Kermit Murray

@kkmurray.bsky.social

2 days ago

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

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




Rationale




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

Kermit Murray

@kkmurray.bsky.social

2 days ago

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

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




Rationale




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

Kermit Murray

@kkmurray.bsky.social

2 days ago

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

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




Rationale




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

Kermit Murray

@kkmurray.bsky.social

3 days ago

Numerical Simulation and Experimental Study of a Dual‐Ionization Source (PI/EI) Quadrupole Mass Spectrometer Based on the CFD–DSMC Method ABSTRACT Background Online analysis of complex gas mixtures is often hindered by spectral congestion resulting from extensive fragmentation in traditional electron ionization (EI) sources. Although photoionization (PI) provides clean mass spectra by preserving molecular ion integrity, its comprehensive detection is limited by an inherent ionization selectivity toward species with low ionization energies. Methods To address these challenges, a dual-ionization source quadrupole mass spectrometer (DISQMS) integrating PI and EI was developed. Its design and optimization were guided by a multiphysics ion trajectory simulation method coupling continuum-rarefied flow fields with electric fields. The flow field, spanning from the sampling capillary to the quadrupole mass analyzer chamber, was numerically simulated using a hybrid computational fluid dynamics–direct simulation Monte Carlo (CFD–DSMC) method. Results Guided by the simulation, the key instrumental parameters were systematically optimized, and the reliability of the simulation model was validated experimentally. During the detection of acetone, benzene, and air mixtures, clean organic spectra were obtained in PI mode, whereas comprehensive detection of inorganic gases with high ionization energies (e.g., N2 and O2) and detailed fragment-ion information were achieved in EI mode. Conclusions A DISQMS was developed and validated, and a multiphysics ion trajectory simulation framework was proposed to numerically optimize the instrument's sensitivity. It was demonstrated that complementary detection of organic and inorganic species is achieved through the dual-mode capability. Specifically, spectral interpretation and molecular structure elucidation are effectively facilitated by combining the detailed fragment-ion information from EI with the clean molecular ion data from PI.

(RCM) Numerical Simulation and Experimental Study of a Dual‐Ionization Source (PI/EI) Quadrupole Mass Spectrometer Based on the CFD–DSMC Method: ABSTRACT




Background




Online analysis of complex gas mixtures is often hindered by spectral congestion… #RapidCommunMassSpectrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 week ago

Lingguizhugan Decoction Alleviates Lung Inflammatory in Obstructive Sleep Apnea by Modulating ROS and HIF‐1α Signaling Pathway Based on UHPLC–MS, Network Pharmacology, Transcriptomics, and Experimental Verification ABSTRACT Rationale Lingguizhugan decoction (LGZG) is a traditional Chinese formula that has been commonly used in obstructive sleep apnea (OSA) for relieving lung inflammation. However, the active substance of LGZG and the specific mechanism remain unclear. This study aims to identify the bioactive components of LGZG and subsequently elucidate the underlying therapeutic mechanisms against OSA based on mass spectrometry analysis, network pharmacology, transcriptomics, and experimental verification. Methods Ultra-high-performance liquid chromatography-high-resolution mass spectrometry (UHPLC–HRMS) was used to identify the main ingredients of LGZG. The OSA animal model was induced by chronic intermittent hypoxia (CIH) for 5 weeks in C57BL/6 mice. Transcriptome sequencing and network pharmacology were used to analyze potential mechanisms, which were further validated by molecular docking. HE staining was used for detecting lung inflammation. Immunohistochemistry (IHC), ELISA, and Western blot were employed to investigate protein expression, while quantitative real-time PCR (RT-qPCR) was used to determine gene expressions. Tissue reactive oxygen species (ROS) levels were measured by the DCFH-DA probe method. Results LGZG inhibited CIH-induced pulmonary inflammatory infiltration, protein concentration in bronchoalveolar lavage fluid (BALF), and suppressed IL-17 and IL-1β gene expression. UHPLC–HRMS identified 482 compounds in the LGZG aqueous decoction. Network pharmacology analysis revealed that IL-6 and HIF-1α pathway were the major targets. Subsequently, transcriptomics analysis revealed that LGZG affected functions associated with ROS production and polymorphonuclear cells. LGZG suppressed the CIH-induced expression of neutrophil elastase and reduced MPO production in BALF. Furthermore, LGZG inhibited the IL-6 expression and secretion, and reduced CIH-induced ROS production. LGZG inhibited the CIH-induced activation of HIF-1α pathway. Moreover, molecular docking identified compounds in LGZG that could directly interact with the core targets IL-6, MPO, CYBB, and HIF-1α. Conclusions LGZG alleviates CIH-induced pulmonary inflammation, neutrophil infiltration, and IL-6 secretion in mice. These effects are associated with the suppression of ROS production and inhibition of the HIF-1α signaling pathway.

(RCM) Lingguizhugan Decoction Alleviates Lung Inflammatory in Obstructive Sleep Apnea by Modulating ROS and HIF‐1α Signaling Pathway Based on UHPLC–MS, Network Pharmacology, Transcriptomics, and Experimental Verification: ABSTRACT




Rationale… #RapidCommunMassSpectrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 weeks ago

Rapid Identification of Chemical Constituents of Zanthoxylum nitidum (Roxb.) DC. by Ultra‐High‐Performance Liquid Chromatography Quadrupole‐Exactive Orbitrap Mass Spectrometry ABSTRACT Rationale Zanthoxylum nitidum (Roxb.) DC. (ZN) is a traditional Chinese medicine known for its diverse pharmacological activities. However, its chemical constituents are complex and not fully elucidated. This study aims to establish a comprehensive chemical profile of ZN to facilitate its further research in the pharmacological substance basis. Methods The comprehensive analysis of chemical constituents in the ZN extract was conducted using ultra-high-performance liquid chromatography coupled with quadrupole-exactive orbitrap mass spectrometry (UHPLC-Q-Exactive Orbitrap MS) cooperated with data postprocessing. The obtained MS data, including quasi-molecular ion peaks, fragment ions, and retention times, were compared with the literature and standard substances to identify the chemical constituents. The characteristic fragments and neutral losses contributed to classify the compounds and infer their cleavage rules. Results Through the nontargeted qualitative identification of ZN constituents, a total of 64 compounds were identified from ZN, comprising 43 alkaloids, four flavonoids, four phenylpropanoids, and 13 others. Among them, eight compounds were newly reported as potential constituents. In addition, the cleavage rules of representative constituents were summarized. Conclusions The UHPLC-Q-Exactive Orbitrap MS and data postprocessing technology were successfully enabled the rapid and comprehensive identification of the chemical constituents of ZN. These findings broaden the understanding of ZN's composition and establish a solid foundation for further pharmacological research.

