Journal of Mass Spectrometry最新文献

{"title":"Sodiation of Enhanced Green Fluorescent Protein (EGFP) in Basic Solution Studied by Electrospray Mass Spectrometry","authors":"Kenzo Hiraoka,&nbsp;Satoshi Ninomiya,&nbsp;Stephanie Rankin-Turner,&nbsp;Noa Suzuki,&nbsp;Satoko Akashi","doi":"10.1002/jms.5111","DOIUrl":"10.1002/jms.5111","url":null,"abstract":"<div>\u0000 \u0000 <p>In our previous work, the sodiation of melittin, cytochrome <i>c</i>, and ubiquitin in a 1 mM NaOH water/methanol solution was studied by electrospray mass spectrometry. It was suggested that the α-helix is more resistant to sodiation than the β-sheet. In this study, sodiation of enhanced green fluorescent protein (EGFP) composed of a β-barrel was studied in 1% CH₃COOH (AcOH) or 1 mM NaOH water/methanol solution by electrospray mass spectrometry. Although EGFP was denatured in an acidic solution, it maintains a near-native structure in a basic solution. For the 1% AcOH solution, the protonated EGFP, [EGFP + nH − mH + mNa]ⁿ⁺, with <i>n</i> = 14 − 36 and <i>m</i> = 0 was detected. For 1 mM NaOH, the number <i>n</i> for [EGFP + nH − mH + mNa]ⁿ⁺ was found to increase with the sodiation number <i>m</i> and vice versa for [EGFP + nH − mH + mNa]ⁿ⁻. Namely, Na⁺ adducts counteract the negative charges of deprotonated acidic residues. The protonated EGFP detected as major ions for basic 1 mM NaOH was ascribed to the more surface-active H₃O⁺(aq) than OH⁻(aq).</p>\u0000 </div>","PeriodicalId":16178,"journal":{"name":"Journal of Mass Spectrometry","volume":"60 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2025-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142932002","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cryogenic TOF-SIMS Around Sublimation Temperature of Quench-Condensed Noble Gas (Ne, Ar, and Kr) Films","authors":"Taku T. Suzuki","doi":"10.1002/jms.5107","DOIUrl":"10.1002/jms.5107","url":null,"abstract":"<div>\u0000 \u0000 <p>A possible TOF-SIMS analysis of surface phase transitions has recently been proposed for limited cases such as polymers and ionic liquids. In the present study, we have extended this analysis to quench-condensed noble gas films. The newly developed cryogenic TOF-SIMS allowed both measurements of TOF-SIMS below 4 K, and low-energy ion scattering spectroscopy that is used to prepare a clean surface. It was found that the TOF-SIMS intensity variation by increasing the temperature at a constant ramp rate (temperature-programmed TOF-SIMS) shows steep changes due to sublimation. Thus, the possibility of analyzing the surface phase transition at the local region defined by the incident ion beam of (cryogenic) TOF-SIMS was demonstrated in the present study.</p>\u0000 </div>","PeriodicalId":16178,"journal":{"name":"Journal of Mass Spectrometry","volume":"60 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142877071","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bothersome Back Exchange in MALDI Plume and Its Impact on Hydrogen/Deuterium Exchange Mass Spectrometry Analysis","authors":"Xianwen Lou,&nbsp;Michel van Houtem,&nbsp;René P. M. Lafleur,&nbsp;Sandra M. C. Schoenmakers,&nbsp;Joost L. J. van Dongen,&nbsp;Anja R. A. Palmans","doi":"10.1002/jms.5108","DOIUrl":"10.1002/jms.5108","url":null,"abstract":"<p>One critical issue in hydrogen/deuterium exchange mass spectrometry (HDX MS) analysis is the deleterious back exchange. Herein, we report that when matrix-assisted laser desorption/ionization (MALDI) is used, the MALDI process itself can also cause significant back exchange. The back exchange occurred inside the reactive MALDI plume was investigated by depositing a fully deuterated sample prepared in D₂O on top of a preloaded dried layer of matrix. A benzene-1,3,5-tricarboxamide (BTA) compound that can form supramolecular polymer in water and five peptides of angiotensin II (AT), pentaglycine (5G), pentaalanine (5A), cyclohexaglycine (C6G), and cyclohexaalanine (C6A) were selected as the testing compounds. Just like the situation in solution, the back exchange for the side chains and end groups is fast in the MALDI plume, while for the backbone amides, it is slow and dependent on the primary structure of the peptide. For the peptides tested, 5%–15% of D-labels in the backbone amides can be lost during the MALDI process. This degree of back exchange, although not an unbearable problem for most HDX MS applications as 85%–95% of the informative labels would still survive, could seriously limit the use of MALDI in the HDX MS analysis of supramolecular assemblies. For these assemblies, the EX1-like mechanism with two distinct distributions is common, and the back exchange could gravely distort or even merge the distinct isotopic distributions, which are the characteristic symbols of EX1.