Kermit Murray

@kkmurray.bsky.social

7 hours ago

[ASAP] Mass Spectrometry-Based Proteomics Methods for Systematic Identification and Quantification of Protein O-Glycosylation in Complex Biological Samples Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00005

(JASMS) [ASAP] Mass Spectrometry-Based Proteomics Methods for Systematic Identification and Quantification of Protein O-Glycosylation in Complex Biological Samples: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00005 (RSS) #MassSpecRSS #JASMS

Kermit Murray

@kkmurray.bsky.social

8 hours ago

[ASAP] Mass Spectrometry-Based Spatial Imaging of the Cochlea Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00436

(JASMS) [ASAP] Mass Spectrometry-Based Spatial Imaging of the Cochlea: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00436 (RSS) #MassSpecRSS #JASMS

Kermit Murray

@kkmurray.bsky.social

20 hours ago

Gallium induces cytotoxicity through disruption of DNA synthesis rather than ferroptosis Background: Gallium (Ga) is a promising anti-tumor agent; however, its precise molecular targets in osteosarcoma remain debated. While current paradigms largely attribute its toxicity to reactive oxygen species (ROS) and ferroptosis, understanding its true mechanism is essential for overcoming therapeutic resistance. This highlights the need for interdisciplinary approaches, such as metabolomics, to unveil novel vulnerabilities in cancer metabolism. Methods:,We employed an interdisciplinary strategy utilizing high-resolution liquid chromatography-mass spectrometry (LC-MS) metabolomics and 13C2-glutamine stable isotope tracing in osteosarcoma cells to elucidate the cytotoxic mechanisms of gallium nitrate. Scanning electron microscopy with energy-dispersive X-ray spectroscopy (SEM-EDS) was utilized for elemental mapping, and in silico modeling was applied to evaluated metal binding dynamics. Furthermore, synergistic effects were tested by combining gallium with the DNA-damaging agent cisplatin. Results: Our metabolic profiling revealed a profound bifurcation characterized by the systemic depletion of glycolysis and pentose phosphate pathway intermediates, coupled with a novel ribonucleotide accumulation bottleneck. The observed distinct signature strongly implicated ribonucleotide reductase (RNR) as the primary enzymatic target. In silico modeling and SEM-EDS visually and thermodynamically confirmedthat gallium acts as a structural decoy for iron within the RNR active site. The co-localization induces functional iron starvation rather than canonical ferroptosis. Furthermore, isotope tracing confirmed that elevated ROS is a consequence of overall metabolic failure, not the primary driver of cell death. Crucially, gallium functioned as a metabolic DNA repair inhibitor, synergizing potently with cisplatin to prevent the repair of platinum-induced DNA lesions. Conclusions: Gallium selectively sensitizes highly proliferative sarcoma cells by disrupting RNR-mediated DNA precursor synthesis, while sparing normal osteoblasts. Leveraging metabolomics to uncover this state of functional iron starvation provides a rational, interdisciplinary framework for developing gallium-based combination therapies designed to break platinum resistance in clinical oncology.

(BioRxiv All) Gallium induces cytotoxicity through disruption of DNA synthesis rather than ferroptosis: Background: Gallium (Ga) is a promising anti-tumor agent; however, its precise molecular targets in osteosarcoma remain debated. While current paradigms largely attribute… #BioRxiv #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 day ago

Proteomic profiling of whole tissue sections in cardiac ATTR amyloidosis reveals increased extracellular matrix remodeling Cardiac transthyretin amyloidosis (ATTR-CA) is caused by myocardial deposition of misfolded transthyretin, leading to progressive heart failure. Disease pathology, however, extends beyond passive amyloid deposition and also involves active processes such as extracellular matrix (ECM) remodeling and immune activation. Mass spectrometry (MS) is the gold standard for amyloid typing in diagnostics. Here, we applied quantitative MS-driven proteomics on formalin-fixed paraffin-embedded whole cardiac tissue sections from six ATTR-CA cases, ten unaffected controls and four AL-CA controls to investigate protein expression changes. In addition to transthyretin, over 500 proteins were upregulated in ATTR-CA biopsies, including complement and coagulation factors as well as extracellular matrix (ECM) remodeling proteins. Among these, members of the A Disintegrin and Metalloproteinase with Thrombospondin Motifs (ADAMTS) family, metalloproteinases (MMPs), and Tissue Inhibitor of Metalloproteinases (TIMP3) showed significant upregulation. These proteins are key regulators of ECM turnover and structural integrity. Immunohistochemistry confirmed ADAMTS4 enrichment in amyloid deposits, while TIMP3 showed strong expression in cardiomyocytes and weaker staining within amyloid deposits. Together, these findings indicate that ECM remodeling, alongside complement and coagulation activation, represents a reproducible feature of cardiac ATTR amyloidosis. Whole-tissue proteomics provides biological insights that extend beyond amyloid typing, with potential implications for biomarker discovery and therapeutic targeting in ATTR-CA.

