#massSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 minute ago

[ASAP] Rapid Analysis of NAD and Other Phosphorylated Metabolites in Complex Biological Samples by Hydrophilic Interaction Liquid Chromatography Coupled with Tandem Mass Spectrometry Analytical ChemistryDOI: 10.1021/acs.analchem.6c00721

(ACS Anal Chem) [ASAP] Rapid Analysis of NAD and Other Phosphorylated Metabolites in Complex Biological Samples by Hydrophilic Interaction Liquid Chromatography Coupled with Tandem Mass Spectrometry: Analytical ChemistryDOI: 10.1021/acs.analchem.6c00721 #MassSpecRSS #ACSAChem

Kermit Murray

@kkmurray.bsky.social

51 minutes ago

Reverse‐Phase High‐Performance Liquid Chromatography/Mass Spectrometry (RP‐LC–MS/MS, Label‐Free Method) for Component Analysis of Gonadotropin Drugs Journal of Mass Spectrometry, Volume 61, Issue 5, May 2026.

(J Mass Spectrom) Reverse‐Phase High‐Performance Liquid Chromatography/Mass Spectrometry (RP‐LC–MS/MS, Label‐Free Method) for Component Analysis of Gonadotropin Drugs: Journal of Mass Spectrometry, Volume 61, Issue 5, May 2026. #JMassSpectrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 hours ago

Numerical Modeling of Ion-Optical Isotrajectory Systems for Space and Plasma Measurements Publication date: Available online 8 April 2026 Source: International Journal of Mass Spectrometry Author(s): Zh.T. Kambarova, A.A. Trubitsyn, A.O. Saulebekov, T. Shugayeva, M.K. Tungushbekova

(IJMS) Numerical Modeling of Ion-Optical Isotrajectory Systems for Space and Plasma Measurements: Publication date: Available online 8 April 2026

Source: International Journal of Mass Spectrometry

Author(s): Zh.T. Kambarova, A.A. Trubitsyn, A.O. Saulebekov, T. Shugayeva, M.K.… #ijms #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

9 hours ago

(BioRxiv All) Critical amino acid residues in the N-terminal domain of NADPH-dependent assimilatory sulfite reductase flavoprotein mediate octameric assembly: How large, flexible enzymes assemble into defined oligomeric architectures remains a central question in biology.… #BioRxiv #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

16 hours ago

Decoding magic numbers in helium droplet mass spectra: An experimental and DFT perspective on corannulene-H₂ and -D₂ cluster stability European Journal of Mass Spectrometry, Ahead of Print. Polycyclic aromatic hydrocarbons (PAHs) are believed to be abundant in the dense regions of the interstellar medium (ISM) and are hypothesized to play a role in the origin of diffuse interstellar bands (DIBs). Among these, corannulene C₂₀H₁₀ stands out ...

(EJMS) Decoding magic numbers in helium droplet mass spectra: An experimental and DFT perspective on corannulene-H₂ and -D₂
cluster stability: European Journal of Mass Spectrometry, Ahead of Print.
Polycyclic aromatic hydrocarbons (PAHs) are believed to be abundant in the dense… #EJMS #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

18 hours ago

Comparison of Extraction Methods for the Quantification of Phytohormones from Tomato Fruits and Leaves by LC-MS/MS Accurate, simultaneous, and efficient quantification of chemically diverse phytohormone species is a critical task towards understanding the complex system of phytohormone signaling pathways. Quantification of phytohormones with the commonly used technique liquid chromatography coupled to tandem mass spectrometry is susceptible to the influence of non-phytohormone components present in the sample, a phenomenon referred to as matrix effect. To reduce matrix effect, some phytohormone quantification methods include additional steps of cleanup of crude extracts. However, to what extent additional purification steps provide increased accuracy compared to simpler, less laborious methods is seldomly evaluated. We evaluated three previously described phytohormone extraction methods, two of which include solid-phase extraction and one that does not, in their ability to minimize matrix effect and generate accurate estimates of phytohormone species spanning six classifications, from fruit and leaf tissue of Solanum lycopersicum cv. Micro-Tom (tomato). Our results show that, while the methods that included solid phase extraction occasionally outperformed each other regarding matrix effect and/or recovery efficiency for broad range of phytohormones, they rarely outperformed the simpler single-phase extraction method.

