Kermit Murray

Characterization of aliA and aliB deletion mutants reveals a dominant role of AliA in Haloferax volcanii lipoprotein lipidation Protein lipidation is a widespread strategy for anchoring proteins to cellular membranes across all domains of life, yet the mechanisms underlying this process in archaea remain poorly understood. Recently, the first archaeal enzymes involved in lipobox-containing protein (lipoprotein) biogenesis, AliA and AliB, were identified and characterized in the model archaeon Haloferax volcanii. Although these paralogs share significant sequence similarity, distinct deletion phenotypes suggest differences in their substrate specificity and function. Here, we employed large-scale Triton X-114 fractionation followed by quantitative proteomics and lipid-specific mass spectrometry to systematically analyze AliA- and AliB-dependent lipoprotein lipidation. Deletion of aliA affected substantially more lipoproteins in Hfx. volcanii than deletion of aliB, markedly diminishing their TX-114 enrichment--indicating reduced hydrophobicity--and abolishing thioether-linked archaeol modification. This establishes AliA as the primary enzyme responsible for archaeal lipoprotein lipidation. In contrast, deletion of aliB affected only a small subset of lipoproteins and did not significantly reduce thioether-linked archaeol levels. In addition to defining distinct and non-redundant roles for AliA and AliB, this study provides the first large-scale experimental validation of predicted archaeal lipoproteins and identifies candidate components of the archaeal lipoprotein biogenesis pathway, substantially advancing mechanistic understanding and enabling improved lipoprotein prediction in this previously underexplored field.

(BioRxiv All) Characterization of aliA and aliB deletion mutants reveals a dominant role of AliA in Haloferax volcanii lipoprotein lipidation: Protein lipidation is a widespread strategy for anchoring proteins to cellular membranes across all domains of life, yet the… #BioRxiv #MassSpecRSS

(Analyst) Separating O-desmethylvenlafaxine and tramadol enantiomers using two-dimensional chiral LC × DMS mass spectrometry: Analyst, 2026, Advance Article
DOI: 10.1039/D6AN00119J, Paper Open Access &nbsp This article is licensed under a Creative Commons Attribution 3.0… (RSS) #MassSpecRSS #analyst

Structural dynamics and immunogenicity of the recombinant and outer membrane vesicle-embedded Meningococcal antigen NadA #nature #MassSpecRSS

(RSC A Meth) The analysis of 80 simple saccharides by ion chromatography mass spectrometry: Anal. Methods, 2026, Advance Article
DOI: 10.1039/D5AY01489A, Paper Open Access &nbsp This article is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported Licence.Hans S. A.… #MassSpecRSS

(J An Atom Spec) Enhanced ion utilization efficiency in IMS-TOFMS using a novel gate-free traveling wave ion guide: J. Anal. At. Spectrom., 2026, Accepted Manuscript
DOI: 10.1039/D5JA00415B, PaperZhekun Wang, Zhongjun Zhao, Zhihao He, Xiaoqin Jiang, Yanting Yang,… #jaas #MassSpecRSS #AtomicSpec

(J Chrom B) Ultrahigh performance liquid chromatography mass spectrometry for the determination of azithromycin in canine serum and skin tissue: Publication date: Available online 11 March 2026

