Mass spectrometry-based single-cell metabolomics and metabolic tracing analysis Publication date: July 2026 Source: TrAC Trends in Analytical Chemistry, Volume 200 Author(s): Xinying Zhu, Jia Yi, Liang Qiao

(TrAC) Mass spectrometry-based single-cell metabolomics and metabolic tracing analysis: Publication date: July 2026

Source: TrAC Trends in Analytical Chemistry, Volume 200

Author(s): Xinying Zhu, Jia Yi, Liang Qiao #TrAC #MassSpecRSS

SugarBase: mapping glycomolecule precursors in microbes Glycan biosynthesis relies on nucleotide-activated sugars, essential metabolites across all domains of life, yet their usage in microbes is poorly understood. Here we present SugarBase, a mass spectrometry and bioinformatic pipeline for untargeted exploration of microbial nucleotide sugar networks. SugarBase resolves the chemical complexity of microbial metabolism by combining narrow-window DIA fragmentation with a chemistry-informed parent ion identification algorithm. Applying SugarBase across a broad phylogenetic range of microbes revealed extensive, species-specific nucleotide sugar profiles, including many candidates with no existing annotation, generating the most comprehensive inventory of nucleotide sugars to date. SugarBase guided identification of gene clusters and allowed discrimination between pseudaminic- and legionaminic acid-producing strains, where genomic and proteomic data provided only ambiguous information. We resolved distinct nonulosonic acid profiles in several Campylobacter jejuni strains, sugars which may alter susceptibility towards distinct flagellotropic phages. We further identify previously undescribed CMP-activated higher-carbon ulosonic acids in Magnetospirillum, expanding the known chemical space in glycan biosynthesis. In summary, SugarBase supports scalable discovery of microbial nucleotide sugar pathways and enzymes, expanding access to chemically complex glycans and providing new targets for antimicrobial development.

(BioRxiv All) SugarBase: mapping glycomolecule precursors in microbes: Glycan biosynthesis relies on nucleotide-activated sugars, essential metabolites across all domains of life, yet their usage in microbes is poorly understood. Here we present SugarBase, a mass spectrometry… #BioRxiv #MassSpecRSS

diagFDR: Verifiable False Discovery Rate Reporting in Proteomics via Scope, Calibration, and Stability Diagnostics In mass spectrometry-based proteomics, false discovery rate (FDR) control underpins the credibility of peptide and protein identifications. In contemporary workflows, including multi-run Data Independent Acquisition (DIA), deep learning-assisted scoring, library-free searches, and extensive post-processing, the statement "1% FDR" has become increasingly ambiguous, potentially referring to different statistical entities, multiple-testing scopes, and null models. We propose a standardized framework requiring explicit specification of three complementary properties: "scope", meaning which statistical universe is controlled; "calibration", meaning whether confidence measures behave consistently with their intended interpretation on the reported unit; and "stability", meaning whether acceptance thresholds and resulting identification lists remain robust to perturbations. Building on routine target/decoy outputs, we introduce pipeline-agnostic diagnostics that audit internal coherence of scores, q-values, and posterior error probabilities, quantify tail support and cutoff fragility, and test plausibility of target-decoy assumptions. We further complement internal checks with external validation via entrapment, which measures empirical false positives on known absent sequences. We highlight a "granularity paradox": as scoring becomes more discriminative, decoy matches can become so sparse near stringent cutoffs that the numerical support for decoy-based estimation deteriorates, making reported FDR thresholds increasingly fragile despite improved separation between the distributions of target and decoy scores. Applications to DIA-NN and MS2Rescore show that scope and aggregation choices can materially alter both estimated error rates and list reproducibility. We provide a practical reporting checklist and an open-source R package (diagFDR, available from CRAN) that generates diagnostic reports from standard software outputs. As a minimal verifiable reporting standard, we recommend that any "FDR = alpha%" claim specify the controlled unit and scope, report tail support at the operating cutoff, and make decoy-inclusive outputs available for independent verification.