(BioRxiv All) Proteomic profiling of whole tissue sections in cardiac ATTR amyloidosis reveals increased extracellular matrix remodeling: Cardiac transthyretin amyloidosis (ATTR-CA) is caused by myocardial deposition of misfolded transthyretin, leading to progressive heart… #BioRxiv #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 day ago

Proteome analyses reveal Endoplasmic Reticulum stress-induced changes in protein abundance associated with Ube2j2 deficiency in human cell culture The unfolded protein response (UPR) helps reinstate cellular proteostasis upon an accumulation of misfolded proteins in the endoplasmic reticulum (ER), in part through ER-associated degradation (ERAD). Ube2j2 is an ER-localized E2 ubiquitin-conjugating enzyme that participates in ERAD. We used mass spectrometry analysis of cultured U2OS cells to investigate how the loss of Ube2j2 affects the cellular proteome in response to tunicamycin-induced ER stress. We constructed a network of twelve statistically distinct modules of protein abundance profiles across conditions. We describe the Gene Ontology annotations for each module along with the hub gene proteins whose abundance levels most closely adhere to each modules protein abundance profile. Our analysis identifies known Ube2j2-associated pathways (e.g., the UPR and ERAD) and cellular functions that were previously unassociated with Ube2j2 (e.g., RNA metabolism, ER-Golgi transport, and cell-cycle progression). These data are available via ProteomeXchange with identifier PXD076153 and provide avenues for further investigation into the cellular functions of Ube2j2 under basal and ER-stressed conditions.

(BioRxiv All) Proteome analyses reveal Endoplasmic Reticulum stress-induced changes in protein abundance associated with Ube2j2 deficiency in human cell culture: The unfolded protein response (UPR) helps reinstate cellular proteostasis upon an accumulation of misfolded… #BioRxiv #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 day ago

A multi-omics approach to identify the impact of miR-411ed on NSCLC TKI resistance Tyrosine Kinase inhibitors (TKIs) are widely used as effective chemotherapeutic agents for treating patients with EGFR-mutated NSCLC. Unfortunately, after treatment, patients eventually develop resistance to TKI therapy. The most common resistance mechanism for the TKI Osimertinib is the overexpression of the MET Proto-Oncogene, Receptor Tyrosine Kinase (MET). We previously demonstrated that miR-411-5p A-to-I edited at position 5 (miR-411ed) can directly target MET in A549 and H1299 cells. MiR-411ed in combination with Osimertinib reduced cell proliferation in two TKI resistant EGFR-mutated cell lines: HCC827R and PC9R. MiR-411ed did not downregulate MET expression in HCC827R, suggesting an alternative mechanism for TKI response. In this study, we aim to identify the mechanism of miR-411ed TKI response using a multi-omics approach of RNAseq and protein mass spectrometry. In our cellular model, we identified miR-411ed affected genes independent of MET activity, resulting in 211 genes (RNAseq) and 36 proteins (proteomics). Pathway analysis identified an increase in interferon signaling for RNAseq and combined omics, and a decrease in ERK/MAPK signaling in proteomics. Using the IsoTar target prediction tool, we identified STAT3 as a key regulator and confirmed STAT3 protein downregulation upon transfection with miR-411ed. We further investigated the effect of miR-411ed in vivo, observing a reduction in tumor size with miR-411ed in combination with Osimertinib but not with miR-411ed or Osimertinib treatment alone, confirming the effectiveness of miR-411ed in TKI response.