Source: Journal of Chromatography B

Author(s): Apurva Patil, Michaela Austel,… #JChrom #MassSpecRSS

Advanced Phosphoproteomics Depth and Quantitative Performance Using an Integrated noFAIMS–FAIMS Approach ABSTRACT Rationale Protein phosphorylation plays a central role in regulating cellular signaling, and its dysregulation is closely linked to diseases such as cancer and neurodegeneration. Mass spectrometry–based phosphoproteomics allows comprehensive mapping of phosphorylation; however, detecting low-abundance and poor ionization phosphopeptides remains a challenge. High-field asymmetric waveform ion mobility spectrometry (FAIMS) offers orthogonal gas-phase fractionation, enhancing phosphopeptide detection. However, FAIMS and conventional non-FAIMS (noFAIMS) analyses often identify partially overlapping yet complementary subsets of phosphopeptides. This suggests that integrating both approaches could significantly increase the depth of phosphoproteomic analysis. Methods Phosphopeptide samples were analyzed using a Vanquish Neo UHPLC system coupled to an Orbitrap Eclipse Tribrid mass spectrometer. Using parallel reaction monitoring (PRM) on a panel of 200 synthetic phosphopeptides, we assessed ionization efficiencies under noFAIMS conditions and at six different FAIMS compensation voltages (CVs). The integrated noFAIMS and FAIMS approach was further evaluated using enriched phosphopeptide samples from HEK293 and HeLa cells, analyzed by data-dependent acquisition (DDA). Results The integrated noFAIMS–FAIMS approach resulted in a substantial increase in phosphopeptide identifications (14.9%–46.5%) compared with either the noFAIMS or FAIMS method alone. This integrated approach also exhibited high reproducibility across technical and biological replicates. Importantly, the integrated approach expanded the coverage of key signaling pathways such as EGF/EGFR, VEGFA–VEGFR2, and PI3K–AKT, by capturing phosphoproteins identified exclusively in either dataset. Conclusions This study demonstrates that an integrated noFAIMS–FAIMS approach significantly enhances phosphoproteomic depth and quantification by leveraging the complementary advantages of each method. By capturing unique phosphopeptides from each analysis, this strategy can be a practical and efficient phosphoproteomic approach, providing deeper insights into cellular signaling pathways.

(RCM) Advanced Phosphoproteomics Depth and Quantitative Performance Using an Integrated noFAIMS–FAIMS Approach: ABSTRACT




Rationale




Protein phosphorylation plays a central role in regulating cellular signaling, and its dysregulation is closely linked to… #RapidCommunMassSpectrom #MassSpecRSS

ESI–MS/MS Characterisation of Phenolic Reaction Products of Nitrogen Mustards and N,N‐Dialkylaminoethyl‐2‐Chlorides and Their Rapid Screening by LC–MS/MS in Neutral Loss Scan Mode ABSTRACT Rationale Nitrogen mustards (HN1, HN2 and HN3) and N,N-dialkylaminoethyl-2-chlorides (where alkyl = methyl, ethyl, isopropyl, or propyl) contain reactive chloride bonds that react with phenol in environmental samples to form phenolic reaction products. Identifying these products is crucial for the Chemical Weapons Convention (CWC) verification, as they serve as markers for the presence of scheduled chemicals. Methods Phenolic reaction products of nitrogen mustards (1–3) and N,N-dialkylaminoethyl-2-chlorides (4–13) were analysed using direct ESI–MS and LC–ESI–MS/MS on an Agilent Q-TOF system. Product ion spectra for [M + H]+ ions (1–13) were collected at varied collision energies. Isomers were separated via LC with an Agilent Eclipse AAA column and gradient elution. A targeted LC–MS/MS in neutral-loss scan (94 u) method was developed and validated for rapid screening of compounds 1–13 in a complex aqueous sample. Results Distinct product ions observed in the MS/MS spectra of 1–13 enabled structural characterisation and differentiation between isomers. Major fragmentation involved loss of a phenol (94 u) and C–C bond cleavages, which were influenced by the structure and size of the alkyl groups. A neutral loss scan LC–MS/MS method was developed for rapid screening of 1–13 at low levels (LOD ~ 10 ppb; LOQ ~ 30 ppb), even within complex matrices. Conclusions Phenolic reaction products of nitrogen mustards and N,N-dialkylaminoethyl-2-chlorides were comprehensively characterised, including isomer differentiation, through their ESI–MS/MS product ion spectra. The validated LC–MS/MS neutral-loss scan method enabled efficient screening of these markers in complex samples. These LC–MS/MS methods are highly valuable for OPCW proficiency testing and CWC verification programs.