(BioRxiv All) diagFDR: Verifiable False Discovery Rate Reporting in Proteomics via Scope, Calibration, and Stability Diagnostics: In mass spectrometry-based proteomics, false discovery rate (FDR) control underpins the credibility of peptide and protein identifications. In… #BioRxiv #MassSpecRSS

Selective Hydrolytic Defluorination of Branched Perfluorooctanoic Acid Isomers by a Haloacid Dehalogenase Per- and polyfluoroalkyl substances (PFAS) are highly resistant to enzymatic C-F bond cleavage, and hydrolytic defluorination of long-chain PFAS has rarely been demonstrated. Here, we report selective hydrolytic defluorination of branched perfluorooctanoic acid (PFOA) isomers by a haloacid dehalogenase (4A) from Delftia acidovorans strain D4B. A fluoride-specific riboswitch biosensor was used for initial substrate screening, followed by scaled-up assays in which fluoride release was quantified using a fluoride ion-selective electrode. Defluorination products were subsequently identified by liquid chromatography-mass spectrometry (LC-MS). Although purified 4A (10 M) readily catalyzed hydrolytic defluorination of fluoroacetic acid, incubation of PFOA (0.5 mM) with purified 4A resulted in a statistically significant increase in fluoride release at elevated enzyme loading (500 M). High-resolution LC-MS/MS analysis revealed that defluorination products originated from minor branched PFOA isomers rather than linear PFOA. Molecular docking analyses supported catalytically plausible binding geometries for branched PFOA isomers, positioning the substrate -carbon within ~4 [A] of the catalytic aspartate residue. These findings demonstrate previously unrecognized hydrolytic reactivity of a haloacid dehalogenase toward branched PFAS isomers and expand the known catalytic scope of the haloacid dehalogenase family.

(BioRxiv All) Selective Hydrolytic Defluorination of Branched Perfluorooctanoic Acid Isomers by a Haloacid Dehalogenase: Per- and polyfluoroalkyl substances (PFAS) are highly resistant to enzymatic C-F bond cleavage, and hydrolytic defluorination of long-chain PFAS has rarely… #BioRxiv #MassSpecRSS

The inner nuclear membrane protein SUN1 regulates cullin-3 neddylation to maintain insulin signaling Metabolic dysfunction-associated steatotic liver disease (MASLD) is the most prevalent chronic liver disease and strongly linked to obesity and insulin resistance. We previously reported that the common nuclear envelope variant rs6461378 (g.842031C>T; SUN1 H118Y) associated with MASLD and related traits including insulin resistance. To gain insight into how wildtype (WT) and H118Y SUN1 might differentially impact insulin signaling, we performed affinity purification-mass spectrometry (AP-MS) in human liver-derived cells stably expressing WT or H118Y SUN1. Unbiased AP-MS revealed a novel SUN1-CUL3 interaction, with comparative analysis showing that WT SUN1 interacted robustly with CUL3, while CUL3 interaction was markedly diminished with H118Y SUN1. Cells in which SUN1 was silenced via siRNA, or in which H118Y SUN1 was ectopically expressed, showed increased CUL3 neddylation, which is required for cullin RING ligase (CRL)-mediated ubiquitination of insulin receptor substrate (IRS) proteins. Inhibition of neddylation restored IRS-1 levels and insulin signaling in H118Y SUN1-expressing cells. Together, our findings provide a potential mechanism of H118Y SUN1-driven insulin resistance and a viable therapeutic approach for its reversal.

(BioRxiv All) The inner nuclear membrane protein SUN1 regulates cullin-3 neddylation to maintain insulin signaling: Metabolic dysfunction-associated steatotic liver disease (MASLD) is the most prevalent chronic liver disease and strongly linked to obesity and insulin… #BioRxiv #MassSpecRSS

[ASAP] Changes to the JASMS Associate Editor Team: Farewell and Welcome Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00098

(JASMS) [ASAP] Changes to the JASMS Associate Editor Team: Farewell and Welcome: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00098 (RSS) #MassSpecRSS #JASMS

[ASAP] Direct Identification of Microplastics by Ambient Pyrolysis Electrospray Ionization Mass Spectrometry Analytical ChemistryDOI: 10.1021/acs.analchem.6c00938

(ACS Anal Chem) [ASAP] Direct Identification of Microplastics by Ambient Pyrolysis Electrospray Ionization Mass Spectrometry: Analytical ChemistryDOI: 10.1021/acs.analchem.6c00938 #MassSpecRSS #ACSAChem