(BioRxiv All) Comparison of Extraction Methods for the Quantification of Phytohormones from Tomato Fruits and Leaves by LC-MS/MS: Accurate, simultaneous, and efficient quantification of chemically diverse phytohormone species is a critical task towards understanding the… #BioRxiv #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

20 hours ago

(J Proteom) Proteomics of the extremotolerant yeast Meyerozyma guilliermondii 4LYP0 isolated from the Yanamate tailings Cerro de Pasco (Peru) upon exposure to Cu2+, Cd2+, and Cr6＋ ions: Publication date: Available online 7 April 2026

Source: Journal of Proteomics

Author(s): Diego… #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

20 hours ago

[ASAP] Minimizing the Coffee Ring Effect: Improving MALDI Dried-Drop Analysis by Sequential Spotting Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00063

(JASMS) [ASAP] Minimizing the Coffee Ring Effect: Improving MALDI Dried-Drop Analysis by Sequential Spotting: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00063 (RSS) #MassSpecRSS #JASMS

Kermit Murray

@kkmurray.bsky.social

22 hours ago

[ASAP] Characterizing Noncovalent Therapeutics in Biomatrices by Native Affinity Capture Mass Spectrometry: Biotransformation of Antibodies Conjugated with Small Molecules and siRNA Analytical ChemistryDOI: 10.1021/acs.analchem.5c07260

(ACS Anal Chem) [ASAP] Characterizing Noncovalent Therapeutics in Biomatrices by Native Affinity Capture Mass Spectrometry: Biotransformation of Antibodies Conjugated with Small Molecules and siRNA: Analytical ChemistryDOI: 10.1021/acs.analchem.5c07260 #MassSpecRSS #ACSAChem

Kermit Murray

@kkmurray.bsky.social

22 hours ago

High‐Throughput N‐Glycan Analysis by IR‐MALDESI With a 1.5‐kHz Pulsed Mid‐IR Laser Journal of Mass Spectrometry, Volume 61, Issue 5, May 2026.

(J Mass Spectrom) High‐Throughput N‐Glycan Analysis by IR‐MALDESI With a 1.5‐kHz Pulsed Mid‐IR Laser: Journal of Mass Spectrometry, Volume 61, Issue 5, May 2026. #JMassSpectrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 day ago

Issue Information Journal of Mass Spectrometry, Volume 61, Issue 5, May 2026.

(J Mass Spectrom) Issue Information: Journal of Mass Spectrometry, Volume 61, Issue 5, May 2026. #JMassSpectrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 day ago

(RSC A Meth) Analysis of the Effect of Glycerol Addition and Heating Temperature on the Puff-by-Puff Release of Volatile Organic Compounds from Heated Tobacco Products: Anal. Methods, 2026, Accepted Manuscript
DOI: 10.1039/D6AY00249H, PaperTing FEI, Junjie LI, Bingyu WU, Jie Yu, Peicai… #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 day ago

Online Study on the Smoke Aerosol of the Heat‐Not‐Burn Cigarette by Photoionization Mass Spectrometry ABSTRACT Online analysis of chemical components in heat-not-burn (HNB) cigarette aerosol is crucial for understanding the product's characteristics and guiding product development. Herein, a synchrotron radiation photoionization time-of-flight mass spectrometry method was established to online distinguish isobars and isomers in HNB cigarette aerosol, where photoionization efficiency (PIE) curves of HNB cigarette aerosol were scanned at different photon energies, and more than 43 components including aldehydes, ketones, alkenes, alkanes, and heterocyclic compounds were identified based on multiple linear regression (MLR) simulation. Additionally, the puff-by-puff dynamic evolutions of some typical components were investigated with the help of a smoking machine.

(RCM) Online Study on the Smoke Aerosol of the Heat‐Not‐Burn Cigarette by Photoionization Mass Spectrometry: ABSTRACT




Online analysis of chemical components in heat-not-burn (HNB) cigarette aerosol is crucial for understanding the product's characteristics… #RapidCommunMassSpectrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 day ago

