Kermit Murray

@kkmurray.bsky.social

30 minutes 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

3 hours 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

5 hours 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

14 hours 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

15 hours 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

16 hours 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

17 hours 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

18 hours 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

19 hours 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

20 hours 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

21 hours 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

22 hours 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

23 hours 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

1 day 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

1 day 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

1 day 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

1 day 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

1 day 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

1 day 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

1 day 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

1 day 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

Kermit Murray

@kkmurray.bsky.social

1 day ago

[ASAP] Implementing Annotation Confidence Scoring in Untargeted Mass Spectrometry Workflows for Small Molecule Analysis Analytical ChemistryDOI: 10.1021/acs.analchem.5c03229

(ACS Anal Chem) [ASAP] Implementing Annotation Confidence Scoring in Untargeted Mass Spectrometry Workflows for Small Molecule Analysis: Analytical ChemistryDOI: 10.1021/acs.analchem.5c03229 #MassSpecRSS #ACSAChem

Kermit Murray

@kkmurray.bsky.social

2 days ago

Inositol phosphates, pyrophosphates and the genes involved in their turnover in the streptophyte green alga Chara braunii Inositol phosphates (InsPs) and inositol pyrophosphates (PP-InsPs) are conserved signalling molecules, but their evolutionary origin and diversification in the green lineage remain poorly understood. Here we investigated the InsP network in the streptophyte alga Chara braunii, a key lineage close to the origin of land plants. Using capillary electrophoresis-electrospray ionization mass spectrometry, we detected a broad spectrum of InsP and PP-InsP species from InsP3 to InsP8, including multiple positional isomers. Developmental profiling across dormant oospores, young thalli and mature thalli revealed extensive metabolic remodeling, with InsP6 as the dominant metabolite and distinct stage-dependent changes in lower InsPs and pyrophosphorylated species. Multiple PP-InsP5 and (PP)2-InsP4 isomers were identified, together with an unassigned additional InsP8-like signal, indicating further pathway complexity. Bioinformatic analyses identified candidate homologs of major InsP metabolic enzymes, supporting the presence of an enzymatic framework for InsP synthesis and turnover similar to land plants. Environmental perturbation revealed isomer-selective effects: prolonged light and dark phases strongly affected the accumulation of specific InsP5 and PP-InsP5 isomers, with 1-PP-InsP5 emerging as the most stimulus-responsive pyrophosphate species, whereas heat stress preferentially reduced 4-PP-InsP5. Together, these findings show that a structurally complex and environmentally responsive InsP network was already established in streptophyte algae before the emergence of land plants.

(BioRxiv All) Inositol phosphates, pyrophosphates and the genes involved in their turnover in the streptophyte green alga Chara braunii: Inositol phosphates (InsPs) and inositol pyrophosphates (PP-InsPs) are conserved signalling molecules, but their evolutionary origin and… #BioRxiv #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 days ago

Methanol-driven esterification of volatile short-chain fatty acids in thermal desorption-based analysis #nature #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 days ago

Enhanced Sensitivity in DESI Mass Spectrometry Imaging via a Dual‐Stage Ion Funnel: A Hybrid Simulation and Experimental Study ABSTRACT Rationale While ambient mass spectrometry imaging (MSI) is essential for biological analysis, its sensitivity remains constrained by ion transmission losses due to collisions and gas dynamics. Methods Here, a high-performance desorption electrospray ionization (DESI) MSI system featuring a high-efficiency dual-stage ion funnel (DIF) was developed. To optimize the system configuration, a hybrid multiphysics simulation model was constructed by coupling gas dynamics, electric field, and ion transport simulations. Results The simulation model was validated against experimental data from mouse brain homogenates, confirming its accuracy in predicting ion transport behavior under realistic conditions. With the optimized DIF assembly, signal enhancements of up to 490-fold and the detection of 303 additional mass peaks in mouse brain sections were achieved compared to the standard S-lens interface. Furthermore, post-photoionization (PI) was introduced to expand molecular coverage to non-polar compounds and simultaneously enhance sensitivity. Conclusions Overall, this study provides theoretical insights into ion motion within complex coupled fields and offers guidelines for the design of high-sensitivity ambient MSI interfaces.