Boosting NADP-malic enzyme 1 enhances seed vigor and longevity in Arabidopsis thaliana Seed longevity is a key determinant of crop establishment, productivity, and germplasm conservation. During storage and germination, reactive oxygen species accumulate and contribute to seed aging through oxidative damage and loss of viability. The maintenance of redox homeostasis therefore relies on NADPH-dependent antioxidant systems, which require a continuous supply of reducing power. NADP-dependent malic enzyme 1 (NADP-ME1), represents a source of NADPH supporting antioxidant defense during seed aging. Here, we show that enhanced expression of NADP-ME1 positively contributes to seed vigor and longevity in Arabidopsis thaliana. NADP-ME1 overexpression lines exhibited faster germination and higher overall germination after accelerated aging, whereas knockout mutants showed markedly reduced germination performance. Enhanced post-aging vigor in the overexpression lines was associated with reduced oxidative damage as indicated by lower malondialdehyde and hydrogen peroxide accumulation, along with preservation of specific polyunsaturated fatty acids, and increased {gamma}-tocopherol levels in aged dry seeds. Enhanced expression of NADP-ME1 reshapes the transcriptome of germinated seeds under fresh conditions compared with the wild type, while only minimal differences between genotypes are detected in aged seeds. These results suggest that NADP-ME1 contributes to the establishment of a transcriptional state associated with enhanced seed vigor and improved post-aging germination. Finally, co-immunoprecipitation coupled to mass spectrometry and bimolecular fluorescence complementation identified aspartate aminotransferase 2 as a NADP-ME1 interactor, pointing to a link between malate metabolism and amino acid-related metabolic adjustment. Together, these results identify NADP-ME1 as a determinant of seed resilience to aging and a potential target for improving seed quality.

(BioRxiv All) Boosting NADP-malic enzyme 1 enhances seed vigor and longevity in Arabidopsis thaliana: Seed longevity is a key determinant of crop establishment, productivity, and germplasm conservation. During storage and germination, reactive oxygen species accumulate and… #BioRxiv #MassSpecRSS

Establishment of a Purge and Trap Continuous‐Flow Isotope Ratio Mass Spectrometer System for Analysis of Stable Nitrate Isotopes (δ15N and δ18O) in Water Samples by Ti(III) Reduction ABSTRACT Rationale Pollution of surface and shallow groundwater by nitrate (NO3−$$ {\mathrm{NO}}_3^{-} $$) is a global concern, resulting in the deterioration of drinking water quality. Stable isotopes of NO3−$$ {\mathrm{NO}}_3^{-} $$ (δ15N and δ18O) can be used to trace its sources and identify prevailing biogeochemical processes. Methods Conversion of aqueous NO3−$$ {\mathrm{NO}}_3^{-} $$ to N2O headspace gas by Ti(III) reduction is a new method for analysis of NO3−$$ {\mathrm{NO}}_3^{-} $$ stable isotopes. Previous literature introduces the analytical procedure but provides limited guidelines for instrument set-up and operation. Here, we present an automated purge-and-trap isotope ratio mass spectrometer (P&T-IRMS) combined with the Ti(III) reduction method for analysis of δ15N and δ18O in NO3−$$ {\mathrm{NO}}_3^{-} $$. Results The P&T-IRMS base analytical precision was ±0.3‰ and ±0.2‰ for δ15N and δ18O, respectively. The limit of quantification (LOQ) for the N2O gas standard was 1 μL L−1 (1.1 nmol N2O-N) for both δ15N and δ18O. The NO3−-N$$ {\mathrm{NO}}_3^{-}\hbox{-} \mathrm{N} $$ range for accurate measurement was 0.2–0.3 mg L−1 (3.3–6.6 nmol). Based on the logarithmic trend of the N2O peak area vs. R15N/14N and R18O/16O, δ15N and δ18O corrections are presented for values outside the range of accuracy. A comparison of δ15N and δ18O from P&T-IRMS and Ti(III) reduction measurements with EA-IRMS values showed high accuracy. The measurement precision and uncertainties for our KNO3−$$ {\mathrm{KNO}}_3^{-} $$ internal standard were ±0.2 (±0.6) and ±0.2 (±0.9) for δ15N and δ18O, respectively. Conclusion The P&T-IRMS and Ti(III) reduction method demonstrated acceptable accuracy and precision, similar to well-established methods for analysis of NO3−$$ {\mathrm{NO}}_3^{-} $$ stable isotopes. This publication will assist laboratories which utilize IRMS headspace gas instrumentation with the process of IRMS set-up and operation, establishment of an independent analytical procedure for the Ti(III) reduction method, and data evaluation and correction.