(RCM) Rapid Identification of Chemical Constituents of Zanthoxylum nitidum (Roxb.) DC. by Ultra‐High‐Performance Liquid Chromatography Quadrupole‐Exactive Orbitrap Mass Spectrometry: ABSTRACT




Rationale




Zanthoxylum nitidum (Roxb.) DC. (ZN) is a… #RapidCommunMassSpectrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 weeks ago

Simultaneous Quantification of Twelve Endogenous HPA Axis Compounds by Protein Precipitation and HILIC‐UPLC–MS/MS in a Mouse Model of Insomnia ABSTRACT Rationale Accurate quantification of neurotransmitters and hormones within the hypothalamic–pituitary–adrenal (HPA) axis is essential for elucidating their pathological roles in neurodegenerative diseases. Methods In this study, a solid-phase extraction (SPE) combined with hydrophilic interaction liquid chromatography–tandem mass spectrometry (HILIC-UPLC-MS/MS) method was developed for the simultaneous determination of 12 endogenous compounds in the HPA axis. The method was fully validated according to FDA standards. Results All analytes showed good linearity over the concentration range of 0.19–19.53 ng/mL, with lower limits of quantification (LLOQs) ranging from 0.19 to 19.53 ng/mL. Accuracy (relative bias) and precision (relative standard deviation) were within ±15%. Matrix effects were evaluated (85.7%–114.3%), and extraction efficiencies were found to be satisfactory (89.1%–108.9%). Compared with other LC-MS-based techniques, this method effectively eliminates interference from endogenous substances by utilizing SPE columns. Conclusions The proposed method exhibited excellent performance in terms of linearity, precision, accuracy, stability, and matrix effects, demonstrating superior practicality and reliability for the analysis of complex biological samples.

(RCM) Simultaneous Quantification of Twelve Endogenous HPA Axis Compounds by Protein Precipitation and HILIC‐UPLC–MS/MS in a Mouse Model of Insomnia: ABSTRACT




Rationale




Accurate quantification of neurotransmitters and hormones within the… #RapidCommunMassSpectrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

3 weeks ago

Ion Useful Yields and Matrix Effects in 26Al–26Mg Dating by Secondary Ion Mass Spectrometry ABSTRACT Rationale Secondary ion mass spectrometry (SIMS) has been widely applied to 26Al–26Mg dating of the earliest Solar System solids. Both 16O− and 16O2 − primary beams have been used for such analyses, yet the influence of primary ion beam species on secondary ion useful yields and matrix effects has not been systematically evaluated. A better understanding of these effects is essential for improving the accuracy and precision of 26Al–26Mg dating. Methods For standard materials used in 26Al–26Mg dating, we determined sputter rates, useful yields, and matrix effects on the relative sensitivity factors (RSFs) of 27Al/24Mg and the instrumental mass fractionations (IMFs) of Mg isotopes under the 16O− and 16O2 − primary beam conditions using SIMS. The sputter rates were evaluated using a rastered beam, whereas the other parameters were obtained under the actual analytical conditions employed for 26Al–26Mg dating. Results The 16O2 − primary beam condition generally provided higher useful yields than the 16O− condition, except for anorthite and melilite analyzed under low ion current conditions. Variations in RSFs among samples of the same mineral species but with different compositions were either larger or smaller between the 16O− and 16O2 − conditions, depending on the mineral species, whereas IMF variations tended to be slightly larger under the 16O2 − condition than under the 16O− condition. Conclusions Our results highlight the necessity of carefully evaluating useful yields, along with the behaviors of RSF and IMF, when optimizing analytical conditions for SIMS-based 26Al–26Mg dating, as well as for other isotopic systems that can be analyzed using SIMS.

(RCM) Ion Useful Yields and Matrix Effects in 26Al–26Mg Dating by Secondary Ion Mass Spectrometry: ABSTRACT




Rationale




Secondary ion mass spectrometry (SIMS) has been widely applied to 26Al–26Mg dating of the earliest Solar System solids. Both 16O− and… #RapidCommunMassSpectrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

3 weeks ago

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

Kermit Murray

@kkmurray.bsky.social

3 weeks ago

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

Kermit Murray

@kkmurray.bsky.social

3 weeks ago

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

Kermit Murray

@kkmurray.bsky.social

1 month ago

δ13C and δ15N Values of Residues Provide Insights Into Identification of the Explosive Source ABSTRACT Rationale Postblast analyses of military and terrorist events will benefit from the capacity to learn more about the explosive materials used in an event. Here stable isotope ratio analyses (δ13C, δ15N) can provide additional information to complement identification of the explosive components. Methods Controlled detonations using different types of military-grade explosives were conducted in 55-gal barrels. Additionally, soil analyses were conducted following Mark-84 field detonations. Swab materials and soils were purified to analyze explosive compounds using established HPLC and IRMS techniques. Results Explosive materials were recovered in the residues of TNT (aromatic-based explosive) and RDX (nonaromatic explosive) detonations in barrel experiments. Explosive residues were not recovered from PETN (nonaromatic explosive). Postblast δ13C and δ15N values of TNT residues were similar to δ values in the source explosive, suggesting minimal enrichment in δ residues. While δ15N values of RDX in postblast residues were also similar to preblast source values, postblast RDX δ13C values were enriched by almost 2‰ relative to the preblast explosive. Similar patterns were observed in HMX, RDX, and NT recovered from soils following Mark-84 detonations. Conclusions δ13C and δ15N values can be effectively measured on explosive compounds recovered in residues following detonations. Residue δ13C and δ15N values can be linked to δ values of undetonated explosive compounds. Additional field studies should be conducted to verify these results.