Time‐Resolved Native Mass Spectrometry Reveals Reversible Light‐Driven Oligomerization of Arabidopsis Cryptochrome 1 and Its Antagonism by BIC1 Time-resolved native mass spectrometry uncovers the blue-light-dependent kinetic mechanism of Arabidopsis CRY1 oligomerization, proceeding sequentially from monomers to dimers and tetramers. ATP promotes assembly, whereas BIC1 actively blocks and disassembles tetramers independent of light, providing mechanistic insight into the regulation of cryptochrome signaling. ABSTRACT Cryptochromes (CRYs) are blue-light photoreceptors that mediate light-dependent signaling in plants. Here, we uncover the molecular mechanism underlying blue-light activation of the Arabidopsis thaliana cryptochrome 1 photolyase homology region (CRY1-PHR) using time-resolved native mass spectrometry combined with kinetic modeling. This approach enables direct monitoring of light-driven complex formation with temporal and molecular resolution. We show that blue-light activation of CRY1-PHR follows a reversible assembly pathway in which monomers rapidly form dimers that further assemble into tetramers. A quantitative two-step kinetic model captures the dynamic interplay between light-induced oligomerization and thermal disassembly. Strikingly, ATP accelerates tetramer formation and stabilizes oligomers by tuning the underlying photochemistry of the flavin adenine dinucleotide (FAD) chromophore. In contrast, the Blue-light Inhibitor of Cryptochromes 1 (BIC1) acts as a potent antagonist. BIC1 binds to CRY1-PHR even in the dark, with significantly increased affinity under blue light, thereby inhibiting oligomerization and actively disassembling pre-formed tetramers. This disassembly is light-independent and occurs regardless of CRY's redox state. Together, these findings provide a kinetic and mechanistic framework for reversible blue-light signaling by plant CRYs and highlight how opposing regulators precisely modulate photoreceptor activation at the molecular level.

(Angew Chem) Time‐Resolved Native Mass Spectrometry Reveals Reversible Light‐Driven Oligomerization of Arabidopsis Cryptochrome 1 and Its Antagonism by BIC1: Time-resolved native mass spectrometry uncovers the blue-light-dependent kinetic mechanism of Arabidopsis CRY1… (RSS) #AngewChem #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 day ago

Component‐Programmed Self‐Assembly for Topological Transformation: From a 2D Network to a Discrete Star of David A novel component-controlled strategy enables an unprecedented 2D to 0D topological transformation, converting a metal-organic network into a discrete hexagon-framed Star of David structure via a modulator ligand. The extended 2D network shows improved photocatalytic performance compared to its 0D analogue. ABSTRACT Controllable modifications on dimensionalities and topologies of supramolecules are crucial for tuning their properties. Here, we report a robust component-controlled topological transformation, initiating with a two-dimensional (2D) layered coordination network S2 formed by the self-assembly of a metallo-organic ligand (MOL) LA with Zn(II). The strategic introduction of a V-shaped modulator LB with peripheral arms into the S2 system triggered a remarkable topological transformation, thus affording a discrete zero-dimensional (0D) hexagon-framed Star of David S1. This unprecedented 2D to 0D control facilitates direct comparison of their intrinsic properties, with structures unequivocally confirmed by nuclear magnetic resonance (NMR) spectroscopy, high-resolution electrospray ionization mass spectrometry (ESI-MS), traveling-wave ion mobility mass spectrometry (TWIM-MS), and microscopy. In the aerobic sulfide oxidation, the extended 2D network S2 exhibited significantly improved photocatalytic performance over S1. This enhanced efficiency was attributed to S2’s pseudo-heterogeneous nature, which maximizes active site exposure and overcomes typical limitations of heterogeneous catalysts. This work not only establishes a novel strategy for controlling supramolecular architecture but also compellingly demonstrates that for catalytic applications, ensuring active site accessibility through judicious structural design can be a more potent strategy than pursuing isolated structural complexity.

(Angew Chem) Component‐Programmed Self‐Assembly for Topological Transformation: From a 2D Network to a Discrete Star of David: A novel component-controlled strategy enables an unprecedented 2D to 0D topological transformation, converting a metal-organic network into a… (RSS) #AngewChem #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 day ago

Controlled Delivery and Light‐Induced Release of Magic Spot Nucleotides in Escherichia coli We synthesized photocaged, clickable and isotope-labeled “magic spot” Nucleotides and delivered them into Escherichia coli comparing different approaches. Light-controlled release inside living cells enabled tracking of their conversion from pppGpp to ppGpp by capillary electrophoresis mass spectrometry and revealed their impact on the growth rate of a (p)ppGpp0 mutant. ABSTRACT The “magic spot” nucleotides (MSNs) ppGpp and pppGpp constitute bacterial alarmones that orchestrate the conserved stringent response, a global regulatory mechanism enabling bacteria to adapt to nutrient deprivation and other environmental stresses. Current strategies to manipulate MSN levels rely mainly on genetic or environmental approaches, which are slow and lack temporal control. Chemical tools such as photocaged MSN analogues could provide such temporal control over MSN levels. However, the high negative charge of MSNs prevents spontaneous passage through the complex bacterial cell envelope. Here, we report the synthesis of photocaged, clickable, and isotope-labeled MSN analogues and their delivery into Escherichia coli comparing different approaches. A cyclodextrin-based synthetic nucleotide transporter facilitated uptake. Upon 400 nm irradiation, these probes were photo-released inside living cells, where we tracked their conversion from pppGpp to ppGpp by capillary electrophoresis mass spectrometry and demonstrated their ability to alter growth in a (p)ppGpp0 mutant. These probes lay the foundation for spatially and temporally controlled studies of MSN function and of other highly negatively charged metabolites in vivo.