(RCM) Establishment of a Purge and Trap Continuous‐Flow Isotope Ratio Mass Spectrometer System for Analysis of Stable Nitrate Isotopes (δ15N and δ18O) in Water Samples by Ti(III) Reduction: ABSTRACT




Rationale




Pollution of surface and shallow groundwater… #RapidCommunMassSpectrom #MassSpecRSS

An N-degron proteolytic pathway modulates recipient susceptibility to T6SS DNase effectors The type VI secretion system (T6SS) is a contractile nanoweapon widely employed by Gram-negative bacteria to gain competitive advantages by injecting effector proteins into recipient cells. Although the biochemical activities of T6SS effectors have been well characterized, how recipient factors modulate effector toxicity remains poorly understood. Using Agrobacterium C58 as a model, previous work identified the Escherichia coli ClpAP protease as a recipient susceptibility (RS) factor that enhances T6SS-mediated interbacterial competition. Agrobacterium C58 deploys two DNase effectors, Tde1 and Tde2, as the major antibacterial weapon. Here, we demonstrate that the recipient ClpAP protease and its adaptor ClpS enhanced C58-mediated interbacterial competition in a Tde2-dependent manner in both intra- and interspecies competition. Ectopic expression of Tde2 in E. coli caused growth inhibition and DNA cleavage in the presence of a functional ClpAPS protease complex, but not in any of the clpP, clpA or clpS mutants. Notably, Tde2 accumulated in these mutants but not in wild-type cells, whereas a catalytic variant accumulated regardless of ClpAPS status, suggesting that Tde2 is not directly degraded by ClpAPS. Instead, Tde2 depends on ClpAPS for full toxicity, likely through degradation of inhibitory N-degron substrate(s). Affinity purification of His-tagged Tde2 in a clpP mutant background, followed by mass spectrometry, identified eight N-degron substrate candidates. Tde2-mediated interbacterial competition was significantly reduced by overexpression of three candidates. Among them, the Tde2 DNase domain directly associated with guanosine 5'-monophosphate reductase GuaC, supporting a model in which Tde2 toxicity is blocked by binding of GuaC. Collectively, our findings reveal an unanticipated layer of recipient-mediated regulation in T6SS competition and highlight proteolytic control of inhibitory substrates as a determinant of bacterial susceptibility during interbacterial conflict.

(BioRxiv All) An N-degron proteolytic pathway modulates recipient susceptibility to T6SS DNase effectors: The type VI secretion system (T6SS) is a contractile nanoweapon widely employed by Gram-negative bacteria to gain competitive advantages by injecting effector proteins… #BioRxiv #MassSpecRSS

A Time-Efficient Cyclic Ion Mobility Spectrometry−Mass Spectrometry method for the Separation and Detection of Ergot Alkaloids Publication date: Available online 18 April 2026 Source: Analytica Chimica Acta Author(s): Laura Carbonell-Rozas, Ane Arrizabalaga-Larranaga, Laura Righetti

(ACA) A Time-Efficient Cyclic Ion Mobility Spectrometry−Mass Spectrometry method for the Separation and Detection of Ergot Alkaloids: Publication date: Available online 18 April 2026

Source: Analytica Chimica Acta

Author(s): Laura Carbonell-Rozas, Ane… #AChimActa #MassSpecRSS

[ASAP] Top-Down Proteomics of Zebrafish Brain Regions Using Capillary Zone Electrophoresis-Tandem Mass Spectrometry Journal of Proteome ResearchDOI: 10.1021/acs.jproteome.6c00007

(J Proteom Res) [ASAP] Top-Down Proteomics of Zebrafish Brain Regions Using Capillary Zone Electrophoresis-Tandem Mass Spectrometry: Journal of Proteome ResearchDOI: 10.1021/acs.jproteome.6c00007 #MassSpecRSS

(IJMS) “Application of trichloroacetimidate-mediated benzylation to the detection of pinacolyl methylphosphonic acid in standardised proficiency test matrices”: Publication date: Available online 17 April 2026

Source: International Journal of Mass Spectrometry

Author(s): Saphon… #ijms #MassSpecRSS

[ASAP] Native Top-Down Mass Spectrometry Combined with High-Resolution Charge Variant Analysis of Trastuzumab Originator and Biosimilars Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00438