(RCM) δ13C and δ15N Values of Residues Provide Insights Into Identification of the Explosive Source: ABSTRACT




Rationale




Postblast analyses of military and terrorist events will benefit from the capacity to learn more about the explosive materials used… #RapidCommunMassSpectrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 month ago

Correction to ‘Analysing Sr Isotopes in Low‐Sr Samples Such as Single Insects With Inductively Coupled Plasma Tandem Mass Spectrometry Using N2O as a Reaction Gas for In‐Line Rb Separation’ Rapid Communications in Mass Spectrometry, Volume 40, Issue 10, 30 May 2026.

(RCM) Correction to ‘Analysing Sr Isotopes in Low‐Sr Samples Such as Single Insects With Inductively Coupled Plasma Tandem Mass Spectrometry Using N2O as a Reaction Gas for In‐Line Rb Separation’: Rapid Communications in Mass Spectrometry, Volume 40, Issue 10,… #RapidCommunMassSpectrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 month ago

UHPLC–MS/MS Quantification of Human Cytosolic Aldehyde Oxidase: Heat‐Assisted In‐Solution Protein Denaturation and Digestion ABSTRACT Rationale The quality of protein denaturation and digestion is critical in determining the performance of a UHPLC–MS/MS method in absolute protein quantification. Previous UHPLC–MS/MS methods on human aldehyde oxidase (AOX1) protein provided little or no methodological information on protein denaturation and digestion. Therefore, we developed and optimized a sample preparation method for the UHPLC–MS/MS quantification of human cytosolic AOX1. Methods Various reagents and conditions in protein denaturation (urea, Rapigest, temperature, heating time, and acetonitrile) and digestion (incubation time) were evaluated. A UHPLC–MS/MS method was developed and validated for quantifying the surrogate peptide 446VFFGEGDGIIR456 for AOX1 and its stable-isotope-labelled internal standard. Results Surrogate peptide yield was improved by our optimized conditions for AOX1 protein denaturation (heating at 80°C for 15 min together with reduction by DL-dithiothreitol, acetonitrile not added during trypsin digestion) and protein digestion (4 h). A solvent composition of 40% water-10% acetonitrile-50% ammonium bicarbonate buffer enhanced peptide solubility and assay linearity and sensitivity. An AOX1-negative cytosol was an appropriate matrix blank for cellular samples. The UPHLC–MS/MS assay validation metrics were within acceptable FDA guidelines, highlighted by peptide stability during sample preparation, a shorter run time (11.5 min), greater sensitivity (7.5 fmol), broader linearity range (7.5–10 000 fmol), allowing for the low femtomole quantification of human cytosolic AOX1. Conclusions Our novel methodological advances, as highlighted by a high temperature, in-solution protein denaturation protocol and optimal digestion time, solvent composition, and matrix blank, enabled the femtomole quantification of AOX1 protein using a validated UHPLC–MS/MS method with better assay performance than previous methods.

(RCM) UHPLC–MS/MS Quantification of Human Cytosolic Aldehyde Oxidase: Heat‐Assisted In‐Solution Protein Denaturation and Digestion: ABSTRACT




Rationale




The quality of protein denaturation and digestion is critical in determining the performance of a… #RapidCommunMassSpectrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 month ago

Sensitive Detection of Salmonella Susceptibility to Ceftriaxone and Azithromycin Using Matrix‐Assisted Laser Desorption/Ionization Time‐of‐Flight Mass Spectrometry ABSTRACT Background The rising incidence of Salmonella-induced diarrhea highlights the critical need for judicious antibiotic use to ensure effective treatment outcomes. Methods This study presents an innovative methodology for evaluating the susceptibility of Salmonella to ceftriaxone and azithromycin through the application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Results The proposed method requires only 2–3 individual Salmonella colonies and yields results within approximately 1 hour, assessing susceptibility to ceftriaxone (70 mg/L) and azithromycin (25 mg/L). In comparison to the Kirby-Bauer method, this technique exhibits a sensitivity of 98.64% and a specificity of 84.38%. Conclusions The method developed in this study is both straightforward and user-friendly, making it suitable for deployment in major laboratories equipped with time-of-flight mass spectrometry. It offers a preliminary assessment of Salmonella susceptibility to ceftriaxone and azithromycin, thereby enhancing the accuracy of clinical interventions for Salmonella infections.

(RCM) Sensitive Detection of Salmonella Susceptibility to Ceftriaxone and Azithromycin Using Matrix‐Assisted Laser Desorption/Ionization Time‐of‐Flight Mass Spectrometry: ABSTRACT




Background




The rising incidence of Salmonella-induced diarrhea highlights… #RapidCommunMassSpectrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 month ago

