Journal of Mass Spectrometry最新文献

{"title":"Interpreting Mass Spectrometry Data From Computational Chemistry: A Practical Guide to Reactivity and the Dissociation Mechanisms of 1,4-Naphthoquinone Derivatives","authors":"Ricardo Vessecchi,&nbsp;Vinicius Corali Bosco,&nbsp;Gabriel Rossi Saraiva,&nbsp;Celso Donizete Lourenço Jr,&nbsp;Flávio da Silva Emery,&nbsp;Norberto Peporine Lopes","doi":"10.1002/jms.70097","DOIUrl":"https://doi.org/10.1002/jms.70097","url":null,"abstract":"<div>\u0000 \u0000 <p>Computational chemistry has played a key role in helping scientists understand ionization and molecular dissociation in the gas phase, which has contributed to its growing popularity among users of various mass spectrometry techniques. Early studies laid a strong foundation for applying computational methods to explore the stability and reactivity of gas-phase ions, making these approaches more accessible and widely used across different research areas. In this work, we present a practical guide for effectively using computational chemistry in mass spectrometry studies. By comparing experimental results obtained in ESI-MS/MS with those from quantum chemical models (DFT and composite methods) and spectra simulations (QCxMS and CFM-ID), we aim to provide researchers with clear steps for studying organic molecules from ESI-MS and MS/MS data and understanding the protonation in mass spectrometry. Proton affinity and gas-phase basicities were calculated and the protonation sites were proposed. These results were compared to atomic charges, molecular orbitals, and Quantum Theory of Atoms-in-Molecules (QTAIM) calculations. Fragmentation mechanisms were proposed from protonated species, and the MS/MS spectra were compared to those predicted using CFM-ID and QCxMS methods. The 2-methyl-1,4-naphthoquinone analysis was used as a reference molecule for computational studies and benchmark. It is suggested the useful toolkits to describe molecular ionization/dissociation in ESI-MS and ESI-MS/MS studies from quantum chemical calculations by using a guide for the systematic application of computational chemistry in mass spectrometry and fragmentation mechanisms studies. Finally, an application was demonstrated for 2-hydroxy-3-benzamine-1,4-naphthoquinone ionized in positive mode, highlighting the versatility of this guideline for studies involving more structural complexity.</p>\u0000 </div>","PeriodicalId":16178,"journal":{"name":"Journal of Mass Spectrometry","volume":"61 9","pages":""},"PeriodicalIF":2.1,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148784051","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":"Discovery of Breast Cancer Diagnostic Markers Using Lipase-Based Plasma Proteomics of Lipid-Bound Proteins","authors":"Eun Joo Kang,&nbsp;Youngshik Choe,&nbsp;Kwan Ho Lee,&nbsp;Sangkyu Lee","doi":"10.1002/jms.70104","DOIUrl":"https://doi.org/10.1002/jms.70104","url":null,"abstract":"<div>\u0000 \u0000 <p>Membrane-associated proteins, including those embedded in exosomal membranes or bound to plasma lipids, are promising disease biomarkers. However, their hydrophobic nature limits detection through conventional proteomic workflows, which primarily capture soluble proteins. In this study, we developed and optimized a lipase-based pretreatment strategy to improve the detection of insoluble membrane proteins in human plasma. Lipase treatment using porcine pancreas-derived enzymes was optimized to 37°C, 3 U, and 1 h, based on overall protein yield and membrane protein enrichment. Sequential application after depletion of high-abundance proteins increased the proportion of membrane proteins from 12%–20%. Using this optimized workflow, we performed data-independent acquisition-based LC–MS/MS analysis of plasma samples from patients with early-stage breast cancer and benign disease (<i>n</i> = 6 each). Notably, 38% of the uniquely detected or enriched proteins in cancer plasma were membrane-associated. Among them, protocadherin 12 (PCDH12) was significantly elevated in the plasma of patients with breast cancer, indicating its potential as a novel diagnostic biomarker. This study highlights the use of lipase-enhanced proteomics for revealing plasma membrane proteins and advancing noninvasive biomarker discovery for cancer.</p>\u0000 </div>","PeriodicalId":16178,"journal":{"name":"Journal of Mass Spectrometry","volume":"61 9","pages":""},"PeriodicalIF":2.1,"publicationDate":"2026-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148784160","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":"Olive Oil Quality Analysis and the Detection of Adulterations by GC-MS With Cold EI","authors":"Benny Neumark,&nbsp;Oneg Elkabets,&nbsp;Zadok Shabi,&nbsp;Aviv Amirav","doi":"10.1002/jms.70103","DOIUrl":"https://doi.org/10.1002/jms.70103","url":null,"abstract":"<p>Olive oil is widely consumed for its nutritional and health benefits, yet its high market value makes it vulnerable to adulteration and mislabeling. Current analytical approaches for assessing olive oil quality and authenticity rely largely on indirect analyses, such as fatty acid methyl ester (FAME) profiles, peroxide values, or UV absorbance, and