(JASMS) [ASAP] Native Top-Down Mass Spectrometry Combined with High-Resolution Charge Variant Analysis of Trastuzumab Originator and Biosimilars: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00438 (RSS) #MassSpecRSS #JASMS

[ASAP] Quantitative Host Cell Protein Analysis of Antibody-Based Protein Therapeutics Using the Orbitrap Astral Mass Spectrometer Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00272

(JASMS) [ASAP] Quantitative Host Cell Protein Analysis of Antibody-Based Protein Therapeutics Using the Orbitrap Astral Mass Spectrometer: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00272 (RSS) #MassSpecRSS #JASMS

Editorial for the Special Honor Issue Honoring Dr. Carlito B. Lebrilla Mass Spectrometry Reviews, EarlyView.

(MS Reviews) Editorial for the Special Honor Issue Honoring Dr. Carlito B. Lebrilla: Mass Spectrometry Reviews, EarlyView. #MassSpectromRev #MassSpecRSS

Personal Reflection on Dr. Carlito Lebrilla Mass Spectrometry Reviews, EarlyView.

(MS Reviews) Personal Reflection on Dr. Carlito Lebrilla: Mass Spectrometry Reviews, EarlyView. #MassSpectromRev #MassSpecRSS

[ASAP] Label-Free High-Throughput Screening of CYP3A4 Inhibitors Using Acoustic Ejection Mass Spectrometry Analytical ChemistryDOI: 10.1021/acs.analchem.5c08059

(ACS Anal Chem) [ASAP] Label-Free High-Throughput Screening of CYP3A4 Inhibitors Using Acoustic Ejection Mass Spectrometry: Analytical ChemistryDOI: 10.1021/acs.analchem.5c08059 #MassSpecRSS #ACSAChem

Ion–Molecule Reaction Products as Probes and Precursors for Preparative Mass Spectrometry Chemistry – A European Journal, Volume 32, Issue 14, 15 April 2026.

(CEJ) Ion–Molecule Reaction Products as Probes and Precursors for Preparative Mass Spectrometry: Chemistry – A European Journal, Volume 32, Issue 14, 15 April 2026. (/CEJ)

Copper(II), a Peculiar Metal Ion for Complexation With Monensin A Ionophore Chemistry – A European Journal, Volume 32, Issue 14, 15 April 2026.

(CEJ) Copper(II), a Peculiar Metal Ion for Complexation With Monensin A Ionophore: Chemistry – A European Journal, Volume 32, Issue 14, 15 April 2026. (/CEJ)

Bridging VPDB and VPDB‐LSVEC: Updated Carbon Isotope Delta Values and Improved Uncertainties for NRC Certified Reference Materials Rapid Communications in Mass Spectrometry, Volume 40, Issue 14, 30 July 2026.

(RCM) Bridging VPDB and VPDB‐LSVEC: Updated Carbon Isotope Delta Values and Improved Uncertainties for NRC Certified Reference Materials: Rapid Communications in Mass Spectrometry, Volume 40, Issue 14, 30 July 2026. #RapidCommunMassSpectrom #MassSpecRSS

Meat Speciation via Deployable Atmospheric Solid Analysis Probe Mass Spectrometry (ASAP‐MS) Using Prototype RADIAN‐ASAP ABSTRACT Rationale Food fraud, particularly meat adulteration, poses risks to consumer trust, public health, and regulatory compliance. Existing detection methods are often slow and require complex preparation. There is a need for rapid, reliable, and accessible analytical approaches to verify meat authenticity in both laboratory and field settings. Methods Atmospheric Solid Analysis Probe Mass Spectrometry (ASAP-MS) was used for direct analysis of meat samples with minimal preparation. Spectral data from seven meat species were processed using chemometric modelling to build a classification system. The model was validated using laboratory-prepared mixed meat samples and subsequently applied to commercial processed products and ready meals. Results The developed model successfully differentiated seven meat species and detected adulteration at levels as low as 5% in mixed samples. Analysis time was under 5 min per sample. When applied to commercial products, the method achieved 100% agreement with declared labelling, demonstrating high accuracy and robustness across different sample types. Conclusions This study demonstrates that ASAP-MS combined with chemometric modelling provides a fast, accurate and minimally invasive approach for meat speciation. Its speed and potential portability make it well suited for real-time, field-based testing, offering a valuable tool to enhance food authenticity monitoring and consumer protection.