(BioRxiv All) A multi-omics approach to identify the impact of miR-411ed on NSCLC TKI resistance: Tyrosine Kinase inhibitors (TKIs) are widely used as effective chemotherapeutic agents for treating patients with EGFR-mutated NSCLC. Unfortunately, after treatment, patients… #BioRxiv #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 day ago

(J Proteom) Curcumin mitigates gas explosion-induced traumatic brain injury in male rats by regulating key molecular signatures: A multiomics analysis: Publication date: Available online 2 April 2026

Source: Journal of Proteomics

Author(s): Xinwen Dong, Yaguang Su, Cuiying Li,… #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 day ago

(Talanta) Development and validation of a gas chromatography – mass spectrometry (GC-MS) method for analyzing the polycyclic aromatic hydrocarbons in microplastics: Publication date: Available online 2 April 2026

Source: Talanta

Author(s): Olga V. Kuznetsova #Talanta #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 day ago

[ASAP] Integrated Single-Cell Mass Spectrometry Imaging and Immunofluorescence Microscopy for Multimodal Characterization of Human Immune Cells Analytical ChemistryDOI: 10.1021/acs.analchem.6c00381

(ACS Anal Chem) [ASAP] Integrated Single-Cell Mass Spectrometry Imaging and Immunofluorescence Microscopy for Multimodal Characterization of Human Immune Cells: Analytical ChemistryDOI: 10.1021/acs.analchem.6c00381 #MassSpecRSS #ACSAChem

Kermit Murray

@kkmurray.bsky.social

1 day ago

A stage-resolved map of dynamic septin interactions required for infection by the rice blast fungus Septin GTPases are essential cytoskeletal regulators that organize membranes and scaffold protein complexes to control cytokinesis, polarity, and morphogenesis. How septins execute these functions remains poorly understood, and comprehensive, stage-resolved interaction maps are lacking. Here, we define a quantitative, time-resolved septin interactome in the rice blast fungus Magnaporthe oryzae using immunoprecipitation coupled to mass spectrometry. We map more than 350 interactors of septins Sep3, Sep4, Sep5 and Sep6, revealing a dynamic network required for appressorium-mediated plant infection. Beyond canonical roles in cytoskeletal organisation and polarity, septins associate with proteins linked to membrane remodelling, metabolism, and virulence, deployed during host invasion. Integration with ultra-high-throughput yeast two-hybrid analysis defines a high-confidence septin interactome and identifies previously uncharacterised factors, including Msi1, a BAR domain protein required for invasive growth. Together, these findings establish septins as dynamic organisers of infection-related processes and provide a framework for understanding how cytoskeletal scaffolds coordinate fungal pathogenesis.

(BioRxiv All) A stage-resolved map of dynamic septin interactions required for infection by the rice blast fungus: Septin GTPases are essential cytoskeletal regulators that organize membranes and scaffold protein complexes to control cytokinesis, polarity, and morphogenesis.… #BioRxiv #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 day ago

Metabolomics Integrated with Mass Spectrometry Imaging Reveals Geographic Variation in Chemical Composition of Ophiopogon japonicus Publication date: Available online 2 April 2026 Source: Journal of Chromatography A Author(s): Muzi Li, Qiao Liu, Guoqian Cui, Shiyan Qian, Yulong Chen, Tao He, Lu Li, Xiaoyan Lu, Guofang Shen, Shengshuang Chen, Xiaohui Fan

(J Chrom A) Metabolomics Integrated with Mass Spectrometry Imaging Reveals Geographic Variation in Chemical Composition of Ophiopogon japonicus: Publication date: Available online 2 April 2026

Source: Journal of Chromatography A

Author(s): Muzi Li, Qiao Liu, Guoqian Cui,… #JChrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 day ago