Automated Near Real‐Time QC for LC‐HRMS ABSTRACT Rationale The quality of analytical measurements is typically evaluated after completion of the entire, or possibly multiple, measurement batch(es). Automated, near real-time quality control (QC) during LC-HRMS acquisition can prevent reruns and sample loss by flagging issues as they occur. Functionality was evaluated by retrospective application to 5 years of river-water surveillance. Methods We present a modular MATLAB workflow that tracks isotopically labelled internal standards for peak height, retention time and mass error against rolling, method-specific expectations; applies multivariate statistical process control (MSPC; PCA with Hotelling's T 2 and SPE on intensity/retention time ratios and mass error); issues immediate email alerts; and logs outcomes to a PostgreSQL database/Grafana dashboard for trend analysis. Also, qualitative target screening via cosine-similarity MS2 checks against a local library, retention time correction, robust peak-height/noise estimation, configurable limits and automated vendor-to-open format conversion. Results In a high-voltage power-supply failure, 25/25 injections were flagged due to abnormal intensity patterns; during an organic-pump malfunction, 17/25 were flagged for retention drift up to and beyond the extraction window; and during an air-conditioning (AC) outage, MSPC detected mass error anomalies even when the ±10 ppm univariate limit was not breached. MSPC closely agreed with univariate thresholds: 95.7% of samples flagged by univariate rules were also flagged by MSPC (≈4.3% Type II), while 92.5% of MSPC-flagged samples violated at least one univariate rule (≈7.5% Type I). Conclusion These capabilities enable immediate detection, triage and documentation of performance excursions, support proactive maintenance (e.g., column aging or pump delivery issues), minimise downtime and safeguard precious samples. Although showcased on a specific LC-HRMS setup and matrix, the workflow is instrument-agnostic and broadly applicable to internal-standardised LC-HRMS methods.

(RCM) Automated Near Real‐Time QC for LC‐HRMS: ABSTRACT




Rationale




The quality of analytical measurements is typically evaluated after completion of the entire, or possibly multiple, measurement batch(es). Automated, near real-time quality control (QC)… #RapidCommunMassSpectrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 month ago

Rapid Detection of Plasticizer Migration From UV‐Aged PVC Films by DART‐HRMS ABSTRACT Rationale The migration of phthalate plasticizers from high-volume polymers, such as poly(vinyl chloride) (PVC), raises significant toxicological concerns, particularly when materials are subjected to aging and environmental stress. As traditional monitoring techniques rely on time-consuming solvent extraction and chromatographic methods that are often expensive and lack the throughput required for large-scale safety screening, this study intends to present a rapid screening method using direct analysis in real time coupled to high-resolution mass spectrometry (DART-HRMS) to monitor plasticizer migration in PVC films subjected to accelerated UV aging. Operational parameters, such as ionization gas temperature and grid voltage, were systematically optimized to balance desorption efficiency with molecular integrity. Methods DART-HRMS analysis of three commercial PVC films subjected to accelerated UV aging (ASTM G154-23) was performed after optimization of the operational parameters: ionization gas temperature: 250 °C, 350 °C, and 500 °C and grid voltage: 50 and 350 V were systematically optimized to balance desorption efficiency with molecular integrity. Results Analytical performance was strongly governed by source energy, with optimal conditions achieved at 350 °C and 50 V, yielding the highest signal stability and minimal in-source fragmentation. Elevated grid voltage (350 V) caused severe signal suppression and fragmentation, particularly for high-molecular-weight plasticizers such as DIDP and DINP. Application of the optimized method revealed formulation-dependent migration behavior during UV aging. Short-chain phthalates showed rapid and, in some cases, transient surface enrichment, whereas medium- and high-molecular-weight plasticizers exhibited delayed or limited migration, becoming detectable only after prolonged exposure. Conclusions DART-HRMS provides a fast, robust, and solvent-free approach for screening plasticizer migration in PVC films. The optimized conditions enable sensitive detection while preserving molecular integrity, allowing differentiation of additive mobility as a function of molecular weight, formulation, and UV-induced degradation. This methodology offers a high-throughput alternative for assessing additive stability and potential release in consumer-grade PVC materials.

(RCM) Rapid Detection of Plasticizer Migration From UV‐Aged PVC Films by DART‐HRMS: ABSTRACT




Rationale




The migration of phthalate plasticizers from high-volume polymers, such as poly(vinyl chloride) (PVC), raises significant toxicological concerns,… #RapidCommunMassSpectrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 month ago

TCEP‐Mediated Protein Hydrolysis: Highly Selective Cleavage C‐Terminal to Aspartic Acid ABSTRACT Background Tris(2-carboxyethyl)phosphine (TCEP) is a commonly used laboratory reagent for the purposes of reducing disulfide bonds. TCEP is often preferred over alternative reducing reagents, such as dithiothreitol (DTT), due to its strong redox potential, effectiveness in a broad pH range, and handling considerations. Despite this, many side reactions involving TCEP have been poorly categorized and understood. Finding Utilizing a combination of gel electrophoresis and mass spectrometry techniques, we have discovered a unique and novel mechanism by which TCEP engages in the hydrolysis of proteins. This behavior has been observed to be site specific to the carboxyl terminus of aspartic acid residues. Conclusion Cleavage at this location is completely independent of the reduction of disulfide bonds in proteins due to the observance of this phenomenon in proteins lacking disulfide bonds, and some lacking cysteines altogether. While the specific chemistry of this hydrolysis is unknown, this discovery has potentially wide-ranging impacts as a sample preparation tool for mass spectrometry analysis, as well as being cautionary towards other common laboratory uses of this ubiquitous reagent where it could potentially cause unwanted hydrolysis of proteins being studied. Impact The broader analytical implications of this finding are that many previously unknown origin artifacts can now be properly attributed to a source, particularly in areas such as proteomic sample preparation, redox chemistries studies, and similar. This also expands our knowledge of TCEP chemistry beyond simply a disulfide bond reductor, offering both methodological opportunities for peptide mapping and important cautionary implications for biochemical sample treatment.