</p>","PeriodicalId":16178,"journal":{"name":"Journal of Mass Spectrometry","volume":"60 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11664201/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142877023","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ghost Peaks of Aromatic Metabolites Induced by Corona Discharge Artifacts in LC-ESI-MS/MS","authors":"Yayoi Hongo,&nbsp;Daisuke Fukuyama,&nbsp;Lee Chuin Chen,&nbsp;Kanako Sekimoto,&nbsp;Hiroshi Watanabe","doi":"10.1002/jms.5102","DOIUrl":"10.1002/jms.5102","url":null,"abstract":"<p>LC-ESI-MS/MS is a preferred method for detecting and identifying metabolites, including those that are unpredictable from the genome, especially in basal metazoans like <i>Cnidaria</i>, which diverged earlier than bilaterians and whose metabolism is poorly understood. However, the unexpected appearance of a “ghost peak” for dopamine, which exhibited the same <i>m/z</i> value and MS/MS product ion spectrum during an analysis of <i>Nematostella vectensis</i>, a model cnidarian, complicated its accurate identification. Understanding the mechanism by which “ghost peaks” appear is crucial to accurately identify the monoamine repertoire in early animals so as to avoid misassignments. Verification experiments showed that <i>in-source</i> oxidation of tyramine, which produced an intense signal, was responsible for this “ghost peak.” This artifact commonly occurs among aromatic compounds with high signal intensities and appears at the same <i>m/z</i> as their respective in vivo oxidized metabolites. In metabolomics, spectra contain diverse signals from complex biological mixtures, making it difficult to recognize artifact peaks. To prevent misassignments, despite +16 Da differences, adequate chromatographic separation of metabolites from their respective in vivo oxidation precursors is necessary. Whereas both electrolysis and gas-phase corona discharge can cause <i>in-source</i> oxidation in ESI, corona discharge proved to be the dominant factor. Additionally, the presence of multiple oxygen atom sources was suggested by the voltage-dependent mass shift of +16 Da to +18 Da of the “ghost peak” when using ¹⁸O-labeled water as a solvent. Accurate metabolite identification using LC-ESI-MS/MS requires accounting for <i>in-source</i> products that can mimic in vivo products.</p>","PeriodicalId":16178,"journal":{"name":"Journal of Mass Spectrometry","volume":"60 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11664113/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142877089","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Performance Optimization of a Large Geometry High Resolution-Secondary Ion Mass Spectrometer (HR-SIMS) for High Precision Measurements of Oxygen Isotopic Composition (δ18O) and U–Pb Geochronology in Zircon","authors":"Deeksha Khandelwal,&nbsp;Pankaj Kumar,&nbsp;P. V. Kumar,&nbsp;Atul K. Singh,&nbsp;Mahadev Rawat,&nbsp;Anit Dawar,&nbsp;R. Sharma,&nbsp;S. Ojha,&nbsp;S. Gargari,&nbsp;P. K. Mukherjee,&nbsp;S. Chopra,&nbsp;A. C. Pandey","doi":"10.1002/jms.5103","DOIUrl":"10.1002/jms.5103","url":null,"abstract":"<div>\u0000 \u0000 <p>A large geometry high resolution secondary ion mass spectrometer (HR-SIMS) has been established as a part of the National Geochronology Facility (NGF) at Inter-University Accelerator Centre (IUAC), New Delhi. The performance of the instrument related to high spatial resolution, high mass resolving power (MRP), sensitivity of the instrument to measure low abundant isotopes, and sensitivity of the instrument for ²⁰⁶Pb signal under different conditions are optimized and presented in this paper. We report the precision of the order of ~ 0.2‰ for oxygen isotopes measurement in 91500 reference material zircon and measured δ¹⁸O value of 10.08‰ ± 0.18‰ (2SD), which is in agreement with the recommended values. For U–Pb age measurement in zircon, Plešovice and FCT reference materials are measured as unknown and their ²⁰⁶Pb/²³⁸U ages agree with the reported values within the uncertainties. A long-term evaluation of ²⁰⁶Pb/²³⁸UO and ²⁰⁶Pb/²³⁸U isotopic measurement ratio is also presented.