FAM134B isoform 2/RETREG1-2 defines a calnexin-TOLLIP-coupled ER-phagy pathway that restricts Ebola virus glycoprotein and is antagonized by VP40 through macro-autophagy Selective autophagy of the endoplasmic reticulum (ER-phagy) is critical for ER proteostasis and host defense, yet how ER quality-control pathways interface with ER-phagy to restrict viral glycoproteins remains poorly defined. Previously, the 1st known ER-phagy receptor gene RETREG1 (RETR1)/FAM134B gene was reported to restrict Ebola virus (EBOV) replication in vivo by inhibiting the viral glycoprotein (GP) and viral protein 40 kDa (VP40) expression, but this mechanism remains unknown. Here, we identify the truncated RETR1/FAM134B isoform 2 (RETR1-2), but not its full-length protein RETR1, as an ER-phagy receptor that targets EBOV-GP for degradation. RETR1-2 broadly triggers GP degradation across ebolavirus species but not Marburg virus and inhibits EBOV replication. Mechanistically, RETR1-2 recognizes EBOV-GP via its luminal domain, undergoes GP-induced oligomerization, and directs GP-containing ER membranes to lysosomes through canonical macro-autophagy. Using unbiased mass spectrometry, we identified TOLLIP as the key cytoplasm adaptor for RETR1-2, which also requires cooperation with the ER chaperone calnexin for EBOV-GP degradation. Notably, the PI3P-binding C2 domain of TOLLIP mediates its interaction with RETR1-2, and the EBOV-GP degradation occurs independently of ubiquitination, revealing an unexpected role for TOLLIP in ER-phagy. Furthermore, EBOV-VP40 antagonizes this pathway by selectively targeting RETR1-2 for macroautophagic degradation independently of TOLLIP, thereby restoring GP expression and viral infectivity. Nevertheless, RETR1-2 reciprocally degrades VP40 via a similar mechanism. Together, these findings define a calnexin-TOLLIP-RETR1-2 axis that links ER quality control to ER-phagy-mediated antiviral restriction and uncover a reciprocal host-virus arms race centered on selective macro-autophagy.

(BioRxiv All) FAM134B isoform 2/RETREG1-2 defines a calnexin-TOLLIP-coupled ER-phagy pathway that restricts Ebola virus glycoprotein and is antagonized by VP40 through macro-autophagy: Selective autophagy of the endoplasmic reticulum (ER-phagy) is critical for ER proteostasis… #BioRxiv #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 days ago

[ASAP] Quantifying Protein Homodimer Affinities and the Effect of Molecular Glues and Interface Residues Using Native Mass Spectrometry Journal of the American Chemical SocietyDOI: 10.1021/jacs.5c18602

(J Am Chem Soc) [ASAP] Quantifying Protein Homodimer Affinities and the Effect of Molecular Glues and Interface Residues Using Native Mass Spectrometry: Journal of the American Chemical SocietyDOI: 10.1021/jacs.5c18602 #JAmChemSoc #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 days ago

The metabolome and proteome of stem cell-derived human primordial germ cells: a multi-omics approach Primordial germ cells (PGCs) are the population of cells that, in the human embryo, specify day 12 post-fertilization, and form the precursor cells for the future egg or sperm cells. Although in vitro differentiation of PGCs from human stem cells has been achieved, these primordial germ cell-like cells (hPGCLCs) fail to further mature. The reason for this is unclear. Previous studies in mice revealed that several specific metabolic changes occur during the maturation of these cells, which are essential for their developmental progress. However, very little is known about the metabolic profile of human primordial germ cells. In the severe scarcity of human PGCs, hPGCLCs serve as a research model to study PGC formation. To investigate this, we differentiated hPGCLCs using induced-pluripotent stem cells and performed a mass spectrometry analysis to establish their metabolome and proteome. These cells revealed distinct metabolic profile, with changes particularly at the proteome level. This included a shift between canonical and non-canonical citric acid cycle in hPGCLC, downregulation of late-stage glycolysis and reduction of nucleotide de novo synthesis. By providing an integrative map of these metabolic networks, we aim to provide insight on the influence of metabolism on human PGC development that could help improve methods for in vitro differentiation and maturation hPGCLCs.

(BioRxiv All) The metabolome and proteome of stem cell-derived human primordial germ cells: a multi-omics approach: Primordial germ cells (PGCs) are the population of cells that, in the human embryo, specify day 12 post-fertilization, and form the precursor cells for the… #BioRxiv #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 days ago