(Angew Chem) Controlled Delivery and Light‐Induced Release of Magic Spot Nucleotides in Escherichia coli: We synthesized photocaged, clickable and isotope-labeled “magic spot” Nucleotides and delivered them into Escherichia coli comparing different approaches.… (RSS) #AngewChem #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 day ago

T‐Shaped Stannyliumylidene Ion: Synthesis, Reactivity, and Redox Catalysis Tin redox catalysis: T-shaped stannyliumylidene ion bearing a rigid pincer ligand has been synthesized and characterized. This cationic Sn(II) complex presents ambiphilic reactivity and engages in the σ-bond activation and catalytic transfer hydrogenation. Experimental and mechanistic investigation reveal a distinct FLP-mediated Sn(II)/Sn(IV) redox platform, offering a new paradigm for main group catalysis. ABSTRACT We report the synthesis and characterization of a T-shaped, 8-electron stannyliumylidene ion bearing a rigid acridane-based pincer ligand. This cationic Sn(II) complex exhibits pronounced ambiphilic reactivity, participating in electrophilic, nucleophilic, and σ-bond activation reactions. All derived compounds were characterized by nuclear magnetic resonance spectroscopy, single crystal x-ray diffraction analysis, and high-resolution mass spectrometry. Density functional theory calculations reveal the coexistence of a lone pair of electrons and a vacant 5p-orbital at the tin center, which rationalizes the experimentally observed dual reactivity. Remarkably, the transition metal-like electronic structure enables this organotin(II) species to act as an efficient catalyst for transfer hydrogenation of azoarenes and imines using NH3BH3 as hydrogen source. Combined experimental and computational mechanistic studies reveal a distinct catalytic platform based on Sn(II)/Sn(IV) redox cycle at a single tin(II) center. This work demonstrates the first Sn(II)/Sn(IV) catalyzed reduction of unsaturated bonds, offering a paradigm for mimicking transition metal reactivity through rationally designed main group systems in mediating diverse chemical transformations.

(Angew Chem) T‐Shaped Stannyliumylidene Ion: Synthesis, Reactivity, and Redox Catalysis: Tin redox catalysis: T-shaped stannyliumylidene ion bearing a rigid pincer ligand has been synthesized and characterized. This cationic Sn(II) complex presents ambiphilic… (RSS) #AngewChem #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 day ago

Soil bacterium Massilia secretes metabolites that promote Leptospira growth Understanding pathogen metabolism is critical for identifying key functions for drug targeting, establishing effective in vitro experimental systems, etc., particularly for metabolically unique organisms such as Leptospira. Pathogenic Leptospira are thought to infect humans from environmental sources; however, direct isolation from environmental samples remains technically challenging and is not yet well established. Here, we report that a ubiquitous environmental bacterium, Massilia sp., produces metabolites that promote the growth of Leptospira interrogans, encountered through an incidental contamination event, and identified in this study. Gas chromatography-tandem mass spectrometry (GC-MS/MS) analysis showed demonstrated that cultivating of Massilia sp. in R2A medium resulted in the accumulation of metabolites, including branched-chain amino acid (BCAA) intermediates, compared to fresh medium. By combining genome-scale metabolic modeling with experimental validation using cell-free culture supernatant supplementation assays, we demonstrate that BCAA intermediates, particularly 2-ketoisocaproic acid (4-methyl-2-oxopentanoate; 4MOP), a leucine biosynthetic intermediate produced by Massilia sp., enhance Leptospira growth. To investigate the metabolic role of 4MOP, we incorporated transcriptomic data into a genome-scale metabolic network model to generate condition-specific models. Resulted flux distributions indicated that Leptospiracatabolized imported 4MOP to produce acetyl-CoA. Our results reveal a previously unrecognized metabolic interaction where metabolites produced by environmental bacteria support the growth of pathogenic Leptospira, offering mechanistic insight into its metabolic requirement. These findings have implications to understand the environmental persistence of Leptospira through its metabolic dependencies on coexisting microbes, and they also help develop better strategies for this pathogen.