(RCM) ESI–MS/MS Characterisation of Phenolic Reaction Products of Nitrogen Mustards and N,N‐Dialkylaminoethyl‐2‐Chlorides and Their Rapid Screening by LC–MS/MS in Neutral Loss Scan Mode: ABSTRACT




Rationale




Nitrogen mustards (HN1, HN2 and HN3) and… #RapidCommunMassSpectrom #MassSpecRSS

Domino Polymerization for the Synthesis of Reductively Degradable Poly(disulfide)s With Arbitrary Side‐Chain Structures We developed a novel domino polymerization to synthesize reductively degradable poly(disulfide)s with tunable side chains. A novel monomer bearing thiolactone and pyridyl disulfide groups reacts with various amines, enabling continuous ring-opening and disulfide exchange. The resulting polymers show reductive degradability, pH-responsive solubility, and can form degradable gels, offering versatile applications. ABSTRACT The environmental persistence of conventional plastics has driven the development of degradable polymers with functional versatility. Poly(disulfide)s are particularly attractive due to their reductive degradability and environmentally triggered disassembly. In this study, we report a domino polymerization strategy that enables the rapid and modular synthesis of functional poly(disulfide)s with degradable main chains and diverse side-chain structures. This method utilizes a single monomer, N-(2-oxotetrahydrothiophen-3-yl)-3-(pyridin-2-yldisulfanyl)propanamide (PDTL), which contains both thiolactone (TL) and pyridyl disulfide (PDS) moieties. Polymerization is initiated by TL ring-opening with commercially available amines, generating thiol groups that undergo disulfide exchange with PDS moieties of other monomers, resulting in chain propagation. The method accommodates primary, secondary amines, and ammonia, allowing incorporation of alkyl, allyl, propargyl, hydroxyl, carboxyl, amide, and tertiary amine functionalities. The reductive degradability of the poly(disulfide)s is confirmed using gel permeation chromatography and mass spectrometry. Furthermore, it is found that pH-responsive properties appear in poly(disulfide)s possessing dimethylamino groups, where water solubility can be regulated in response to pH. Domino polymerization is further applied to synthesize reductively degradable poly(disulfide) gels using multi-functional amines. This polymerization technique will lead to the development of reductively degradable polymers with various functions for use in various applications in the future.

(Angew Chem) Domino Polymerization for the Synthesis of Reductively Degradable Poly(disulfide)s With Arbitrary Side‐Chain Structures: We developed a novel domino polymerization to synthesize reductively degradable poly(disulfide)s with tunable side chains. A novel… (RSS) #AngewChem #MassSpecRSS

PhosSight: a Unified Deep Learning Framework Boosting and Accelerating Phosphoproteome Identification to Enable Biological Discoveries Protein phosphorylation is a key regulator of signaling, with mass spectrometry (MS) based phosphoproteomics serving as the premier technology for its analysis. However, phosphorylation profiling is hindered by acquisition biases: Data-Dependent Acquisition (DDA) suffers from stochastic undersampling and missing values, while Data-Independent Acquisition (DIA) faces computational bottlenecks and inefficiencies from vast spectral libraries. We present PhosSight, a unified deep learning framework designed to augment identification depth and accelerate search efficiency. PhosSight features PhosDetect, a model that explicitly encodes phosphorylation specific physicochemical features to accurately predict peptide detectability. For DDA, PhosSight leverages predicted retention time, fragment intensity, and detectability to refine site localization and rescoring, recovering marginal, low-abundance spectra. For DIA, PhosSight utilizes detectability-guided library pruning to remove non-detectable noise, accelerating search speeds without compromising sensitivity. Benchmarking on synthetic and real world datasets confirms PhosSight's superior performance in both modes. Applying PhosSight to a large-scale Uterine Corpus Endometrial Carcinoma (UCEC) cohort significantly reduced missing values and expanded the quantifiable phosphoproteome. This enhanced completeness enabled the discovery of novel prognosis associated kinase targets, such as MARK2, underscoring PhosSight as a powerful tool for biological discovery in precision oncology.