Ovarian extracellular matrix mechanics regulate oocyte-follicle interactions during female reproductive aging Female reproductive aging is associated with ovarian functional decline, leading to infertility. During aging, biochemical and biophysical changes in the ovarian extracellular matrix (ECM) occur, yet how these properties affect follicle growth and oocyte quality remains poorly understood. Here we describe spatiotemporal changes in the ovarian ECM with age using mass spectrometry, immunohistochemistry, and nanoindentation. While follicle stiffness remains unchanged, stromal matrix remodeling is associated with a ~2.5-fold increase in stiffness. To understand how this increase in stromal stiffness affects age-related follicular dysfunction, isolated young follicles were cultured in soft and stiff hydrogels mimicking young and aged ovarian stromal stiffness, respectively. Higher stiffness leads to a decrease in granulosa cell (GC) proliferation, oocyte quality, and GC-oocyte interactions mediated via transzonal projections (TZPs). RNA-seq revealed TGF-{beta} signaling as a major pathway affected by stiffness, and activation of TGF-{beta} signaling through Mongersen treatment rescued TZP formation and oocyte quality in stiff matrix. These findings provide mechanistic insight into how changes in ECM mechanics contribute to ovarian aging functional decline and reveal potential therapeutic targets to counter fertility loss associated with tissue aging and fibrosis.

(BioRxiv All) Ovarian extracellular matrix mechanics regulate oocyte-follicle interactions during female reproductive aging: Female reproductive aging is associated with ovarian functional decline, leading to infertility. During aging, biochemical and biophysical changes in… #BioRxiv #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 days ago

Proteomic analysis of ammonia-induced stress in Chinese hamster ovary (CHO) cell cultures Publication date: Available online 1 April 2026 Source: Journal of Proteomics Author(s): David Ryan, Michael Henry, Christiana-Kondylo Sideri, Esen Efeoglu, Paula Meleady

(J Proteom) Proteomic analysis of ammonia-induced stress in Chinese hamster ovary (CHO) cell cultures: Publication date: Available online 1 April 2026

Source: Journal of Proteomics

Author(s): David Ryan, Michael Henry, Christiana-Kondylo Sideri, Esen Efeoglu, Paula Meleady #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 days ago

First Establishment of LC–MS/MS Method for Quantitative Analysis of Pharmacokinetics and Tissue Distribution of Trilobatin—Comparison of Three Administration Modes ABSTRACT Trilobatin is a novel dihydrochalcone natural food additive. It has multiple functions such as anti-inflammatory, antioxidant, and anticancer effects. This study first developed and validated a method based on liquid chromatography–tandem mass spectrometry for the quantitative determination of trilobatin in rat plasma and tissues. The method demonstrated high precision, high accuracy, good extraction recovery, and minimal matrix effects. Subsequently, this method was used to study the pharmacokinetics and tissue distribution of trilobatin after oral, intravenous, and intraperitoneal administration in rats. Pharmacokinetic analysis showed that trilobatin was rapidly absorbed after oral administration with a T max of 1 h, and T max was also approximately 1 h after intraperitoneal administration. Compared to intravenous injection, the relative bioavailability of oral administration and intraperitoneal injection is only 0.004% and 0.3%, respectively. Tissue distribution results from the three administration routes indicated that trilobatin exhibits widespread tissue distribution. These findings provide a theoretical basis for further research on trilobatin. This study provides detailed insights into the pharmacokinetic and tissue distribution characteristics of trilobatin in rats for the first time, laying the foundation for further research on trilobatin as a potential new drug candidate.

(Biomed Chrom) First Establishment of LC–MS/MS Method for Quantitative Analysis of Pharmacokinetics and Tissue Distribution of Trilobatin—Comparison of Three Administration Modes: ABSTRACT




Trilobatin is a novel dihydrochalcone natural food additive. It has multiple… #massSpecRSS #biomedchrom

Kermit Murray

@kkmurray.bsky.social

2 days ago

[ASAP] Integrating Mass Spectrometry Imaging with Tumor Organoid-Immunity Platform to Identify Metabolic Adaptations in Tumor Immune Resistance Analytical ChemistryDOI: 10.1021/acs.analchem.6c00013

(ACS Anal Chem) [ASAP] Integrating Mass Spectrometry Imaging with Tumor Organoid-Immunity Platform to Identify Metabolic Adaptations in Tumor Immune Resistance: Analytical ChemistryDOI: 10.1021/acs.analchem.6c00013 #MassSpecRSS #ACSAChem

Kermit Murray

@kkmurray.bsky.social

2 days ago

[ASAP] Direct Current Arc Plasma-Excited Nebulizer Gas-Assisted Electrospray Ionization Mass Spectrometry Analytical ChemistryDOI: 10.1021/acs.analchem.6c00669