(BioRxiv All) Soil bacterium Massilia secretes metabolites that promote Leptospira growth: Understanding pathogen metabolism is critical for identifying key functions for drug targeting, establishing effective in vitro experimental systems, etc., particularly for metabolically… #BioRxiv #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 day ago

Defining the RNA Modification Landscape of Multiple Myeloma Reveals METTL3-Dependent m6A Regulation of NEAT1 RNA modifications play critical roles in gene regulation. N6-methyladenosine (m6A) is the most abundant modification on mRNA and long noncoding RNA (lncRNA) and regulates RNA processing, stability, and translation. RNA modifications are not well characterized in multiple myeloma (MM), a plasma cell malignancy characterized by relapse and disease progression, and the contribution of m6A -modified lncRNAs to the disease remains unclear. Here, we define the RNA modification landscape of MM by combining mass spectrometry, Nanopore Direct RNA sequencing, and methylated RNA immunoprecipitation sequencing. We identify 20 RNA modification types and > 15,000 m6A sites, including sites on 2,398 lncRNAs. Among these, we validate m6A sites on the paraspeckle-associated lncRNA NEAT1. Functional studies reveal that NEAT1 expression is regulated by the methyltransferase METTL3 and site-specific demethylation of a NEAT1 m6A site reduces MM cell viability. Single-cell RNA sequencing shows consistent NEAT1 enrichment in malignant plasma cells but minimal expression in healthy cells. These findings identify m6A-modified lncRNAs as key regulators of MM biology and establish NEAT1 as an epitranscriptomically controlled driver of MM cell survival.

(BioRxiv All) Defining the RNA Modification Landscape of Multiple Myeloma Reveals METTL3-Dependent m6A Regulation of NEAT1: RNA modifications play critical roles in gene regulation. N6-methyladenosine (m6A) is the most abundant modification on mRNA and long noncoding RNA… #BioRxiv #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 day ago

Defining the RNA Modification Landscape of Multiple Myeloma Reveals METTL3-Dependent m6A Regulation of NEAT1 RNA modifications play critical roles in gene regulation. N6-methyladenosine (m6A) is the most abundant modification on mRNA and long noncoding RNA (lncRNA) and regulates RNA processing, stability, and translation. RNA modifications are not well characterized in multiple myeloma (MM), a plasma cell malignancy characterized by relapse and disease progression, and the contribution of m6A -modified lncRNAs to the disease remains unclear. Here, we define the RNA modification landscape of MM by combining mass spectrometry, Nanopore Direct RNA sequencing, and methylated RNA immunoprecipitation sequencing. We identify 20 RNA modification types and > 15,000 m6A sites, including sites on 2,398 lncRNAs. Among these, we validate m6A sites on the paraspeckle-associated lncRNA NEAT1. Functional studies reveal that NEAT1 expression is regulated by the methyltransferase METTL3 and site-specific demethylation of a NEAT1 m6A site reduces MM cell viability. Single-cell RNA sequencing shows consistent NEAT1 enrichment in malignant plasma cells but minimal expression in healthy cells. These findings identify m6A-modified lncRNAs as key regulators of MM biology and establish NEAT1 as an epitranscriptomically controlled driver of MM cell survival.

(BioRxiv All) Defining the RNA Modification Landscape of Multiple Myeloma Reveals METTL3-Dependent m6A Regulation of NEAT1: RNA modifications play critical roles in gene regulation. N6-methyladenosine (m6A) is the most abundant modification on mRNA and long noncoding RNA… #BioRxiv #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 day ago