(BioRxiv All) PhosSight: a Unified Deep Learning Framework Boosting and Accelerating Phosphoproteome Identification to Enable Biological Discoveries: Protein phosphorylation is a key regulator of signaling, with mass spectrometry (MS) based phosphoproteomics serving as the… #BioRxiv #MassSpecRSS

From Stress to Survival: Trophoblast-Derived Extracellular Vesicle Proteome Captures Aspirin-Driven Cellular Reprogramming in a Preeclampsia Model. Background: Low-dose aspirin (LDA) reduces preeclampsia (PE) risk by up to 40%, yet its molecular effects on chorion trophoblast cells (CTCs) a fetal membrane lineage at the feto-maternal interface remain obscure. CTCs form a structural and immunoregulatory barrier whose dysfunction drives inflammation-associated membrane pathology in PE. Extracellular vesicles (EVs) released by CTCs may encode cellular stress and adaptation states, offering a molecular window into aspirin's timing-dependent effects on PE risk modification. Methods: Human CTCs were challenged with cigarette smoke extract (CSE) to model oxidative stress-driven PE pathology. Two paradigms were tested: (1) prophylactic aspirin (4 and 40 ug/ml) before and/or flanking CSE, and (2) therapeutic aspirin after CSE challenge. EVs were isolated via ultracentrifugation and size exclusion chromatography, characterized by nanoparticle tracking and immunoblotting, and profiled by quantitative mass spectrometry. Network pathway analysis and machine-learning biomarker selection defined EV-encoded molecular states. Results: CTC-derived EVs from CSE-exposed cells carried a PE-like proteomic signature marked by suppressed VEGF/ECM remodeling, activated TNF-p53 apoptotic signaling, and heightened inflammation. Prophylactic low-dose aspirin shifted EV cargo toward preserved angiogenic capacity (VEGFA, COL1A1, MMP14) with attenuated apoptotic and NF-kB signatures. High-dose aspirin produced broad transcriptional suppression without vascular benefit in EVs. Therapeutic aspirin partially rescued injury-associated EV cargo but failed to restore angiogenic signatures. Machine-learning analysis of EV proteomes identified a prophylactic biomarker panel anchored by HSPA8, SERPINF2, COL4A1, and PLOD1, linked to angiogenic recovery and redox balance. Conclusions: CTC-derived EV proteomic signatures capture dose and timing-dependent aspirin effects, positioning the chorion as a pharmacological "secondary responder" favoring cellular resilience over classical anti-inflammatory suppression. EV-based molecular profiling might offer a framework for stratifying aspirin responders from non-responders toward personalized PE prevention.

(BioRxiv All) From Stress to Survival: Trophoblast-Derived Extracellular Vesicle Proteome Captures Aspirin-Driven Cellular Reprogramming in a Preeclampsia Model.: Background: Low-dose aspirin (LDA) reduces preeclampsia (PE) risk by up to 40%, yet its molecular effects on… #BioRxiv #MassSpecRSS

DIA-NN EasyFilter workflow for the fast and user-friendly critical assessment and visualization of DIA-NN proteomics analysis outcome Liquid chromatography-tandem mass spectrometry (LC-MS/MS) based proteomics, particularly data-independent acquisition (DIA), has become widely adopted across in One Health approaches for biological and clinical research for quantitative protein characterization. Among the many computational tools available, DIA-NN has demonstrated superior performance; however, the primary output of the current versions is provided as a compact, compressed PARQUET file that can be difficult to interrogate without programming expertise. To address this limitation, we developed DIA-NN EasyFilter (DEF), a fast, user-friendly, KNIME-based workflow for comprehensive protein filtering, and visualization. DEF integrates chromatographic peak-based filtering, curated contaminant libraries, and quantity-quality assessment, along with interactive modules for qualitative and quantitative data exploration. The workflow is optimized for efficient execution within the KNIME local desktop environment and is designed to support end-users in improving accuracy and interpretability without requiring coding skills. We provide detailed description on how to run DEF and demonstrate the utility and robustness of DEF using published large-scale proteomics datasets, showing high comparability across studies regardless of instrument platform or dataset size.