(ACS Anal Chem) [ASAP] Direct Current Arc Plasma-Excited Nebulizer Gas-Assisted Electrospray Ionization Mass Spectrometry: Analytical ChemistryDOI: 10.1021/acs.analchem.6c00669 #MassSpecRSS #ACSAChem

Kermit Murray

@kkmurray.bsky.social

2 days ago

Identification and characterization of unknown photo-oxidation degradation components of ganciclovir by high-performance liquid chromatography and quadrupole time-of-flight mass spectrometry European Journal of Mass Spectrometry, Ahead of Print. Ganciclovir (GCV) is an antiviral drug used to treat cytomegalovirus infections associated with AIDS. The study of the GCV drug substance under photo-oxidation stress conditions identified five impurities. This study aims to interpret the chemical ...

(EJMS) Identification and characterization of
unknown photo-oxidation degradation components of ganciclovir by high-performance liquid chromatography and quadrupole time-of-flight mass spectrometry: European Journal of Mass Spectrometry, Ahead of Print.
Ganciclovir (GCV) is an… #EJMS #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 days ago

(IJMS) Graphical abstract TOC: Publication date: May 2026

Source: International Journal of Mass Spectrometry, Volume 523

Author(s): #ijms #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 days ago

(IJMS) Graphical abstract TOC: Publication date: May 2026

Source: International Journal of Mass Spectrometry, Volume 523

Author(s): #ijms #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 days ago

Sex-specific remodeling of the tRNA epitranscriptome in Alzheimers disease tRNA modifications are critical regulators of RNA stability, decoding fidelity, and cellular stress adaptation, yet their contribution to human neurodegenerative disease remains poorly understood. Beyond their established functions in translational control, emerging evidence shows that RNA modifications influence neurogenesis, neurodevelopment, neuronal function, brain-cell differentiation, and cellular plasticity. Consequently, dysregulation of these molecular processes is increasingly recognized as a mechanistic contributor to neurodegenerative disorders. Alzheimers disease (AD), characterized by amyloid pathology, synaptic dysfunction, and progressive neuronal loss, has recently been linked to disturbances in RNA metabolism, suggesting that alterations in the epitranscriptome may represent an underexplored dimension of AD pathophysiology. Here, we systematically profiled the tRNA epitranscriptome across cellular and animal models of AD, as well as in human postmortem brain tissue from non-demented controls and AD patients, using liquid chromatography-tandem mass spectrometry (LC-MS/MS). This method enables highly sensitive quantification of RNA modifications, with limits of detection in the low femtomole range. Across our models, we identified a conserved yet sex-specific remodeling of the tRNA modification landscape in AD. Because therapeutic options and early diagnostic tools for AD remain limited, we leveraged these findings to develop a tRNA-centered RNA-modification score that integrates both nucleobase-specific modification patterns and neuropathological disease severity into a quantitative metric. Together, our findings identify the tRNA epitranscriptome as a unifying molecular sex-specific signature of AD, linking disease pathology and sex to impaired RNA metabolism. This line of research opens a new path toward establishing early biomarkers or diagnostic tools for AD.

(BioRxiv All) Sex-specific remodeling of the tRNA epitranscriptome in Alzheimers disease: tRNA modifications are critical regulators of RNA stability, decoding fidelity, and cellular stress adaptation, yet their contribution to human neurodegenerative disease remains poorly… #BioRxiv #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 days ago

Versatile and sensitive detection of mono- and poly(ADP-ribosyl)ation reveals XRCC1-dependent remodelling of PARP1 signalling #nature #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 days ago

Distribution of extraterrestrial nucleobases, other N-heterocycles, and their precursors in a sample from asteroid Bennu - Communications Chemistry The presence of all canonical nucleobases in samples from Bennu has previously provided evidence that some of life’s ingredients were synthesized abiotically in the parent body of this asteroid and/or its precedent components. Here, the authors extend research on the distribution of nucleobases and other N-heterocycles in Bennu by using a larger sample and an updated analytical protocol, reporting the concentrations of a diverse suite of N-heterocycles including nucleobases and their precursors extracted from a homogenized Bennu sample.