Defining the RNA Modification Landscape of Multiple Myeloma Reveals METTL3-Dependent m6A Regulation of NEAT1 RNA modifications play critical roles in gene regulation. N6-methyladenosine (m6A) is the most abundant modification on mRNA and long noncoding RNA (lncRNA) and regulates RNA processing, stability, and translation. RNA modifications are not well characterized in multiple myeloma (MM), a plasma cell malignancy characterized by relapse and disease progression, and the contribution of m6A -modified lncRNAs to the disease remains unclear. Here, we define the RNA modification landscape of MM by combining mass spectrometry, Nanopore Direct RNA sequencing, and methylated RNA immunoprecipitation sequencing. We identify 20 RNA modification types and > 15,000 m6A sites, including sites on 2,398 lncRNAs. Among these, we validate m6A sites on the paraspeckle-associated lncRNA NEAT1. Functional studies reveal that NEAT1 expression is regulated by the methyltransferase METTL3 and site-specific demethylation of a NEAT1 m6A site reduces MM cell viability. Single-cell RNA sequencing shows consistent NEAT1 enrichment in malignant plasma cells but minimal expression in healthy cells. These findings identify m6A-modified lncRNAs as key regulators of MM biology and establish NEAT1 as an epitranscriptomically controlled driver of MM cell survival.

(BioRxiv All) Defining the RNA Modification Landscape of Multiple Myeloma Reveals METTL3-Dependent m6A Regulation of NEAT1: RNA modifications play critical roles in gene regulation. N6-methyladenosine (m6A) is the most abundant modification on mRNA and long noncoding RNA… #BioRxiv #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 day ago

Design and Characteristics of a Collision Cell with Axial Field for Quadrupole Time-of-Flight Mass Spectrometer Publication date: Available online 6 April 2026 Source: International Journal of Mass Spectrometry Author(s): Yixue Cao, Chenxin Wu, Xuesong Zhang, Jilong Wang, Lei Hua, Ping Chen, Haiyang Li

(IJMS) Design and Characteristics of a Collision Cell with Axial Field for Quadrupole Time-of-Flight Mass Spectrometer: Publication date: Available online 6 April 2026

Source: International Journal of Mass Spectrometry

Author(s): Yixue Cao, Chenxin Wu, Xuesong Zhang, Jilong… #ijms #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 day ago

A Context-Aware Single-Cell Proteomics Analysis pipeline. Single-cell proteomics (SCP) by mass spectrometry can now quantify hundreds to thousands of proteins per cell, but the field still lacks standardised analytical pipelines that accommodate the diversity of instruments, sample preparation workflows and biological contexts encountered in practice. Existing workflows, largely adapted from single-cell transcriptomics, do not account for the informative missingness, pervasive ambient protein contamination and limited feature space that distinguish proteomic from transcriptomic data. In addition, cell type annotation remains a manual bottleneck that is subjective, difficult to reproduce and hard to scale. Here we present an end-to-end pipeline that integrates adaptive quality control, entropy-guided iterative batch correction, multi-modal marker discovery that exploits detection patterns unique to proteomics, and context-aware annotation by large language models (LLMs) coupled to structured contradiction reasoning and orthogonal data-driven validation. Benchmarking on published single-cell proteomic datasets from developing human brain and glioblastoma-associated neutrophils revealed systematic LLM failure modes, including context-insensitive marker vocabulary and misinterpretation of phagocytic or lytic cell states. We addressed these errors using a three-round prompt architecture that combines general biological principles with auto-generated dataset-specific constraints. In held-out validation on a skin tumour dataset acquired, the pipeline showed high concordance with FACS-sorted ground truth. In the caerulein-injured pancreas, orthogonal immunohistochemistry further supported annotations of macrophage, stellate and immune populations. The pipeline is fully automated under fixed settings, and available as Context-Aware Single-Cell Proteomics Analysis (CASPA), providing SCP laboratories and facilities with a reproducible workflow that delivers interpretable, confidence-quantified annotations suitable for downstream expert review.

(BioRxiv All) A Context-Aware Single-Cell Proteomics Analysis pipeline.: Single-cell proteomics (SCP) by mass spectrometry can now quantify hundreds to thousands of proteins per cell, but the field still lacks standardised analytical pipelines that accommodate the diversity of… #BioRxiv #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 day ago

[ASAP] Ion Mobility Separation of Six Isomeric Cyclobutane Thymidine Photodimers Relevant to the Photochemistry of Non-B DNA Structures Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00014

(JASMS) [ASAP] Ion Mobility Separation of Six Isomeric Cyclobutane Thymidine Photodimers Relevant to the Photochemistry of Non-B DNA Structures: Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.6c00014 (RSS) #MassSpecRSS #JASMS

Kermit Murray

@kkmurray.bsky.social

1 day ago

[ASAP] Single-Cell Metabolic Profiling in a Glioblastoma Coculture Model Using AP-MALDI-Based Mass Spectrometry Imaging Analytical ChemistryDOI: 10.1021/acs.analchem.5c07924