(RCM) Meat Speciation via Deployable Atmospheric Solid Analysis Probe Mass Spectrometry (ASAP‐MS) Using Prototype RADIAN‐ASAP: ABSTRACT




Rationale




Food fraud, particularly meat adulteration, poses risks to consumer trust, public health, and regulatory… #RapidCommunMassSpectrom #MassSpecRSS

ARMH3 acts as a central scaffold at the Golgi/TGN through interactions with Arl5, GBF1, and PI4KB The armadillo repeat protein ARMH3 regulates the activity and localisation of the Golgi resident lipid kinase phosphatidylinositol 4 kinase III{beta} (PI4KB) and the Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 (GBF1) that activates Arf1. ARMH3 localises to the trans Golgi network (TGN) via the GTPase Arl5. We used hydrogen deuterium exchange mass spectrometry (HDX-MS) and AI-enabled modeling to define the interfaces of ARMH3 with its binding partners Arl5, PI4KB, and GBF1. The ARMH3-Arl5 interface was determined to consist of the N and C termini of ARMH3, with Arl5 binding causing conformational changes in ARMH3 located at a shared PI4KB/GBF1 interface. Both PI4KB and GBF1 form mutually exclusive complexes with ARMH3, with GBF1 binding to ARMH3 through a disordered loop we have named the ARMH3 binding region (ABR). The ARMH3 interfaces in PI4KB and GBF1 contain phosphosites, with the phosphomimetic mutation of GBF1 blocking complex formation. These findings provide new insights into the role of ARMH3 as a master coordinator of GTPase and phosphoinositide signaling at the Golgi/TGN.

(BioRxiv All) ARMH3 acts as a central scaffold at the Golgi/TGN through interactions with Arl5, GBF1, and PI4KB: The armadillo repeat protein ARMH3 regulates the activity and localisation of the Golgi resident lipid kinase phosphatidylinositol 4 kinase III{beta} (PI4KB) and… #BioRxiv #MassSpecRSS

Native entanglement misfolding contributes to age-associated structural changes across the Saccharomyces cerevisiae proteome Aging at the subcellular level involves the simultaneous decline in the cell's ability to maintain protein homeostasis and rise in misfolded proteins through a positive feedback loop. Here, we test if a widespread class of protein misfolding could contribute to proteome aging by examining if statistical associations exist between age-related changes in protein structure, measured by limited proteolysis mass spectrometry data of the aging Saccharomyces cerevisiae proteome, with structural annotations and molecular simulations. We find that globular proteins that are likely to exhibit entanglement misfolding are 121% more likely to exhibit age-related structural changes, and these changes are 59% more likely to be localized to natively entangled regions. Proteins containing native entanglements are seven-fold more likely to misfold, according to simulations, and populate long-lived, near-native misfolded states. Thus, the age-related structural changes in yeast proteins can be explained in part by the accumulation of misfolded proteins involving entanglements.

(BioRxiv All) Native entanglement misfolding contributes to age-associated structural changes across the Saccharomyces cerevisiae proteome: Aging at the subcellular level involves the simultaneous decline in the cell's ability to maintain protein homeostasis and rise in… #BioRxiv #MassSpecRSS

[ASAP] Conformational Dynamics of Amylin Receptors Revealed by Hydrogen–Deuterium Exchange Mass Spectrometry Journal of the American Chemical SocietyDOI: 10.1021/jacs.5c20644

(J Am Chem Soc) [ASAP] Conformational Dynamics of Amylin Receptors Revealed by Hydrogen–Deuterium Exchange Mass Spectrometry: Journal of the American Chemical SocietyDOI: 10.1021/jacs.5c20644 #JAmChemSoc #MassSpecRSS

[ASAP] Avoiding False Identification of 7-Hydroxymitragynine in Kratom Products Using a Multicriteria LC–MS Confirmation Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00088

(JASMS) [ASAP] Avoiding False Identification of 7-Hydroxymitragynine in Kratom Products Using a Multicriteria LC–MS Confirmation: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00088 (RSS) #MassSpecRSS #JASMS