(RCM) TCEP‐Mediated Protein Hydrolysis: Highly Selective Cleavage C‐Terminal to Aspartic Acid: ABSTRACT




Background




Tris(2-carboxyethyl)phosphine (TCEP) is a commonly used laboratory reagent for the purposes of reducing disulfide bonds. TCEP is often… #RapidCommunMassSpectrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

1 month ago

Combustion and Pyrolysis EA‐IRMS Techniques to Determine the δ2H of Diamonds ABSTRACT Rationale Diamonds are generally considered to be metasomatic minerals originating from the Earth's mantle. They formed through the interaction of carbon-bearing fluids or melts with the surrounding deep lithology. Most knowledge about the formation of diamonds comes from studying their mineral inclusions or stable isotopes. Furthermore, diamonds are the only geological samples that provide insight into the volatile element composition of the Earth's mantle. While hydrogen has been known since the early 1970s to be a common impurity in natural diamonds, only a few studies have provided satisfactory quantitative measurements of its concentration and isotopic composition. Methods Here, we compare the results obtained using two different techniques involving EA-IRMS. The first analytical procedure involves H-pyrolysis and is a modification from existing techniques. The second innovative setup, which has not yet been described, involves diamond combustion followed by hydrogen reduction. Results As diamond test samples are rare, we first analysed analogous samples (graphite) to validate the method, before analysing polycrystalline diamonds (from the Orapa mine in Botswana) with both techniques. After assessing the consistency between the two procedures, we analysed three natural diamonds. The results obtained using both techniques were highly comparable. This confirmed the validity of the H-Pyrolysis method, which is slightly more sensitive. Conclusions We designed and validated a novel methodology to incorporate an additional isotopic record into diamonds, namely, carbon, oxygen and nitrogen, with the objective of tracing the formation process of natural diamonds. Diamond in situ analyses might enhance our comprehension of the deep water cycle. Those measurements require precisely calibrated materials. This technique could provide such references.

(RCM) Combustion and Pyrolysis EA‐IRMS Techniques to Determine the δ2H of Diamonds: ABSTRACT




Rationale




Diamonds are generally considered to be metasomatic minerals originating from the Earth's mantle. They formed through the interaction of… #RapidCommunMassSpectrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 months ago

Phospholipid Profiling Established by Structure‐Rich Fragments for Molecular Species Level Shotgun Analysis ABSTRACT Rationale Accurate identification of phospholipid molecular species remains a major challenge in shotgun lipidomics because conventional tandem mass spectrometry typically resolves only one structural moiety at a time. This structural ambiguity limits confident lipid biomarker discovery and biological interpretation. Improving structural specificity without sacrificing analytical speed is therefore critical for lipidomics and disease-related studies. Methods Electrospray ionization tandem mass spectrometry was performed using direct infusion on a triple quadrupole mass spectrometer operated in multiple reaction monitoring (MRM) mode. MRMs were designed based on structure-rich phospholipid fragments containing both the headgroup and one fatty acyl chain. Lipids were extracted from mouse liver and brain tissues and analysed without chromatographic separation, and normal-phase LC was used for lipid headgroup confirmation only. Results Structure-rich MS/MS transitions enabled molecular species identification of both diacyl and ether phospholipids. 15 PUFA-containing phospholipids were identified as candidate biomarkers differentiating healthy and metabolic syndrome mouse livers, revealing opposing regulation among structurally similar species supported by complementary fragmentation and LC evidence. In mouse brains, three ether lipid biomarkers were discovered, including plasmalogens and plasmanyl lipids, with distinct disease-associated trends. Conclusion This study demonstrates that structure-rich MS/MS transitions substantially improve phospholipid structural specificity in shotgun lipidomics while maintaining high throughput. The method enables reliable identification of individual lipid species with minimal isomer interference and is readily compatible with existing workflows. This strategy offers a practical path toward more precise lipid biomarker discovery and mechanistic insight into metabolic disease.

(RCM) Phospholipid Profiling Established by Structure‐Rich Fragments for Molecular Species Level Shotgun Analysis: ABSTRACT




Rationale




Accurate identification of phospholipid molecular species remains a major challenge in shotgun lipidomics because… #RapidCommunMassSpectrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 months ago

In Vitro Metabolism and Analytical Characterization of SLU‐PP‐332 and SLU‐PP‐915: Novel Pan‐ERR Agonists With Doping Potential ABSTRACT Rationale Estrogen-related receptor (ERR) agonists such as the drug candidates SLU-PP-332 and SLU-PP-915 are currently being investigated as exercise mimetics, given their ability to trigger human physiological processes similar to those initiated by actual physical activity. This capability prompted the consideration of these compounds as drugs potentially relevant for sports drug testing programs. Methods The two pan-ERR agonists SLU-PP-332 and SLU-PP-915 were characterized using liquid chromatography-high resolution (tandem) mass spectrometry (LC–HRMS/MS). Furthermore, the in vitro metabolic transformation products of both compounds prepared by means of human liver S9 fraction (S9 fraction) and human liver microsomes (HLMs) were analyzed. In addition, selected metabolites of SLU-PP-915 were synthesized and their structures were analyzed by nuclear magnetic resonance (NMR) spectroscopy. Results A total of nine metabolites were identified for SLU-PP-332, consisting of six Phase-I metabolites and three Phase-II conjugates. Conversely, the analysis of SLU-PP-915 yielded only Phase-I transformation products, with a total of seven metabolites identified. In both cases, an in-depth structural elucidation was conducted to obtain a comprehensive overview of the detected metabolites. Furthermore, three metabolites of SLU-PP-915 were confirmed through chemical synthesis and NMR. Conclusion The results obtained in this study gave an in-depth view into the analysis and in vitro metabolism of the newly developed pan-ERR agonists SLU-PP-332 and SLU-PP-915. This may help to uncover the illicit use of these novel compounds as potential performance-enhancing substances.