(ACS Anal Chem) [ASAP] Single-Cell Metabolic Profiling in a Glioblastoma Coculture Model Using AP-MALDI-Based Mass Spectrometry Imaging: Analytical ChemistryDOI: 10.1021/acs.analchem.5c07924 #MassSpecRSS #ACSAChem

Kermit Murray

@kkmurray.bsky.social

1 day ago

Integrating Ultra‐High‐Performance Liquid Chromatography‐Photodiode Array Detector Coupled to Quadrupole Time‐of‐Flight Mass Spectrometry, Network Pharmacology, and Antidepressant Effects to Determine the Optimal Cultivation Years for Paeonia lactiflora Roots ABSTRACT Paeoniae Radix Alba (called Baishao in China, BS), the dried root of Paeonia lactiflora Pall., is a key ingredient in classic Chinese medicine formulas used to treat depression. This study aimed to optimize its cultivation period by integrating analysis of chemical constituents and antidepressant effects. Chemical profiling of 5-year-old roots (BS_5Year) using ultra-high-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry led to the identification of 44 major constituents. Network pharmacology analysis predicted that 12 primary constituents, five monoterpenes (oxypaeoniflorin, albiflorin, paeoniflorin, 6'-O-galloylpaeoniflorin, and benzoylpaeoniflorin) and seven polyphenols (gallic acid, methyl gallate, catechin, 1,3,6-trigalloylglucose, 1,2,3,6-tetragalloylglucose, benzoic acid, and 1,2,3,4,6-pentagalloylglucose) were key contributors to the antidepressant effects. Quantitative analysis by ultra-high-performance liquid chromatography-diode array detection showed that the content of these active constituents in BS_5Year was comparable to that in 4-year-old roots (BS_4Year). Behavioral tests (forced swimming and tail suspension) confirmed no significant difference in antidepressant efficacy between the two groups. These findings indicate that a 4-year growth period is sufficient to achieve the desired quality, thus establishing it as the optimal harvest time. Therefore, this study not only guides the cultivation of P. lactiflora but also highlights the importance of integrating chemical and bioactivity data to determine the optimal harvest time for herbal medicines.

(J Sep Sci) Integrating Ultra‐High‐Performance Liquid Chromatography‐Photodiode Array Detector Coupled to Quadrupole Time‐of‐Flight Mass Spectrometry, Network Pharmacology, and Antidepressant Effects to Determine the Optimal Cultivation Years for Paeonia lactiflora Roots:… #JSepSci #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 days ago

Prediction and Analysis of Quality Markers for Hedysari Radix Using Ultra‐High‐Performance Liquid Chromatography‐Tandem Mass Spectrometry, Network Pharmacology, Molecular Dynamics, and Chemometrics ABSTRACT To establish a scientific and reliable quality evaluation method for Hedysari Radix (HR), this study investigated changes in chemical components before and after the “Rubbing strip” (RS) was processed based on Quality Marker (Q-Marker) theory. By integrating ultra-high-performance liquid chromatography-tandem mass spectrometry quantitative analysis, network pharmacology, molecular dynamics, and chemometrics to elucidate compositional variations and predict potential quality markers systematically. Results showed significantly increased contents of formononetin, calycosin, liquiritigenin, and γ-aminobutyric acid after the RS was processed, while the contents of ononin, calycosin-7-glucoside, and vanillic acid were reduced. These findings suggest that RS processing may facilitate the transformation of isoflavone glycosides into aglycones through mechanochemical effects. Network pharmacology analysis further identified 10 immune-related compounds, including medicarpin, calycosin-7-glucoside, calycosin, ononin, and formononetin, as potential quality markers. Using chemometric methods such as hierarchical cluster analysis, principal component analysis, and Orthogonal partial least-squares discriminant analysis, robust discrimination models distinguishing RS from “Non-rubbing strip” samples were successfully developed based on the identified Q-Marker. This study, integrating chemical profiling and bioinformatics approaches, identified and predicted potential Q-Markers for HR, providing theoretical and methodological support for establishing a robust and scientifically quality evaluation system for HR.

