomics? No? Okay what about normal spatial lipidomics with deep visual proteomics? The diagram pretty much shows what the paper did, but the co-registration of the spatial data from the laser capture microdissection work (now called deep visual proteomics, y'all, get on the hip terminology) to the lipidomics is a star. This does come from the very small but valuable bank of post-mortem human brain tissue in Baltimore that one of these authors definitely didn't […]
- Analytical ChemistryDOI: 10.1021/acs.analchem.5c04150
- Analytical ChemistryDOI: 10.1021/acs.analchem.5c05700
- Loss-of-function mutations in cyclin-dependent kinase 12 (CDK12) define an aggressive subtype of metastatic castration-resistant prostate cancer (mCRPC) characterized by genomic instability, and depletion of CDK12 activity downregulates the expression of long DNA repair genes. While these transcriptional defects are well-documented, potential alterations in chromatin that may topologically affect this silencing and the subsequent adaptive survival mechanisms of tumor cells remain poorly understood. Here, we employ a dynamic multi-omics strategy to map the remodeling of the RNA Polymerase II (RNA Pol […]
- Environmental Science & TechnologyDOI: 10.1021/acs.est.5c08824
- Not for posting – maybe keep it to write a tutorial on writing a mass spec method section. I should probably start with a HOW TO write your proteomics methods paper's method section. But I'm just all around annoyed with this manuscript as well as whoever peer reviewed it. And the editor, and maybe whatever this journal is. I'm also probably annoyed with the premise of injurying bunnies with a balloon. And maybe about the entire state of the world. So here we go! First, […]
- Microbial metabolites play a critical role in regulating ecosystems, including the human body and its microbiota. However, understanding the physiologically relevant role of these molecules, especially through liquid chromatography tandem mass spectrometry (LC-MS/MS)-based untargeted metabolomics, poses significant challenges and often requires manual parsing of a large amount of literature, databases, and webpages. To address this gap, we established the Collaborative Microbial Metabolite Center knowledgebase (CMMC-KB), a platform that fosters collaborative efforts within the scientific community to curate knowledge about microbial […]
- Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00395
- Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00356
- ABSTRACT Nitrooxidative stress, driven by excess reactive nitrogen species like peroxynitrite, contributes to the pathogenesis of many chronic diseases. Among its molecular footprints, 3-nitrotyrosine (3NT) has emerged as a biologically relevant marker of protein nitration. Its accumulation reflects oxidative damage and altered protein function, positioning it as a promising biomarker. Proteomics has advanced our understanding of nitrooxidative stress and its clinical implications. The integration of high-resolution MS with immunoaffinity and structural modeling enables precise mapping of nitration sites and functional […]
- ABSTRACT Modified Xihuang Pills (MXP), a widely used traditional Chinese patent medicine in China, has been clinically applied for treating inflammatory and infectious diseases. However, there are only a few reports on its chemical components at present, which hinders its further research, development, and application. In this study, an ultra-high-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF-MS) method was developed firstly to investigate the major components in MXP. A total of 105 compounds were identified or characterized, among which 12 […]
- ABSTRACT N-(1,3-Dimethylbutyl)-Nâ˛-phenyl-p-phenylenediamine (6-PPD), a tire rubber antioxidant, and its oxidation product 6-PPD-quinone (6-PPDQ) have raised environmental and health concerns due to their widespread occurrence and toxicity. This study aimed to develop and validate a sensitive liquid chromatographyâtandem mass spectrometry (LCâMS/MS) method for the simultaneous quantification of 6-PPD and 6-PPDQ in murine tissues. The method showed excellent linearity (rââĽâ0.9977), low detection limits (0.056â0.967âng/mL), and high accuracy and precision across multiple tissue matrices, enabling reliable quantification at trace levels. Following repeated intratracheal […]
- Journal of Mass Spectrometry, Volume 61, Issue 2, February 2026.
- ABSTRACT A novel derivatization method was developed for the analysis of hydroxy degradation products of the Chemical Weapons Convention (CWC)-related chemicals present in aqueous and soil samples. The analytes were acetylated with acetyl chloride and quantitatively identified by liquid chromatographyâtandem mass spectrometry technique in electrospray ionization and atmospheric pressure chemical ionization modes. The acetylated products showed good separation and peak shapes with characteristic fragmentation. The developed method was validated, and the results showed linearity in the range of 1â5000Â ng/mL quantities […]
- Mascot Newsletter, January 2026:Ion intensity: peak area vs signal to noise?Duplexing deuterated water-labeled samples for protein turnover rate estimation.Role-based access with Mascot Security is useful in a variety of cases.https://www.matrixscience.com/nl/202601/newsletter.html#proteomics #massspec
- Biomolecular condensates, such as germ granules, organize RNAi pathways critical for fertility and genome regulation. Yet, the protein composition and functional contributions of these condensates remain poorly defined. Here, we applied TurboID proximity labeling to the Caenorhabditis elegans germ granule protein SIMR-1, integrating mass spectrometry with genetic screening, CRISPR-based tagging, and small RNA sequencing. This systematic approach identified several previously uncharacterized germ granule proteins that contribute to fertility, germline immortality, exogenous RNAi, and transgenerational inheritance. Small RNA sequencing of 21 […]