(BioRxiv All) DIA-NN EasyFilter workflow for the fast and user-friendly critical assessment and visualization of DIA-NN proteomics analysis outcome: Liquid chromatography-tandem mass spectrometry (LC-MS/MS) based proteomics, particularly data-independent acquisition (DIA), has… #BioRxiv #MassSpecRSS

Loss-of-function phenomics, ncORFs, and ambiguity of mutant phenotypes in Medicago truncatula Non-canonical open reading frames (ncORFs) are an emerging area of research that is quickly gaining momentum. Many peptides and proteins missed in initial annotation efforts (ncProts) were subsequently shown to be crucial for a wide range of biological processes. The discovery of ncORFs continues to improve the accuracy of loss-of-function studies because they often occupy the same genomic spaces as annotated ORFs. While databases of mutant phenotypes linked to genomic loci are available in a few species, none of these databases integrate the information on ncORFs present in already characterized loci. In this study, we introduce a nearly comprehensive loss-of-function phenomics dataset of Medicago truncatula (673 loci characterized over the past 30 years), which should become an integral part of the genome browser of this organism. We used this dataset to provide a critical analysis of the potential contribution of ncORFs to published phenotypes. We detected mass spectrometry (MS)-validated ncORFs in 10 functionally characterized genes, including major regulators of development and symbiotic relationships. We also found conserved ncORFs in 113 characterized genes, including four genes with highly conserved ncORFs. We show that in some studies, the contribution of ncORFs can be ruled out, while in others it cannot. Using real examples, we systematized ambiguities associated with ncORFs. Furthermore, we highlighted little-known trans effects of insertional mutagenesis on splicing as contributors to that ambiguity. Finally, our meta-analysis of published phenotypes indicates that different protein classes have significantly different (unique) proportions of unconditional, conditional, and neutral phenotypes, potentially reflecting their relative functional importance.

(BioRxiv All) Loss-of-function phenomics, ncORFs, and ambiguity of mutant phenotypes in Medicago truncatula: Non-canonical open reading frames (ncORFs) are an emerging area of research that is quickly gaining momentum. Many peptides and proteins missed in initial annotation… #BioRxiv #MassSpecRSS

Quantitative Neuropeptidomics Reveals Thermal Acclimation-Induced Remodeling of Peptidergic Signaling in the American Lobster Homarus americanus Global warming and rising ocean temperatures pose substantial challenges to marine ecosystems and crustacean populations. As an ectothermic species, the American lobster (Homarus americanus) relies on physiological and neurochemical mechanisms to maintain homeostasis under varying environmental conditions. To elucidate the role of neuropeptides in neuronal plasticity and systemic adaptation to temperature fluctuations, we employed a quantitative mass spectrometry-based approach to probe key neuropeptides involving thermal adaptation in four lobster neural tissues at three temperatures: 4 degrees C (cold), 11 degrees C (control), and 18 degrees C (warm). Peptidomic profiling revealed a global reduction in peptide abundance during cold exposure, alongside coordinated, tissue-specific reconfigurations of the neuropeptidome between experimental groups. Cold exposure led to a significant downregulation of RFamide, leucokinin, and pyrokinin peptides in the commissural ganglia, whereas B-type allatostatin (AST-B), natalisin, and RYamide peptides were drastically elevated in the brain of warm-acclimated animals, with comparatively fewer detectable peptide abundance changes in the sinus gland and the stomatogastric ganglion. Collectively, our findings elucidate neuropeptide signaling pathways underlying thermal tolerance and adaptive resilience in Homarus americanus, offering insights into the survival mechanism and neurochemical basis of neural circuits in response to thermal acclimation.

(BioRxiv All) Quantitative Neuropeptidomics Reveals Thermal Acclimation-Induced Remodeling of Peptidergic Signaling in the American Lobster Homarus americanus: Global warming and rising ocean temperatures pose substantial challenges to marine ecosystems and crustacean… #BioRxiv #MassSpecRSS

(J Proteom) Structural diversity of lipid A modulates neutrophil proteome and secretome responses: Publication date: Available online 10 March 2026

Source: Journal of Proteomics

Author(s): Jose R. Pittaluga-Villarreal, Doeun Kim, Sung Hwan-Yoon, Vanya Bhushan, Jiraphorn… #MassSpecRSS

[ASAP] Optimization of Radially Segmented Ion Mirrors for High Resolution Charge Detection Mass Spectrometry Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00337

