Kermit Murray

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  Kermit Murray kkmurray.bsky.social · 1h
  (J Proteom) Comparative proteomics of amaranth and quinoa seeds reveals species-specific solubility traits of 11S globulins after Osborne and polarity-based extractions: Publication date: Available online 5 February 2026 Source: Journal of Proteomics Author(s): Esaú… #MassSpecRSS
  

  Comparative proteomics of amaranth and quinoa seeds reveals species-specific solubility traits of 11S globulins after Osborne and polarity-based extractions

  Publication date: Available online 5 February 2026 Source: Journal of Proteomics Author(s): Esaú Bojórquez-Velázquez, Abraham M. Vidal-Limón, Jesús Alejandro Zamora-Briseño, Miriam L. Llamas-García, Alberto Barrera-Pacheco, Eduardo Espitia-Rangel, Ana P. Barba de la Rosa

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  Kermit Murray kkmurray.bsky.social · 2h
  (Biomed Chrom) Metabolomic Characterization of Neonates Born to Hyperthyroid Mothers: ABSTRACT The aim of this study was to compare blood metabolic profiles between neonates born to propylthiouracil (PTU)-treated hyperthyroid mothers and those born to healthy mothers… #massSpecRSS #biomedchrom
  

  Metabolomic Characterization of Neonates Born to Hyperthyroid Mothers

  ABSTRACT The aim of this study was to compare blood metabolic profiles between neonates born to propylthiouracil (PTU)-treated hyperthyroid mothers and those born to healthy mothers and to evaluate potential impacts on fetal health despite maternal treatment. Blood metabolites from 31 neonates exposed to PTU and 36 healthy controls were analyzed using liquid chromatography–tandem mass spectrometry (LC–MS/MS) at the Sixth Affiliated Hospital, Sun Yat-sen University, and the Maternal and Child Health Care Hospital of Huadu. Metabolite differences were assessed, and enriched pathway analysis was performed to identify significantly altered metabolic pathways. Neonates exposed to PTU exhibited distinct metabolic profiles compared with controls, characterized by significantly reduced levels of histidine and aspartic acid. These differential metabolites were primarily enriched in ammonia recycling as well as glycine and serine metabolism pathways—closely associated with protein and nucleotide biosynthesis. These findings indicate that prenatal exposure to PTU in hyperthyroid mothers leads to characteristic alterations in neonatal blood metabolic profiles, suggesting the need for close monitoring of growth and developmental outcomes in this population.

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  Kermit Murray kkmurray.bsky.social · 7h
  (BioRxiv All) A searchable metadata network graph for microbiome metabolomics: Establishing the biological context of microbial metabolites remains a major challenge. We present microbiomeMASST, a metadata-driven network graph that maps metabolites across 467 available… #BioRxiv #MassSpecRSS
  

  A searchable metadata network graph for microbiome metabolomics

  Establishing the biological context of microbial metabolites remains a major challenge. We present microbiomeMASST, a metadata-driven network graph that maps metabolites across 467 available datasets with 144,424 mass spectrometry files from humans, animals, and microbial culture systems. MicrobiomeMASST integrates monocultures, synthetic communities, and host-associated samples across multiple body sites and plants. MS/MS spectra can be queried to trace occurrence across hosts, experimental conditions, and interventions, enabling cross-study integration. We demonstrate this framework by contextualizing microbial-conjugated bile acids and interrogating microbiome-mediated drug metabolism. Screening gut bacteria revealed deprolylation of the angiotensin-converting enzyme (ACE) inhibitor prodrug enalapril. Using microbiomeMASST, we traced this metabolite across human cohorts, microbial isolates, environmental samples, and in Gorillas. Structural modeling and enzymatic assays showed that microbial deprolylation abolishes ACE inhibition, thereby inactivating its therapeutic effect. Together, microbiomeMASST links MS/MS spectra to biological context, converting isolated observations into an interpretable microbiome map for cross-study analysis.

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  Kermit Murray kkmurray.bsky.social · 10h
  (BioRxiv All) Bacterial exo-α-sialidases subvert the complement system through desialylation: The complement system is a central pillar of innate immunity, yet how bacterial glycan-modifying enzymes subvert complement function remains poorly understood. Bacterial sialidases… #BioRxiv #MassSpecRSS
  

  Bacterial exo-α-sialidases subvert the complement system through desialylation

  The complement system is a central pillar of innate immunity, yet how bacterial glycan-modifying enzymes subvert complement function remains poorly understood. Bacterial sialidases remove terminal sialic acids from host sialoglycans, but their direct impact on complement immunity is unclear. Here, we investigate the impact of six sialidases from five human pathogens on complement immunity using an integrated approach combining genetics, biochemistry, glycobiology, mass spectrometry, and structural biology. We demonstrate that major complement components (IgG, C1q, C4, and C5) and regulators (Factor I, Factor H, and C4bp) are sialylated, and that bacterial sialidase-mediated desialylation suppresses complement activation and surface deposition, thereby enabling complement evasion. Despite extensive sequence diversity, biochemical and structural analyses reveal that all examined sialidases share a conserved six-bladed {beta}-propeller catalytic domain and cleave both N-acetylneuraminic and N-glycolylneuraminic acids, the predominant mammalian sialic acids. Together, these findings uncover a conserved mechanism by which diverse bacterial pathogens disable complement immunity through desialylation.