Distribution of extraterrestrial nucleobases, other N-heterocycles, and their precursors in a sample from asteroid Bennu #nature #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

3 days ago

(J An Atom Spec) Polyvinyl chloride microplastic detection by single particle inductively coupled plasma mass spectrometry for the characterization of model microplastics: J. Anal. At. Spectrom., 2026, Advance Article
DOI: 10.1039/D5JA00455A, Technical Note Open… #jaas #MassSpecRSS #AtomicSpec

Kermit Murray

@kkmurray.bsky.social

3 days ago

Single Cell-Type Spatial Proteomics Uncovers Regional Heterogeneity of Astrocytes Astrocytes are a subset of glial cells in the central nervous system (CNS) that support numerous processes essential for brain function. Their functional diversity is thought to arise from specialized subpopulations with distinct molecular profiles. Although single-cell and single-nucleus RNA sequencing (scRNA-seq and snRNA-seq) have greatly advanced our understanding of astrocyte transcriptomic heterogeneity, mRNA abundance does not always correlate with protein levels because of post-transcriptional and translational regulation. Therefore, studying protein profiles remains essential to accurately capture astrocyte functional states and heterogeneity. Here, we used Microscoop Mint, a microscopy-guided spatial proteomics platform that integrates subcellular, region-specific sample preparation with LC-MS/MS-based mass spectrometry, enabling direct protein profiling of astrocytes in paraformaldehyde-fixed, optimal cutting temperature (OCT)-embedded mouse brain tissue. By applying this approach, we uncovered distinct regional-associated astrocyte proteomic signatures in the cerebral cortex and hippocampus and selected novel candidate protein markers for subsequent validation by immunofluorescence. Notably, MINK1 and PLEKHB1 showed preferential expression in hippocampal and cortical astrocytes, respectively, highlighting their potential as region-specific astrocyte markers. Overall, this strategy enables high-precision, unbiased spatial proteomic discovery at subcellular resolution, providing a powerful framework for linking molecular diversity to functional specialization in astrocyte biology.

(BioRxiv All) Single Cell-Type Spatial Proteomics Uncovers Regional Heterogeneity of Astrocytes: Astrocytes are a subset of glial cells in the central nervous system (CNS) that support numerous processes essential for brain function. Their functional diversity is thought to… #BioRxiv #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

3 days ago

[ASAP] Improved Methods for Recording Accurate Collision Cross Sections Using Cyclic Ion Mobility-Mass Spectrometry Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00022

(JASMS) [ASAP] Improved Methods for Recording Accurate Collision Cross Sections Using Cyclic Ion Mobility-Mass Spectrometry: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00022 (RSS) #MassSpecRSS #JASMS

Kermit Murray

@kkmurray.bsky.social

3 days ago

[ASAP] Residue-Level Determination of Small-Molecule–Protein Affinities by Hydrogen–Deuterium Exchange Mass Spectrometry Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00020

(JASMS) [ASAP] Residue-Level Determination of Small-Molecule–Protein Affinities by Hydrogen–Deuterium Exchange Mass Spectrometry: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00020 (RSS) #MassSpecRSS #JASMS

Kermit Murray

@kkmurray.bsky.social

3 days ago

Ion Activation Methods for Top‐Down Proteomics ABSTRACT Mass spectrometry (MS) has emerged as a premier method used to characterize the sequences of proteins. Top-down proteomics aims to capture the multiple sources of structural diversity reflected in proteins, such as those that arise from alternative RNA splicing events or the addition of post-translational modifications. Tandem MS (i.e., MS/MS) represents a critical component of a top-down proteomics experiment, as the resulting fragmentation patterns unveil various structural features associated with protein function. This review spotlights recent developments and applications of ion activation methods used to decipher the structural properties of intact proteins, including collisional activation and those based on the use of electrons and photons. The analysis of fragment ions generated by these MS/MS methods are also discussed, along with an outlook on future developments in the field related to instrumentation and burgeoning approaches to top-down proteomics, such as single-cell methods.

(MS Reviews) Ion Activation Methods for Top‐Down Proteomics: ABSTRACT




Mass spectrometry (MS) has emerged as a premier method used to characterize the sequences of proteins. Top-down proteomics aims to capture the multiple sources of structural diversity reflected… #MassSpectromRev #MassSpecRSS