(RCM) Enhanced Sensitivity in DESI Mass Spectrometry Imaging via a Dual‐Stage Ion Funnel: A Hybrid Simulation and Experimental Study: ABSTRACT




Rationale




While ambient mass spectrometry imaging (MSI) is essential for biological analysis, its sensitivity… #RapidCommunMassSpectrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 days ago

Comparative Metabolomic Profiling of Roasted Coffee Beans From Taiwan and Brazil ABSTRACT Rationale Taiwan produces high-value specialty coffee on a limited scale, whereas Brazil is the largest global supplier and a major source of imports to Taiwan. For food authenticity, differentiation of roasted coffee from these origins is important. However, few metabolomics-based traceability studies have yet been conducted on Taiwan-roasted coffee. Methods In this study, metabolic profiling was applied to evaluate origin-related chemical signatures in Arabica roasted coffee beans from Taiwan and Brazil. An untargeted metabolomic workflow of integrating full scan and data-dependent acquisition (IFSDDA) was implemented using UHPLC-QTOF-MS. Roasted coffee beans were extracted using optimized 50% ethanol, profiled by LC-MS/MS, and analyzed using multivariate statistics, ROC analysis, and spectral-library–based metabolite annotation. Results Multivariate analyses revealed a clear separation of Taiwanese and Brazilian roasted coffee samples. Among 26 annotated metabolites, four compounds showed the highest discriminatory power (VIP > 1.0), including 4-(1H-indol-3-yl)butan-2-one, citrulline, 7-methanesulfinylheptanenitrile, and phytosphingosine. The four-potential markers achieved excellent classification performance (AUC > 0.98), reflecting consistent origin-associated patterns. Conclusions This study demonstrated that untargeted metabolic profiling can effectively distinguish roasted coffee from Taiwan and Brazil. Such profiling provided an approach for food safety surveillance by capturing chemical signatures linked to regional production environments and agricultural inputs. The annotated markers offer a practical framework for monitoring both imported and domestic roasted coffee.

(RCM) Comparative Metabolomic Profiling of Roasted Coffee Beans From Taiwan and Brazil: ABSTRACT




Rationale




Taiwan produces high-value specialty coffee on a limited scale, whereas Brazil is the largest global supplier and a major source of imports to… #RapidCommunMassSpectrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 days ago

Decoding Sickle Cell Disorders Using Flow Injection Analysis Mass Spectrometry ABSTRACT Rationale Chromatographic and electrophoretic methods reliably distinguish the heterozygous and homozygous sickle cell states with hemoglobin variants appearing at consistent percentages with specific retention or migration times. However, co-migrating variants alter the overall hemoglobin profile, complicating interpretation in compound heterozygous conditions such as βS/βD-Punjab since these variants electrophoretically migrate close to each other. These cases often require hematological correlation or molecular confirmation. As molecular testing is not available in all laboratories, mass spectrometry (MS) may serve as an alternate approach for examining complex compound heterozygous sickle cell disorders. Methods Hemoglobin extracted from K2 EDTA blood samples (n = 154) was analyzed using flow-injection triple quadrupole MS. Summed intensities of three charge states each of βS and β globin monomers enabled calculation of the βS/β ratio to differentiate sickle cell trait (SCT) from sickle cell disease (SCD). Additional globin ratios (α/β, γ/β, δ/α (%)) were evaluated to subclassify SCD into Group 1 (βSβE, βSβD-Punjab, βSβC, βSLepore-BW), Group 2 (βSβ0), and Group 3 (βSβS). Statistical analysis was performed using SPSS v27. Results The βS/β ratio effectively differentiated SCT from SCD with an optimal cut-off value of 0.71 yielding 90.3% sensitivity and 98.4% specificity. The ratios α/β, γ/β, δ/α (%), βS/β, significantly discriminated against Group 1 from Group 3 (p 

(RCM) Decoding Sickle Cell Disorders Using Flow Injection Analysis Mass Spectrometry: ABSTRACT




Rationale




Chromatographic and electrophoretic methods reliably distinguish the heterozygous and homozygous sickle cell states with hemoglobin variants… #RapidCommunMassSpectrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 days ago