(RCM) In Vitro Metabolism and Analytical Characterization of SLU‐PP‐332 and SLU‐PP‐915: Novel Pan‐ERR Agonists With Doping Potential: ABSTRACT




Rationale




Estrogen-related receptor (ERR) agonists such as the drug candidates SLU-PP-332 and SLU-PP-915 are… #RapidCommunMassSpectrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 months ago

Colicin‐Bearing Plasmids Carried by Shiga Toxin‐Producing E. coli (STEC) Analyzed by Targeted Top‐Down MS Analysis ABSTRACT Rationale Colicins are protein toxins produced by bacteria that destroy the nucleic acids or outer membranes of their bacterial neighbors. Their genes are encoded in small extra-chromosomal plasmids that play an important role in bacterial survival. Although colicins do not contribute to bacterial pathogen virulence, it is important to develop methods to identify molecular determinants that facilitate pathogen survival. Methods Shiga toxin-producing Escherichia coli (STEC) were analyzed for the presence of colicin-bearing plasmids using antibiotic induction, MALDI-TOF-TOF, Orbitrap mass spectrometry, and targeted top-down analysis using in-house software. Small plasmid sequencing was used to confirm plasmid-encoded genes as well as their upstream regulation. AlphaFold3 was used to rationalize expected (as well as anomalous) fragment ions detected by MS/MS post-source decay (PSD). Results Colicin immunity (Imm) proteins were detected and identified by targeted top-down mass spectrometry in two STEC strains (serotypes O26:H11 and O104:H7) that carried one or more colicin plasmids. ImBac, ImmD, and a 7.8 kDa hypothetical protein (whose gene resides on a plasmid that encodes a pore-forming colicin) were detected and identified. Whole genome sequencing (by other groups) and our small plasmid sequencing confirmed the colicin/immunity genes as well as their upstream regulatory control. Conclusions MALDI-TOF-TOF-MS/MS-PSD is an effective platform for rapid detection and identification of inducible antibacterial protein toxins. We also note that the previously reported glycine-enhanced aspartic acid effect (AAE) appears to occur most often at unstructured/linker regions of the polypeptide backbone.

(RCM) Colicin‐Bearing Plasmids Carried by Shiga Toxin‐Producing E. coli (STEC) Analyzed by Targeted Top‐Down MS Analysis: ABSTRACT




Rationale




Colicins are protein toxins produced by bacteria that destroy the nucleic acids or outer membranes of their… #RapidCommunMassSpectrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 months ago

Label‐Free Quantitative Proteomics Analysis Revealed the Peptide and Keratin Protein Pattern in Different Types of Sunda Porcupine (Hystrix javanica) Quill ABSTRACT Rationale Sunda porcupine (Hystrix javanica) has quills that exhibit considerable morphological diversity and functionality, yet the molecular variation underlying these differences remains insufficiently explored. Comprehensive proteomic profiling provides an opportunity to examine peptide composition and keratin expression patterns across quill types. This study aims to characterize molecular distinctions among Sunda porcupine quills using label-free quantitative proteomic analysis. Methods Three quill types—spine, true quill, and rattle quill—were collected, cleaned, pulverized, and subjected to keratin-specific extraction employing reducing agents. Extracted proteins underwent in-solution digestion before analysis using LC–MS/MS on a high-resolution Orbitrap system. Peptide and protein identification utilized SequestHT against curated rodent keratin databases. Data were processed through multivariate statistical analyses, including PCA, PLS-DA, SOM, and heatmap clustering to assess quill-specific clustering, peptide distribution, and keratin profile variation among quill types. Results LC–MS/MS identified 653 peptides and 70 homologous proteins, revealing molecular variation among quill types. True quill and spine displayed overlapping peptide abundance patterns, whereas rattle quill demonstrated distinct clustering. Amino acid composition varied among quills, reflecting structural and functional differentiation. True quill and spine showed higher intensity of proteins than rattle quill. Keratin type I cuticular and cytoskeletal proteins were the most matched proteins. Protein profile indicated high similarity to keratins from Hystricomorpha rodent species. Conclusion The study demonstrates clear molecular differentiation among quill types, with true quill and spine exhibiting closer proteomic similarity than rattle quill. Distinct peptides identified in each quill category highlight their potential as biomarkers for quill-type discrimination, although further validation is required to confirm their diagnostic reliability.

(RCM) Label‐Free Quantitative Proteomics Analysis Revealed the Peptide and Keratin Protein Pattern in Different Types of Sunda Porcupine (Hystrix javanica) Quill: ABSTRACT




Rationale




Sunda porcupine (Hystrix javanica) has quills that exhibit considerable… #RapidCommunMassSpectrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 months ago

A Novel 1,3‐Sigmatropic Rearrangement in an Iminium Ion Generated in Collision‐Induced Decomposition During Electrospray Ionization High Resolution Multistage Mass Spectrometry ABSTRACT Rationale Rapid structural elucidation of unknown pharmaceutical impurities is critical throughout the whole life cycle of drug development. It can be achieved by using multistage mass spectrometric analysis, in conjunction with the understanding of dissociation mechanisms of the ions generated by electrospray ionization. Methods Liquid chromatography-UV/photo diode array detection—high resolution multistage mass spectrometric analysis (HiRes MSn) was used to elucidate the structure of an impurity of silodosin. The structure was confirmed by 1D and 2D NMR spectroscopy. Results The impurity is identified as N-cyanomethylsilodosin, a solution degradant of silodosin. A novel 1,3-sigmatropic rearrangement was observed during one of its MS3 dissociation pathways. A mechanism is proposed for the 1,3-sigmatropic rearrangement, which is supported by the MSn behavior of a 13C-isotope labeled derivative of N-cyanomethylsilodosin. Conclusion Elucidation of such an intra-molecular rearrangement mechanism not only enriches our understanding of the gas phase dissociation chemistry, but also should facilitate future rapid structural characterization of unknown pharmaceutical impurities and metabolites using multistage mass spectrometric analysis.