(JASMS) [ASAP] Optimization of Radially Segmented Ion Mirrors for High Resolution Charge Detection Mass Spectrometry: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00337 (RSS) #MassSpecRSS #JASMS

From Raw Signals to AI and Omics-Agnostic Algorithms for Multidimensional Mass Spectrometry Publication date: Available online 9 March 2026 Source: International Journal of Mass Spectrometry Author(s): Aivett Bilbao

(IJMS) From Raw Signals to AI and Omics-Agnostic Algorithms for Multidimensional Mass Spectrometry: Publication date: Available online 9 March 2026

Source: International Journal of Mass Spectrometry

Author(s): Aivett Bilbao #ijms #MassSpecRSS

(Analyst) Dielectric Barrier Discharge Ionization (DBDI) Enables Rapid Analysis of New Psychoactive Substances with Ion Mobility-Mass Spectrometry: Analyst, 2026, Accepted Manuscript
DOI: 10.1039/D6AN00028B, Paper Open Access &nbsp This article is licensed under a… (RSS) #MassSpecRSS #analyst

High-throughput analysis of arsenic-based pigments in historical book bindings using laser ablation coupled to inductively coupled plasma-mass spectrometry and micro-X-ray fluorescence Publication date: 1 August 2026 Source: Talanta, Volume 305 Author(s): Johannes Schmeinck, David Husmann, Kirsten Krumeich, Fabian Knechtel, Uwe Karst

(Talanta) High-throughput analysis of arsenic-based pigments in historical book bindings using laser ablation coupled to inductively coupled plasma-mass spectrometry and micro-X-ray fluorescence: Publication date: 1 August 2026

Source: Talanta, Volume 305

Author(s): Johannes… #Talanta #MassSpecRSS

[ASAP] Online Chemical Analysis of Flowing n-Hexane in a Pyrolysis Reactor by Optical Spectroscopy and Molecular Beam Mass Spectrometry The Journal of Physical Chemistry ADOI: 10.1021/acs.jpca.6c00148

(J Phys Chem A) [ASAP] Online Chemical Analysis of Flowing n-Hexane in a Pyrolysis Reactor by Optical Spectroscopy and Molecular Beam Mass Spectrometry: The Journal of Physical Chemistry ADOI: 10.1021/acs.jpca.6c00148 #MassSpecRSS

(ACS Anal Chem) [ASAP] Resolving sn-Positional Isomers of Docosahexaenoic Acid-Bound Phospholipids in the Mouse Brain by Cyclic Ion Mobility Mass Spectrometry Imaging: Analytical ChemistryDOI: 10.1021/acs.analchem.5c06621 #MassSpecRSS #ACSAChem

Issue Information Journal of Mass Spectrometry, Volume 61, Issue 4, April 2026.

(J Mass Spectrom) Issue Information: Journal of Mass Spectrometry, Volume 61, Issue 4, April 2026. #JMassSpectrom #MassSpecRSS

On the Fate of Protonated Aldehydes in the Gas Phase Journal of Mass Spectrometry, Volume 61, Issue 4, April 2026.

(J Mass Spectrom) On the Fate of Protonated Aldehydes in the Gas Phase: Journal of Mass Spectrometry, Volume 61, Issue 4, April 2026. #JMassSpectrom #MassSpecRSS

Marine Aspergillus terreus produces a chitinase exhibiting a dual mode of enzymatic action Marine Aspergillus terreus has been explored as an important chitinase-producing fungal strain for N-Acetyl-D-Glucosamine (GlcNAc) production from chitin substrates. Here, a purified extracellular 45 kDa chitinase of marine Aspergillus terreus (accession number JQ248076) was characterized in terms of substrate specificity. Conventionally, endochitinase cleaves the chitin substrate randomly to produce GlcNAc and its different multimers. So, it requires at least tetramer to characterize the endochitinases; whereas, exochitinases cleaves the chitin substrate from its reducing end and produce either GlcNAc or chitobiose (GlcNAc dimer). In present chitinase characterization, the HPLC followed by HRMS analyses revealed differential product formation from the chitin substrates of varied chain length. With swollen chitin polymer, the enzyme produced GlcNAc as a sole product; whereas with chitohexaose substrate, a mixture of GlcNAc and its oligomers were obtained. Although, mass spectrometry-based proteomics analysis identified the isolated chitinase as an endochitinase 1 precursor (Accession XP_001217186). However, the enzyme kinetic study exhibited higher catalytic efficiency for exochitinase specific dimeric chromogenic substrate in comparison to endochitinase specific tetrameric fluorogenic substrate, which indicated predominantly exochitinase behavior of the enzyme. Further, the in-silico study predicted the differential cleavage pattern of the enzyme, which could be due to different mode of substrate binding and processive mechanism through the tunnel shaped binding cleft of the enzyme. The dual mode of catalytic activity of the present chitinase was further confirmed by a molecular docking study with different lengths of substrates. With the unique dual mode of action, the chitinase of marine Aspergillus terreus offers a great promise towards its utility in the production of GlcNAc.