ER-Lysosome Cholesterol Exchange Regulates Lysosomal Motility Through mTOR-Dependent LAMTOR1 Phosphorylation The subcellular distribution of lysosomes, the main degradative organelles of mammalian cells, responds to metabolic cues in a highly dynamic way. While lysosomal positioning due to amino acid levels is well-characterized, cholesterol-dependent regulation of lysosomal motility is incompletely understood. We explored impaired lysosomal cholesterol export using a mass spectrometry-based multi-OMICs approach, identifying widespread reallocation of resources and signaling pathway modulation. We identified increased phosphorylation at LAMTOR1 serine 56 in response to cholesterol level perturbations. We demonstrate that this phosphorylation site is sufficient to disrupt Rag GTPases/SLC38A9 binding to the Ragulator complex, inhibiting canonical mTORC1 and facilitating binding of BORC, therefore promoting lysosomal retrograde movement. LAMTOR1 S56 phosphorylation responds exclusively to depletion of lysosomal limiting membrane cholesterol, is facilitated by mTOR, and presents a negative feedback loop for amino acid independent displacement of Ragulator bound Rag GTPases, limiting canonical mTORC1 activity. Mass spectrometry data are available via ProteomeXchange with identifier PXD073489.

(BioRxiv All) ER-Lysosome Cholesterol Exchange Regulates Lysosomal Motility Through mTOR-Dependent LAMTOR1 Phosphorylation: The subcellular distribution of lysosomes, the main degradative organelles of mammalian cells, responds to metabolic cues in a highly dynamic way. While… #BioRxiv #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 days ago

A lateral linker histone binding mode scaffolds dinucleosome stacking in chromatin fibers Linker histones are essential for chromatin compaction, yet how they contribute to higher-order fiber assembly remains poorly understood. Here, we determined cryo-electron microscopy structures of Arabidopsis dodeca-nucleosome fibers containing distinct H2A/H3 variants and linker histone H1.3, revealing a noncanonical binding mode that a laterally positioned H1.3 connects the acidic patch of one nucleosome and the DNA of the neighboring nucleosome, thereby scaffolding dinucleosomes into two-start chromatin fibers. This noncanonical binding mode is structurally conserved when H1.3 is replaced by Gallus gallus H5. Furthermore, incorporation of H2A.W and H3.3 further induces back-to-back fiber dimerization. Cryo-electron tomography and in vivo cross-linking mass spectrometry analyses support the physiological relevance of H1 lateral engagement. Our findings establish that linker histones act as active architectural scaffolds in higher-order chromatin organization.

(BioRxiv All) A lateral linker histone binding mode scaffolds dinucleosome stacking in chromatin fibers: Linker histones are essential for chromatin compaction, yet how they contribute to higher-order fiber assembly remains poorly understood. Here, we determined cryo-electron… #BioRxiv #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 days ago

Distribution, assembly and mechanism of GluN1/GluN3A excitatory glycine receptors NMDA receptors play key roles in brain development, plasticity and diseases. While glutamate and glycine co-gated GluN2-containing NMDARs have been extensively characterized, little is known regarding GluN3A-containing NMDARs that form receptors gated by glycine only. Here, combining native purification, mass spectrometry, cryo-EM and electrophysiology, we provide key insights on the molecular logic of GluN3A-NMDARs. We demonstrate that native GluN3A receptors account for a sizeable fraction of total NMDARs, are enriched at extrasynaptic compartments in the adult brain, and assemble specifically as diheteromeric GluN1/GluN3A excitatory glycine receptors (eGlyRs) rather than as triheteromeric GluN1/GluN2/GluN3A receptors. The architecture of eGlyRs reveal splayed and loosely packed extracellular domains, strikingly different from conventional GluN1/GluN2 receptors. Through back-and-forth structural and functional validations, we demonstrate how the combined effects of a weak ligand-binding domain (LBD) dimer interface and high intrinsic mobility of the N-terminal domains (NTDs) shape the atypical gating of eGlyRs. These findings illuminate GluN3A-NMDAR physiology and mechanism, with implications for neuronal signaling and pharmacology.

(BioRxiv All) Distribution, assembly and mechanism of GluN1/GluN3A excitatory glycine receptors: NMDA receptors play key roles in brain development, plasticity and diseases. While glutamate and glycine co-gated GluN2-containing NMDARs have been extensively characterized,… #BioRxiv #MassSpecRSS