(RCM) A Novel 1,3‐Sigmatropic Rearrangement in an Iminium Ion Generated in Collision‐Induced Decomposition During Electrospray Ionization High Resolution Multistage Mass Spectrometry: ABSTRACT




Rationale




Rapid structural elucidation of unknown… #RapidCommunMassSpectrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 months ago

Mass Spectrometry‐Based Proteomics to Understand Immune Thrombocytopenic Purpura: A Review ABSTRACT Background Immune thrombocytopenic purpura (ITP) is an autoimmune bleeding disorder with substantial variability in bleeding manifestations and a generally low risk of fatal outcomes. Diagnosis is based on exclusion and is supported by thrombocytopenia in peripheral blood and characteristic megakaryocytic findings in bone marrow examination. In many adults, treatment remains suboptimal, and morbidity may result from both bleeding and the adverse effects of immunosuppressive therapies. Rationale Identifying the underlying disease process is essential for improving diagnostic precision, developing targeted therapies, and enhancing patient outcomes. Objective This review summarizes mass spectrometry-based proteomics studies investigating the pathogenesis of ITP and their diagnostic, prognostic, and therapeutic implications. Conclusion Despite significant clinical heterogeneity, proteomic research in ITP remains limited, underscoring the need for comprehensive molecular studies to better elucidate disease mechanisms.

(RCM) Mass Spectrometry‐Based Proteomics to Understand Immune Thrombocytopenic Purpura: A Review: ABSTRACT




Background




Immune thrombocytopenic purpura (ITP) is an autoimmune bleeding disorder with substantial variability in bleeding manifestations and a… #RapidCommunMassSpectrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 months ago

Recursive Attention–Based Prediction of Theoretical MS/MS Spectra From Peptide Sequences ABSTRACT Rationale In tandem mass spectrometry (MS/MS)–based proteomics, precise prediction of peptide spectra is key to improving peptide identification accuracy and the overall reliability of proteomic studies. However, existing theoretical MS/MS prediction methods are limited by their focus on predicting only b and y backbone fragment ions and their inability to effectively capture the complex long-range dependencies among distant residues within peptide sequences. Methods To address these issues, we propose DeepMultiIon, a novel prediction framework based on a mathematically grounded recursive attention mechanism, designed to enhance MS/MS spectral fitting and improve peptide detection sensitivity. By combining local chunking with recursive attention, the model enables deep modeling of long-range residue interactions and the corresponding fragment intensity dependencies. In addition to conventional b and y backbone fragment ions, DeepMultiIon further extends its predictive coverage to a ions and precursor ions, while also encompassing their neutral loss ions (–H2O, –NH3) and isotopic peaks, offering comprehensive coverage of all major spectral peak types. Results Performance is evaluated using Pearson correlation coefficient (PCC) and entropy similarity (ES), with comparisons against b/y-only models such as Prosit, pDeep, and AlphaPeptDeep. Experimental results show that DeepMultiIon achieves notable improvements, with average increases of 0.18 in PCC and 0.22 in ES. Conclusions These findings demonstrate that incorporating recursive attention and multi-ion prediction significantly improve both the peak coverage and accuracy of theoretical MS/MS spectrum prediction, thereby enhancing peptide-spectrum fitting and contributing to improved peptide detection sensitivity, making DeepMultiIon a powerful tool for advanced proteomics analysis.

(RCM) Recursive Attention–Based Prediction of Theoretical MS/MS Spectra From Peptide Sequences: ABSTRACT




Rationale




In tandem mass spectrometry (MS/MS)–based proteomics, precise prediction of peptide spectra is key to improving peptide identification… #RapidCommunMassSpectrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 months ago

Clumped Isotope Temperature Reconstruction Using Stalagmite Drip Cups ABSTRACT Rationale Application of clumped isotope palaeothermometry to speleothems (carbonate cave deposits, e.g., stalagmites and flowstones) has been restricted largely to subaqueous samples because of kinetic fractionation processes that occur during subaerial speleothem formation, which lead to erroneously high inferred temperatures. Speleothems are spatially near-ubiquitous terrestrial archives that can be dated accurately over million-year timescales. Thus, wider application of the clumped isotope technique in speleothems could dramatically increase our understanding of terrestrial thermal history. In this study, we assessed the potential of speleothem drip cups (concave depressions at a stalagmite apex in which dripwater accumulates to create a subaqueous environment) to yield reliable palaeotemperature inferences. Methods We sampled along two isochronous layers that extend across both sides of a pronounced drip cup in stalagmite MAYA 22-7 from Cenote Ch'en Mul, Yucatán, Mexico, which was dated to 1650 ce ± 23 years. We measured bulk stable (δ18O and δ13C) and clumped (Δ47) isotope values at increasing distances from the drip cup centre to test for kinetic fractionation effects. Results Lower δ18O, δ13C, and higher Δ47 values were obtained from the drip cup's central subaqueous zone compared with the subaerial flanks, demonstrating reduced isotope fractionation in the subaqueous zone. Average clumped isotope temperatures (T Δ47) inferred from subaqueous drip cup samples are 1°C–2°C higher than modern cave temperatures and 3°C–7°C warmer than estimated formation paleotemperatures derived from nearby regional reconstructions and TEX86 analysis of our sample. This suggests a persistent degree of clumped isotope kinetic effects. Conclusions Despite persistent kinetic effects, lower inferred temperatures from subaqueous drip cup samples suggest closer to equilibrium precipitation compared with subaerial samples. We propose that drip cup carbonates have the potential to yield reliable palaeotemperatures and describe a widely applicable test for clumped isotope kinetic effects in speleothem drip cups by sampling across isochronous layers.