</p>\u0000 </div>","PeriodicalId":16178,"journal":{"name":"Journal of Mass Spectrometry","volume":"60 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142877109","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mass Spectrometry Imaging for Spatial Toxicology Research","authors":"Tian (Autumn) Qiu","doi":"10.1002/jms.5104","DOIUrl":"https://doi.org/10.1002/jms.5104","url":null,"abstract":"<p>The spatial information of xenobiotics distribution, metabolism, and toxicity mechanisms in situ has drawn increasing attention in both pharmaceutical and environmental toxicology research to aid drug development and environmental risk assessments. Mass spectrometry imaging (MSI) provides a label-free, multiplexed, and high-throughput tool to characterize xenobiotics, their metabolites, and endogenous molecules in situ with spatial resolution, providing knowledge on spatially resolved absorption, distribution, metabolism, excretion, and toxicity on the molecular level. In this perspective, we briefly summarize applications of MSI in toxicology on xenobiotic distribution and metabolism, quantification, toxicity mechanisms, and biomarker discovery. We identified several challenges regarding how we can fully harness the power of MSI in both fundamental toxicology research and regulatory practices. First, how can we increase the coverage, sensitivity, and specificity in detecting xenobiotics and their metabolites in complex biological matrices? Second, how can we link the spatial molecular information of xenobiotics to toxicity consequences to understand toxicity mechanisms, predict exposure outcomes, and aid biomarker discovery? Finally, how can we standardize the MSI experiment and data analysis workflow to provide robust conclusions for regulation and drug development? With these questions in mind, we provide our perspectives on the future directions of MSI as a promising tool in spatial toxicology research.</p>","PeriodicalId":16178,"journal":{"name":"Journal of Mass Spectrometry","volume":"59 12","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jms.5104","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142764011","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular Ion: An Extended, Fully Collective, and More Contemporary Definition","authors":"Caroline P. Carvalho,&nbsp;Thiago C. Canevari,&nbsp;Marcos N. Eberlin","doi":"10.1002/jms.5106","DOIUrl":"https://doi.org/10.1002/jms.5106","url":null,"abstract":"","PeriodicalId":16178,"journal":{"name":"Journal of Mass Spectrometry","volume":"59 12","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142764012","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dissociation Chemistry of Protonated α-, β- and Other Amino Acids Using Multiple Stage Tandem Mass Spectrometry","authors":"Daiki Asakawa","doi":"10.1002/jms.5100","DOIUrl":"https://doi.org/10.1002/jms.5100","url":null,"abstract":"<div>\u0000 \u0000 <p>To discriminate amino acid isomers by multiple stage tandem mass spectrometry (MSⁿ), the fragmentation of protonated amino acids were investigated by MSⁿ with collision-induced dissociation (CID) and density functional theory calculations. The CID of protonated α-amino acids results in a loss of 46 Da, corresponding to H₂O and CO, and iminium ions appear as resultant fragments. The CID of protonated β-amino acids also produces iminium ions, but the corresponding loss is 60 Da instead of 46 Da. H₂O loss initiates the fragmentation of protonated β-amino acids, producing protonated β-lactams as an intermediate. Subsequently, protonated β-lactams are easily converted to iminium ions and CH₂CO. By contrast, H₂O loss from the protonated forms of γ- and ε-amino acids provides protonated lactams with 5- and 7-membered rings, respectively. Protonated lactams with more than 5-membered rings provide stable fragments and do not undergo further degradation during CID. In addition, protonated forms of γ- and ε-amino acids undergo NH₃ loss as a competitive fragmentation pathway of H₂O loss, producing protonated lactones. Because the fragmentation of protonated amino acid by CID depends on the position of amino and carboxyl groups, the tandem mass spectrometry with CID can discriminate α-, β-, and other amino acids.