(BioRxiv All) Marine Aspergillus terreus produces a chitinase exhibiting a dual mode of enzymatic action: Marine Aspergillus terreus has been explored as an important chitinase-producing fungal strain for N-Acetyl-D-Glucosamine (GlcNAc) production from chitin substrates. Here,… #BioRxiv #MassSpecRSS

A Novel Glycoproteomics Platform for High-Throughput Identification of Disease-Associated Glycoforms Glycosylation is a critical post-translational modification, and its aberrant forms are potent disease biomarkers; however, the comprehensive, site-specific identification of all glycosites and glycoforms across an entire proteome remains prohibitively slow and computationally demanding. To address this bottleneck and accelerate biomarker discovery, we introduce the Glycoproteomics Data Analysis Software (GDAS), a novel, high-throughput platform designed to provide confident, proteome-scale identification of disease-specific glycoforms. GDAS streamlines the analysis through a core, multi-step workflow: it initially employs an ultrafast open search (e.g., MSFragger-Glyco) on mass spectrometry data to rapidly screen and statistically reduce the vast proteome database to a manageable subset of significantly regulated glycoproteins, conserving computational resources for subsequent, in-depth, targeted N- and O-glycosylation analysis using specialized tools (e.g., GlycReSoft and O-Pair). Furthermore, a unique Final Analysis Module utilizes an advanced statistical and machine learning pipeline (incorporating Bootstrap/Bayesian methods, XGBoost, and Random Forest) to integrate quantitative results and generate a robust, comprehensive glycosylation score. We demonstrate GDAS's power to recognize biologically relevant glycosylation changes in targeted proteins by validating it using published Alzheimer's disease data. GDAS can be downloaded from https://github.com/yang-lab/GDAS.

(BioRxiv All) A Novel Glycoproteomics Platform for High-Throughput Identification of Disease-Associated Glycoforms: Glycosylation is a critical post-translational modification, and its aberrant forms are potent disease biomarkers; however, the comprehensive, site-specific… #BioRxiv #MassSpecRSS

(BioRxiv All) Astrocyte-neuron mitochondrial transfer via mitoEVs supports neuronal energy metabolism and is impaired in early Alzheimer's disease: Background: Mitochondrial dysfunction is an early and central feature of Alzheimer's disease (AD). In particular, intercellular… #BioRxiv #MassSpecRSS