(J Sep Sci) Prediction and Analysis of Quality Markers for Hedysari Radix Using Ultra‐High‐Performance Liquid Chromatography‐Tandem Mass Spectrometry, Network Pharmacology, Molecular Dynamics, and Chemometrics: ABSTRACT




To establish a scientific and reliable quality… #JSepSci #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 days ago

Unraveling the Oligomer‐specific Uptake Dynamics of PEG600 With 9–18 Subunits in HepG2 Cells by Ultra‐High‐Performance Liquid Chromatography‐Tandem Mass Spectrometry Coupled With Ammonium Adduct Strategy to Enhance Sensitivity This study establishes an UHPLC-MS/MS method for quantifying PEG600 oligomers (n=9-18) in HepG2 cells. The method shows good linearity, reveals low cellular uptake ( 0.99) across 10–1000 ng/mL for PEG600 oligomers (n = 9–18). PEG600 oligomers (n = 9–18) internalization in HepG2 cells was quantified by the validated UHPLC-MS/MS method. PEG600 polymers with 9–18 subunits could be absorbed into HepG2 cells with a small quantity (less than 0.04%). The cytotoxicity study suggested that the half-maximal inhibitory concentration of PEG600 on HepG2 cells is 31.42 mg/mL. PEG600 oligomers demonstrated negligible anti-proliferative effects in HepG2 hepatocytes. This study could provide analytical techniques and critical reference data for cytotoxicity and whole cellular uptake profiles of PEG600 polymers with 9–18 subunits in HepG2 cells. This work establishes an analytical framework for assessing the cytotoxicity and cellular uptake kinetics of PEG600 oligomers (n = 9–18) in HepG2 cells.

(J Sep Sci) Unraveling the Oligomer‐specific Uptake Dynamics of PEG600 With 9–18 Subunits in HepG2 Cells by Ultra‐High‐Performance Liquid Chromatography‐Tandem Mass Spectrometry Coupled With Ammonium Adduct Strategy to Enhance Sensitivity: This study establishes an UHPLC-MS/MS… #JSepSci #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 days ago

Molecular architecture of the ciliary base in mammalian multiciliated cells Multiciliated epithelial cells (MCCs) generate tens to hundreds of motile cilia to drive fluid flow in diverse physiological contexts. While the axonemal structure of motile cilia has been described extensively in recent years, the molecular architecture of the transition zone, basal body, and surrounding ciliary environment of MCCs remain more elusive. Here, we use cryo-focused ion beam (cryo-FIB) milling and cryo-electron tomography (cryo-ET) to obtain in situ 3D views of the ciliary base within intact MCCs from mammalian trachea, complemented by in situ cross-linking mass spectrometry (XL/MS) and ultrastructure expansion microscopy (U-ExM) for molecular identification. Our data reveal spatially-defined modifications of microtubule architecture from the proximal centriole to the early axoneme, including transition zone-specific features such as an A-B linker bridging microtubule doublets and a helical assembly of microtubule inner proteins (MIPs). We show that the ciliary necklace, a feature observed in many motile cilia, is spatially aligned with the transition zone and quantify its regular organization within the membrane. Our in situ data capture rarely observed events, including intraflagellar transport (IFT) trains connecting to ciliary vesicles tethered to undocked centrioles. The surrounding ciliary environment contains intermediate filaments that encircle the basal bodies and bundled actin filaments that elaborate microvilli structures between the cilia. Integration of XL/MS and U-ExM identified novel microtubule associated proteins (MAPs), MIPs, and membrane-associated proteins localized to these distinct subdomains. This work provides a molecular and structural map of the mammalian MCC ciliary base, revealing architectural principles that underlie its assembly, organization, and function.

(BioRxiv All) Molecular architecture of the ciliary base in mammalian multiciliated cells: Multiciliated epithelial cells (MCCs) generate tens to hundreds of motile cilia to drive fluid flow in diverse physiological contexts. While the axonemal structure of motile cilia has… #BioRxiv #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 days ago

Evidence-Driven m/z Alignment in Mass Spectrometry Imaging: Physics Models, Observed-Data Recalibration, and Deep Learning Publication date: Available online 7 April 2026 Source: TrAC Trends in Analytical Chemistry Author(s): Zhuohao Yu, Kai Cheng, Danijela Mišić, Marina Soković, Daniel Figeys, Hongxi Xu, Yang Ye, Jia Liu

(TrAC) Evidence-Driven m/z Alignment in Mass Spectrometry Imaging: Physics Models, Observed-Data Recalibration, and Deep Learning: Publication date: Available online 7 April 2026

Source: TrAC Trends in Analytical Chemistry

Author(s): Zhuohao Yu, Kai Cheng, Danijela Mišić,… #TrAC #MassSpecRSS