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  Kermit Murray kkmurray.bsky.social · 14h
  (JASMS) [ASAP] Efficient and Cost-Effective Enzyme Deposition onto Tissues for Mass Spectrometry Imaging of N-Glycans Using a Mini-Humidifier: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00435 (RSS) #MassSpecRSS #JASMS
  

  [ASAP] Efficient and Cost-Effective Enzyme Deposition onto Tissues for Mass Spectrometry Imaging of N-Glycans Using a Mini-Humidifier

  Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00435

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  Kermit Murray kkmurray.bsky.social · 15h
  (ACS Anal Chem) [ASAP] Cyclic Peptide–Polymer Conjugate Characterization Using 193 nm Ultraviolet Photodissociation Tandem Mass Spectrometry: Analytical ChemistryDOI: 10.1021/acs.analchem.5c03375 #MassSpecRSS #ACSAChem
  

  [ASAP] Cyclic Peptide–Polymer Conjugate Characterization Using 193 nm Ultraviolet Photodissociation Tandem Mass Spectrometry

  Analytical ChemistryDOI: 10.1021/acs.analchem.5c03375

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  Kermit Murray kkmurray.bsky.social · 16h
  (BioRxiv All) Bootstrap resampling of mass spectral pairs with SpecReBoot reveals hidden molecular relationships: Mass spectral molecular networking (MN) has emerged as a key computational approach to organize and analyze the vast volumes of tandem mass spectrometry (MS/MS)… #BioRxiv #MassSpecRSS
  

  Bootstrap resampling of mass spectral pairs with SpecReBoot reveals hidden molecular relationships

  Mass spectral molecular networking (MN) has emerged as a key computational approach to organize and analyze the vast volumes of tandem mass spectrometry (MS/MS) data generated in natural product research. MN connections are based on mass spectral similarities derived from cosine-based scores or machine learning-based scores such as Spec2Vec and MS2DeepScore. These similarity scores are single, deterministic values and provide no estimate of the statistical robustness of the inferred mass spectral connections. As a result, molecular networks frequently contain edges arising from noise, missing fragments, or experimental variability, while, simultaneously, authentic chemical relationships remain hidden. To remedy this situation, here, we introduce SpecReBoot, a statistical framework that adapts Felsensteins bootstrap principle from phylogenetics to metabolomics. Within this framework, mass fragmentation peaks are treated as resampling units with replacement to generate pseudo-replicate spectra. Spectral similarities are recalculated across replicates, and the robustness of each edge between a pair of spectra is quantified by how frequently they appear as mutual top-k neighbors across bootstrap replicates. This approach generates bootstrap-derived confidence scores for every spectral connection, transforming mass spectral similarity from an absolute score into a distribution-based, confidence-aware measure. We show how, across public GNPS spectral library and natural products discovery case study datasets on bioactive metabolites produced by bacteria and fungi, SpecReBoot reliably identifies high-confidence spectral connections, filters unstable or noise-driven edges, and rescues chemically meaningful relationships that conventional metrics systematically miss. Applying SpecReBoot to study the polyketide-lactones produced by the endophytic fungus Diaporthe caliensis revealed previously hidden spectral relationships leading to the discovery of the novel caliensomycin macrolactone scaffold, biosynthetically and biochemically related to the bioactive phomol known polyketide present in D. caliensis. In conclusion, this study provides the first statistical framework for quantifying uncertainty in MS/MS mass spectral similarity. Due to its context-agnostic nature, we anticipate that our computational metabolomics framework can also be adopted across other disciplines like clinical and environmental metabolomics. Altogether, SpecReBoot introduces statistical rigor, improves reproducibility, thus enhancing molecular networking-based natural product discovery.

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  Kermit Murray kkmurray.bsky.social · 21h
  (J An Atom Spec) Thiol-Functionalized Magnetic Biochar as an Efficient Sorbent for Magnetic Dispersive Micro-SPE Coupled with ICP-MS Determination of Pb(II), Cd(II), and Hg(II) in Environmental Waters: J. Anal. At. Spectrom., 2026, Accepted Manuscript DOI:… #jaas #MassSpecRSS #AtomicSpec

  Thiol-Functionalized Magnetic Biochar as an Efficient Sorbent for Magnetic Dispersive Micro-SPE Coupled with ICP-MS Determination of Pb(II), Cd(II), and Hg(II) in Environmental Waters

  J. Anal. At. Spectrom., 2026, Accepted Manuscript DOI: 10.1039/D5JA00439J, PaperVu Thi Hoa, Van Cuong Nguyen A thiol-functionalized magnetic biochar (MB-SH) was synthesized and utilized as an efficient sorbent for magnetic dispersive micro-solid-phase extraction (MD-µSPE) coupled with inductively coupled plasma mass spectrometry (ICP-MS) for the simultaneous... The content of this RSS Feed (c) The Royal Society of Chemistry

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  Kermit Murray kkmurray.bsky.social · 23h
  (J Proteom) Prospective serial proteomic analysis uncovers mechanistic pathways of chemotherapy resistance in advanced non-small cell lung cancer: Publication date: Available online 5 February 2026 Source: Journal of Proteomics Author(s): Wei-Ke Kuo, Hsin-Yu Chu, Yen-Kun Ko,… #MassSpecRSS
  

  Prospective serial proteomic analysis uncovers mechanistic pathways of chemotherapy resistance in advanced non-small cell lung cancer

  Publication date: Available online 5 February 2026 Source: Journal of Proteomics Author(s): Wei-Ke Kuo, Hsin-Yu Chu, Yen-Kun Ko, Pang-Hung Hsu

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  Kermit Murray kkmurray.bsky.social · Feb 5
  (CEJ) Bimetallic MOFs With Enzyme‐Mimetic Active Sites for Nerve Agent Detoxification: Synergistic Insights Into Impeccable Performance From Experiment and Theory: Chemistry – A European Journal, EarlyView. (/CEJ)
  

  Bimetallic MOFs With Enzyme‐Mimetic Active Sites for Nerve Agent Detoxification: Synergistic Insights Into Impeccable Performance From Experiment and Theory

  Chemistry – A European Journal, EarlyView.

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