Mechanism of Baxian Huazhuo Decoction in the Treatment of Gouty Arthritis Based on Network Pharmacology, Molecular Docking, and Experimental Verification ABSTRACT The global prevalence of gout continues to rise. Baxian Huazhuo Decoction (BHD) has demonstrated significant efficacy in the clinical treatment of acute gouty arthritis (AGA); however, its mechanism of action remains unclear. This study first employed network pharmacology analysis to identify the key components, targets, and pathways of BHD against AGA. Molecular docking studies validated the binding affinity between the components of BHD and their potential targets. Ultrahigh-performance liquid chromatography–high-resolution mass spectrometry (UHPLC–HRMS) was utilized to identify the active components in BHD and elucidate their fragmentation pathways. Subsequently, a monosodium urate crystal–induced AGA rabbit model was established to evaluate the in vivo therapeutic efficacy of BHD. The results revealed 62 predicted active components and 268 target molecules in BHD, identifying core constituents such as gentiopicroside, limonin, and indirubin, which exhibited high affinity for targets including MAPK1, PPARG, and IL-6. In vivo experiments confirmed that BHD significantly suppressed the phosphorylation of MAPK1, reduced the levels of pro-inflammatory factors such as TNF-α and IL-6, mitigated synovial damage, and inhibited the activation of the PI3K-Akt signaling pathway. This study systematically elucidates the pharmacological basis and mechanisms of action of BHD in the treatment of AGA, providing a scientific basis for its clinical application.

(Biomed Chrom) Mechanism of Baxian Huazhuo Decoction in the Treatment of Gouty Arthritis Based on Network Pharmacology, Molecular Docking, and Experimental Verification: ABSTRACT




The global prevalence of gout continues to rise. Baxian Huazhuo Decoction (BHD) has… #massSpecRSS #biomedchrom

[ASAP] Noncontact Extraction Mass Spectrometry with Bubble Extraction Ionization Facilitates Operando Monitoring Electrochemical Reactions Analytical ChemistryDOI: 10.1021/acs.analchem.6c01350

(ACS Anal Chem) [ASAP] Noncontact Extraction Mass Spectrometry with Bubble Extraction Ionization Facilitates Operando Monitoring Electrochemical Reactions: Analytical ChemistryDOI: 10.1021/acs.analchem.6c01350 #MassSpecRSS #ACSAChem

Detecting misfolded non-covalent lasso entanglements in protein structures, simulation trajectories, and mass spectrometry data A previously overlooked class of protein entanglements, non-covalent lasso entanglements (NCLEs), has been found to play a role in widespread protein misfolding. However, understanding the influence NCLEs have on biological processes is hindered by the absence of dedicated algorithms and computational tools to detect and characterize these geometries in protein structures, molecular dynamics simulations, and in comparison to experimental data from limited proteolysis (LiP) and cross-linking (XL) mass spectrometry (MS). Here, we present EntDetect, a software tool designed to: (1) identify non-redundant NCLEs in protein structures, (2) detect misfolded states by comparing NCLE changes through pairwise comparisons of structures, (3) extract structural ensembles consistent with experimental signals from LiP-MS and XL-MS, and (4) investigate proteome-wide protein misfolding using high-throughput MS data. We demonstrate the utility of EntDetect on a simulated structural ensemble of phosphoglycerate kinase (PGK), alongside corresponding LiP- and XL-MS experimental data. Additionally, we detail the application of EntDetect to detect misfolding associated with native NCLEs on a proteome-wide MS dataset and select candidate proteins for further investigation. This protocol is intended for biophysicists, structural biologists, and molecular biologists with domain knowledge of protein structure, mass spectrometry proteomics data, and beginner experience with Python who want to interpret their experimental observations and computer simulations results through the presence and potential misfolding of NCLE topologies. EntDetect is open-source and freely available (https://github.com/obrien-lab-psu/EntDetect). NCLEweb is also available which is a webserver that identifies NCLEs within a given user-uploaded structure (https://www.ncleweb.org/).

(BioRxiv All) Detecting misfolded non-covalent lasso entanglements in protein structures, simulation trajectories, and mass spectrometry data: A previously overlooked class of protein entanglements, non-covalent lasso entanglements (NCLEs), has been found to play a role in… #BioRxiv #MassSpecRSS

A Novel Heterometallic Ring {Cr5Ni3} and New {Cr6Co2} and {Cr6Zn2} Rings Chemistry – A European Journal, EarlyView.

(CEJ) A Novel Heterometallic Ring {Cr5Ni3} and New {Cr6Co2} and {Cr6Zn2} Rings: Chemistry – A European Journal, EarlyView. (/CEJ)