Characterization of Amidine‐Based Degradation Products of Novichok A‐Series Nerve Agents Using Single‐Quadrupole GC–MS ABSTRACT Rationale The identification of Novichok A-series nerve agents depends primarily on the detection of stable degradation products, as intact agents are rarely encountered in environmental or forensic samples. However, limited GC–MS reference data exist for amidine-based degradation products of A-series nerve agents relevant to Chemical Weapons Convention (CWC) verification. This study aims to address a critical analytical gap supporting forensic attribution and international chemical weapons verification. Methods A series of eight N,N-dialkylethanimidamide compounds relevant to predicted Novichok degradation pathways was synthesized under controlled conditions. Samples were analyzed by GC–MS using electron ionization (EI) and positive chemical ionization (PCI) with isobutane reagent gas. Spectral data, comprising major fragment ions, protonated molecules, and adduct ions, were acquired using a GC–MS system under optimized analytical conditions. GCRI were determined using the Van den Dool and Kratz method with n-alkane standards. Results EI mass spectra showed reproducible fragmentation dominated by α-cleavage, producing characteristic low-mass ions, particularly m/z 42 [C2H4N]+ and m/z 71 [C3H7N2]+, with isomer dependent base peaks and relative abundances. As a complementary technique, PCI with isobutane yielded spectra with molecular mass confirmation via [M+H]+ ions, with minimal adduct formation (≤ 12%). RI ranged from 938 to 1145 and increased systematically with alkyl substitution, enabling discrimination of structural isomers. The combined EI and PCI data provide reliable spectral fingerprints and retention behavior for amidine-based degradation products of A-series nerve agents. Conclusions This work establishes comprehensive GC–MS reference data for amidine-based degradation products associated with Novichok A-series nerve agents. The developed method enabled the successful identification of spiked amidine compounds in the 56th and 57th OPCW proficiency test (PT) samples. These results will enhance the capability of forensic and verification laboratories to detect, confirm, and interpret degradation markers, thereby supporting OPCW PT, chemical weapons attribution, and compliance with the CWC.

(RCM) Characterization of Amidine‐Based Degradation Products of Novichok A‐Series Nerve Agents Using Single‐Quadrupole GC–MS: ABSTRACT




Rationale




The identification of Novichok A-series nerve agents depends primarily on the detection of stable… #RapidCommunMassSpectrom #MassSpecRSS

Small extracellular vesicles in clinical Cancer research - A quantitative proteomics perspective Publication date: Available online 8 March 2026 Source: Journal of Proteomics Author(s): Divya Pandey, Vineeta Tiwari, Dipanjana Ghosh

(J Proteom) Small extracellular vesicles in clinical Cancer research - A quantitative proteomics perspective: Publication date: Available online 8 March 2026

Source: Journal of Proteomics

Author(s): Divya Pandey, Vineeta Tiwari, Dipanjana Ghosh #MassSpecRSS

Simultaneous Quantification of Eight Chiral and Achiral Components in Notopterygii Rhizoma et Radix Extract and Rat Plasma Based on Chiral Stationary Phase‐HPLC‐MS/MS ABSTRACT A chiral stationary phase-high performance liquid chromatography-tandem mass spectrometry (CSP-HPLC-MS/MS) approach was developed and validated for the first time to quantify quantification of eight components: the enantiomers of three chiral components notopterol, oxypeucedanin hydrate, oxypeucedanin (in total six configurations), and achiral components nodakenin, imperatorin, isoimperatorin, bergapten, and ferulic acid, in Notopterygii Rhizoma et Radix. By adjusting the types of chiral stationary phase and the composition ratio of the mobile phase, methanol–acetonitrile (75:25, v/v) was selected as the mobile phase (flow rate 0.5 mL/min), and three chiral components notopterol, oxypeucedanin hydrate, and oxypeucedanin were successfully separated into their enantiomers with Chiralpak IG. The method was applied to analyze both plant extracts and rat plasma samples. A considerable variation in content was observed among the eight components in the plant extracts, with their individual concentrations covering a wide range from 1.04 to 20 400 µg/mL (see Section 3 for details). Similarly, their plasma concentrations also spanned from 0.2 to 262.76 ng/mL. The results demonstrated significant differences in the contents of the components. Notably, the chiral components exhibited marked differences between their enantiomers, suggesting that chiral components should be considered in the quality assessment and control of natural products.

(J Sep Sci) Simultaneous Quantification of Eight Chiral and Achiral Components in Notopterygii Rhizoma et Radix Extract and Rat Plasma Based on Chiral Stationary Phase‐HPLC‐MS/MS: ABSTRACT




A chiral stationary phase-high performance liquid chromatography-tandem mass… #JSepSci #MassSpecRSS

(Clin Chim Acta) Performance evaluation of automated magnetic beads extraction method for the measurement of 23 plasma steroids using dual liquid chromatography-tandem mass spectrometry (LC-MS/MS) method: Publication date: Available online 7 March 2026

Source: Clinica… #ClinChemActa #MassSpecRSS