do not account for olive oil's triglycerides content. In this manuscript, we demonstrate the application of gas chromatography–mass spectrometry (GC-MS) with cold electron ionization (Cold EI) for the direct analysis of olive oil based on its glyceride profiling. Cold EI employs a supersonic molecular beam interface with a contact-free fly-through ion source, providing vibrational cooling that enhances the abundance of molecular ions. This enables direct GC-MS analysis of all glycerides and acids without derivatization, with total analysis time of 19 min. We analyzed multiple commercial olive oil brands, certified reference material, and intentionally adulterated samples containing canola and/or sunflower oil. The resulting mass chromatograms and triglyceride molecular ion patterns allowed clear discrimination between pure olive oil, adulterated oils, and degraded (oxidized) samples. Adulteration at the 30% level was detected through distinct hybrid triglyceride patterns, although aging effects were uniquely identified by increased diglyceride and free fatty acid signals. High sensitivity was demonstrated by the confident detection of olive oil at trace levels down to 100 pg on-column using selective ion monitoring. These results establish GC-MS with Cold EI as a rapid, sensitive, and highly informative technique for ensuring the authenticity, quality, and consumer safety of olive oil.</p>","PeriodicalId":16178,"journal":{"name":"Journal of Mass Spectrometry","volume":"61 9","pages":""},"PeriodicalIF":2.1,"publicationDate":"2026-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jms.70103","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148753754","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":"Enhancing the MALDI-TOF MS Detection Mass Range of Saccharides Using a Reactive Composite Matrix","authors":"Shuyi Wang,&nbsp;Meiying Liu,&nbsp;Ling Ling,&nbsp;Chuan-fan Ding","doi":"10.1002/jms.70102","DOIUrl":"https://doi.org/10.1002/jms.70102","url":null,"abstract":"<div>\u0000 \u0000 <p>Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis of saccharides, particularly high-molecular-weight polysaccharides, is often hampered by low ionization efficiency. To overcome this limitation, we developed a novel composite matrix comprising 4-hydrazinoquinazoline (4-HQ) and caffeic acid (CA). This matrix synergistically enhances saccharide detection: 4-HQ specifically targets the hemiacetal termini of reducing saccharides via hydrazone formation, thereby improving ionization efficiency, while CA maintains an acidic condition for derivatization and extends the detectable mass range. Using dextran 6 k as a model, we systematically optimized the 4-HQ/CA ratio, reaction temperature, and reaction time. The optimized 4-HQ/CA matrix enabled direct profiling of oligo/polysaccharides in inulin and garlic extracts, as well as N-glycans from ovalbumin and fetuin. Notably, even for non-reducing saccharides where derivatization is precluded, 4-HQ/CA outperformed conventional 2,5-dihydroxybenzoic acid (DHB) by detecting more species with higher signal-to-noise ratios. This versatile composite matrix shows potential for robust analysis of saccharides in glycobiology and food science.</p>\u0000 </div>","PeriodicalId":16178,"journal":{"name":"Journal of Mass Spectrometry","volume":"61 9","pages":""},"PeriodicalIF":2.1,"publicationDate":"2026-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148699899","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":"Interactive Software for Interpreting and Curating High-Resolution Electron Ionization Mass Spectra","authors":"Dmitriy D. Matyushin,&nbsp;Anastasia Yu. Sholokhova","doi":"10.1002/jms.70096","DOIUrl":"10.1002/jms.70096","url":null,"abstract":"<div>\u0000 \u0000 <p>Gas chromatography coupled with electron ionization and high-resolution mass spectrometry (GC-EI-HRMS) has been increasingly used in analytical chemistry in recent years. Databases (libraries) of such mass spectra are emerging, and various studies require processing batches of such data. This necessitates the development of user-friendly software for curation and batch processing of such data sets. In this work, we propose the “gchrmsexplain” software specifically developed for this purpose. It includes both a graphical user interface and a command-line interface. The software receives a peak list as input and finds a formula for each peak using in silico fragmentation or combinatorial enumeration. The isotopic pattern is checked. The fraction of the ion current due to the annotated peaks is calculated. The absolute error in determining <i>m</i>/<i>z</i> can be specified in either millidaltons or parts per million. Batch processing is possible. The software was applied to six publicly available GC-EI-HRMS data sets: RECETOX (exposome and metabolome libraries), HREI-MSDB, library from Castro's work (2022), and two subsets of MassBank EU. In total, these data sets contain 1811 mass spectra. Impurity peaks, systematic errors in <i>m</i>/<i>z</i>, and completely incorrect mass spectra were detected. It was shown that some of the data sets contain low-quality mass spectra. It was demonstrated that the presented software can be used for the curation of such data. The software is free and available online: https://github.com/mtshn/gchrmsexplain.