(RCM) Clumped Isotope Temperature Reconstruction Using Stalagmite Drip Cups: ABSTRACT




Rationale




Application of clumped isotope palaeothermometry to speleothems (carbonate cave deposits, e.g., stalagmites and flowstones) has been restricted largely to… #RapidCommunMassSpectrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 months ago

Pyrene‐Conjugated, 2‐Pyridinecarboxaldehyde Derivatives as N‐Terminus‐Specific Tags for MALDI‐ and LALDI‐MS ABSTRACT Background Proteolytic processing is a fundamental post-translational modification. Liquid chromatography–tandem mass spectrometry (LC–MS/MS) workflows are powerful for degradomic analyses but inherently sacrifice spatial information, a critical aspect for investigating biological systems such as aberrant extracellular matrix remodeling and alterations of the tumor microenvironment. Matrix-assisted laser desorption/ionization (MALDI) offers potential for fast spatial profiling, but MALDI imaging of tryptic peptides is still challenged by spectral crowding and restricted abilities for MALDI MS/MS identification. Methods To address these limitations, we developed pyrene-conjugated 2-pyridinecarboxaldehyde (pyr-2PCA) tags for selective N-terminal labeling and enhanced detection sensitivity. The 2PCA reagent exclusively modifies N-terminal α-amines, not lysine ε-amines, as could be confirmed in MALDI-MS, with concentration-dependent side reactions minimized by dilution. A distinct reporter ion produced by 2PCA-labeled peptides in prm-PASEF (MALDI MS/MS) serves as a unique marker for successful labeling. Results The covalent conjugation of 2PCA with a pyrene structure results in the pyr-2PCA tag that enables matrix-free, label-assisted laser desorption ionization mass spectrometry (LALDI-MS) measurements of peptides. We demonstrate that labeling with a pyrene-coupled 2PCA tag (pyr-2PCA) prior to tryptic digestion results in the selective detection of N-terminal peptides in LALDI, with no significant off-target labeling. Conclusions This study presents the first presentation and characterization of this novel pyr-2PCA tag, thereby laying the groundwork and demonstrating its future potential for MALDI/LALDI-based in situ spatial N-terminomics to study proteolytic processes.

(RCM) Pyrene‐Conjugated, 2‐Pyridinecarboxaldehyde Derivatives as N‐Terminus‐Specific Tags for MALDI‐ and LALDI‐MS: ABSTRACT




Background




Proteolytic processing is a fundamental post-translational modification. Liquid chromatography–tandem mass… #RapidCommunMassSpectrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 months ago

Chamber‐by‐Chamber Measurements of Planktonic Foraminiferal Mg, Sr, and Na to Ca Ratios With Femtosecond LA‐ICP‐MS ABSTRACT Rationale Distribution patterns of foraminifera are controlled by environmental parameters such as temperature, salinity, and nutrient concentrations in each water mass. Since trace elements to Ca ratios of marine microfossil calcite test of foraminifera record environmental and ecological habitat information, we used femtosecond (fs) LA-ICP-MS to obtain accurate chamber-by-chamber Mg/Ca, Sr/Ca, and Na/Ca of four foraminifera species to clarify the impact of foraminiferal depth migration on paleoceanographic reconstruction. The Mg/Ca and Sr/Ca ratios were measured with precision better than 5%, fulfilling the accuracy typically required for paleoceanographic reconstructions. We also examined the differences in element ratios due to the pretreatment cleaning methods for extracting accurate paleoceanographic information. Methods The fsLA-ICP-MS has the advantage of less matrix and instrumental element fractionation effects on elements with high condensation temperatures. We also applied the use of multiple carbonate standard materials for concentration standardization. Results The fsLA-ICP-MS analysis was optimized using a spot size of 30 μm or larger with a laser repetition frequency of 5 to 15 Hz in a circular analytical trajectory. A comparison between ultrasonic and oxidative cleaning protocols revealed that oxidative test cleaning with perchloric acid and hydrogen peroxide achieved higher reproducibility and more efficient impurity removal compared to ultrasonic cleaning with ultrapure water and methanol. Repeated analysis on the same chambers of two species, O. universa and P. obliquiloculata, yielded mean relative standard deviations for Mg/Ca and Sr/Ca of

(RCM) Chamber‐by‐Chamber Measurements of Planktonic Foraminiferal Mg, Sr, and Na to Ca Ratios With Femtosecond LA‐ICP‐MS: ABSTRACT




Rationale




Distribution patterns of foraminifera are controlled by environmental parameters such as temperature, salinity,… #RapidCommunMassSpectrom #MassSpecRSS

Kermit Murray

@kkmurray.bsky.social

2 months ago

Gas‐Phase F‐Atom Migration Reactions of Perfluoroalkyl and Polyfluoroalkyl Sulfonic/Sulfinic Anions ABSTRACT Rationale Many perfluoroalkyl and polyfluoroalkyl sulfonic/sulfinic acids and their derivatives are classified as perfluoroalkyl and polyfluoroalkyl substances (PFASs). The use of mass spectrometry techniques to analyze these compounds has attracted considerable research attention. Methods In this article, we employed high-resolution electrospray ionization tandem mass spectrometry (HR-ESI-MS/MS) and all-ion fragmentation (AIF) in negative ion mode to investigate gas-phase F-atom migration reactions of various perfluoroalkyl and polyfluoroalkyl sulfonic/sulfinic anions, particularly those yielding FSO3 − or FSO2 −. Results HR-ESI-MS/MS of CF3SO3 − yielded an unexpected product ion FSO3 −, representing a distinct pathway of gas-phase F-atom migration from C-atom to S-atom accompanied by the loss of CF2. Similarly, HR-ESI-MS/MS of CF3SO2 − produced a dominant product ion FSO2 − also via CF2 elimination. Complementary ESI-MS/MS and AIF experiments on these anions confirmed that FSO2 − and/or FSO3 − are their characteristic fragmentation ions. Conclusion Theoretical calculations of gas-phase reactions CF3SO3 − → FSO3 − + CF2 and CF3SO2 − → FSO2 − + CF2 were performed to investigate the possible F-atom migration mechanisms. These results show that FSO3 − at m/z 99 and/or FSO2 − at m/z 83 could serve as diagnostic ions for structural elucidation of perfluoroalkyl and polyfluoroalkyl sulfonic/sulfinic acids and their derivatives in non-target PFASs analyses by using mass spectrometry.

(RCM) Gas‐Phase F‐Atom Migration Reactions of Perfluoroalkyl and Polyfluoroalkyl Sulfonic/Sulfinic Anions: ABSTRACT




Rationale




Many perfluoroalkyl and polyfluoroalkyl sulfonic/sulfinic acids and their derivatives are classified as perfluoroalkyl and… #RapidCommunMassSpectrom #MassSpecRSS