</p>\u0000 </div>","PeriodicalId":16178,"journal":{"name":"Journal of Mass Spectrometry","volume":"59 12","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142674090","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phytochemical Profiling by HPLC-ESI-MS/MS and In Vitro Investigation of the Antidiabetic Activity of Cassia bakeriana Bark Extract and Fractions","authors":"Diego G. Prado,&nbsp;Allisson B. Justino,&nbsp;Tiara da C. Silva,&nbsp;Sérgio A. L. de Morais,&nbsp;Mário M. Martins,&nbsp;Paula de S. Santos,&nbsp;Luís C. S. Cunha,&nbsp;Raquel M. F. de Sousa,&nbsp;Francisco J. T. de Aquino,&nbsp;Foued S. Espindola,&nbsp;Alberto de Oliveira","doi":"10.1002/jms.5099","DOIUrl":"10.1002/jms.5099","url":null,"abstract":"<div>\u0000 \u0000 <p>Type 2 diabetes mellitus is a global health problem, placing patients at a higher risk of developing cardiovascular diseases and cancer. This study investigates the antidiabetic potential of <i>Cassia bakeriana</i> bark extracts and fractions. We evaluate their ability to inhibit α-amylase and α-glucosidase enzymes and advanced glycation end-products (AGEs). The antioxidant potential was also examined. Extracts were prepared through maceration with hexane (HE) and ethanol (EE), and the fractions were obtained via liquid–liquid extraction from EE. Anti-enzymatic, anti-glycation, antioxidant, and cytotoxic assays were conducted in 96-well plates using different concentrations of samples to determine the half-maximal inhibitory concentration (IC₅₀). Active samples were further analyzed using HPLC-(−)-ESI-MS/MS. The ethyl acetate fraction (EAF) demonstrated a high percentage of α-amylase inhibition (94.0%) with a promising IC₅₀ value of 1.05 μg mL⁻¹. Additionally, EAF displayed 61.5% inhibition of α-glucosidase, with an IC₅₀ value of 537 μg mL⁻¹. The EE, EAF, and <i>n</i>-butanol fraction (BF) exhibited strong anti-glycation capacities. Furthermore, the EE, EAF, BF, and dichloromethane fractions showed promising antioxidant activity using the DPPH and ORAC methodologies. Cytotoxic activity was also evaluated with Vero cells, revealing no adverse effects on cell viability (CC₅₀ &gt; 512.0 μg mL⁻¹). Active samples predominantly comprised proanthocyanidins, flavonoids, and anthraquinone, representing the main constituents of C. <i>bakeriana</i> bark. This study provides the first assessment of the antidiabetic potential of <i>C. bakeriana</i> bark and a comprehensive analysis of the chemical composition of its active extracts and fractions, offering hope for future treatments.</p>\u0000 </div>","PeriodicalId":16178,"journal":{"name":"Journal of Mass Spectrometry","volume":"59 12","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142621923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Advancing Native Mass Spectrometry Toward Cellular Biology","authors":"Kazumi Saikusa","doi":"10.1002/jms.5095","DOIUrl":"10.1002/jms.5095","url":null,"abstract":"<div>\u0000 \u0000 <p>Protein structure, including various post-translational modifications and higher-order structures, regulates diverse biological functions. Native mass spectrometry (native MS) is a powerful analytical technique used to determine the masses of biomolecules, such as proteins and their complexes, while preserving their native folding in solution. This method provides structural information on the composition of monomers or complexes and the stoichiometry of subunits within each complex, significantly contributing to protein structural analysis. Native MS has evolved to incorporate top–down approaches, enabling the characterization of proteoforms and non-covalent interactions between metabolites or proteins and specific targets. This perspective highlights the advancements in native MS for intracellular proteins and protein complexes, and discusses future research directions toward cellular biology.</p>\u0000 </div>","PeriodicalId":16178,"journal":{"name":"Journal of Mass Spectrometry","volume":"59 11","pages":""},"PeriodicalIF":1.9,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142502157","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}