</p>\u0000 </div>","PeriodicalId":16178,"journal":{"name":"Journal of Mass Spectrometry","volume":"61 8","pages":""},"PeriodicalIF":2.1,"publicationDate":"2026-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148669857","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":"Evaluation of a Targeted LC-MS/MS Assay for Clinical Quantification of Urinary Organic Acids.","authors":"Earnest J P Daniel, Emily Garnett, Deepthi Rajapakshe, Sridevi Devaraj","doi":"10.1002/jms.70099","DOIUrl":"10.1002/jms.70099","url":null,"abstract":"<p><p>Gas chromatography-mass spectrometry (GC-MS) is the reference method for urine organic acid analysis but requires complex sample preparation and derivatization, limiting routine clinical use. We developed and validated a targeted Liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for quantifying urinary organic acids relevant to the evaluation of inborn errors of metabolism. The assay demonstrated excellent linearity, precision, accuracy, analytical sensitivity, and good agreement with GC-MS. Organic acidurias and other metabolic disorders were accurately identified through characteristic metabolite elevations. The simplified workflow eliminates derivatization and enables rapid, high-throughput implementation for newborn screening confirmation, metabolic screening, and patient monitoring in pediatric clinical laboratories.</p>","PeriodicalId":16178,"journal":{"name":"Journal of Mass Spectrometry","volume":"61 8","pages":"e70099"},"PeriodicalIF":2.1,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13445640/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148678459","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":"A Platform for High-Throughput Chemical Analysis of Foods: Characterization of Extra Virgin Olive by Direct Mass Spectrometry and Machine Learning.","authors":"Nandhini Sokkalingam, Frances Chu, Joan Zou, Siamak Ashrafi, Mark W Duncan","doi":"10.1002/jms.70100","DOIUrl":"10.1002/jms.70100","url":null,"abstract":"<p><p>Poor diet is now the leading cause of early death globally. In part, this is because our complex food supply chains are increasingly at risk of overprocessing, contamination, low nutrient content, and economically motivated fraud. Chemical testing can offer insights into these concerns, but testing methods are frequently impractical. Extra virgin olive oil (EVOO) is a premium food of high nutritional value, but because of its growing popularity and high price, it can be a target for mislabeling, substitution, dilution, and/or false claims of origin. Rapid and accurate testing methods for its characterization are therefore increasingly important. We used two direct forms of mass spectrometry (MS)-laser desorption/ionization (LDI) MS and direct analysis in real time (DART) MS-to obtain complex chemical signatures of edible oils. The data generated on a set of reference samples were then used to develop and train three independent machine learning (ML) models that assess key characteristics of a test oil. We also developed a proof-of-concept DART-MS/MS assay add-on for the quantification of bioactive phenols in EVOO. Our approach accurately predicts several attributes of an edible oil based on novel markers and intricate patterns within the acquired data. Further, pure reference standards and an isotopically-labeled internal standard allow accurate quantification of the constituent phenols. Because there is no chromatography, both the mass fingerprints and quantification can be performed in seconds-minutes. The method uses low (milliliter) volumes of sample and green solvents, and when combined with ML, it offers rapid data analysis and comprehensive result interpretation.</p>","PeriodicalId":16178,"journal":{"name":"Journal of Mass Spectrometry","volume":"61 8","pages":"e70100"},"PeriodicalIF":2.1,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13439961/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148673692","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":"Mass Spectrometric Characterization of Native Insulin Hexamers and Non-Native Heptamers: Formation and Stability Across Insulin Analogs","authors":"Emmanuel Dare,&nbsp;Colton G. Dixon,&nbsp;Kenneth W. Lee","doi":"10.1002/jms.70098","DOIUrl":"https://doi.org/10.1002/jms.70098","url":null,"abstract":"<div>\u0000 \u0000 <p>Insulin aggregation and oligomerization present significant challenges in both therapeutic formulation and fundamental studies of amyloid formation, particularly due to the transient and heterogeneous nature of early-stage oligomers. Here, we employ ion mobility–mass spectrometry (IM–MS) to characterize the oligomeric distributions of human insulin and two clinically relevant analogs, aspart (rapid-acting) and glargine (long-acting), in excipient-containing solutions designed to stabilize native forms of insulin and under aggregation-inducing conditions. Comparison of insulin analogs revealed distinct aggregation propensities that correlate with each analog's therapeutic design. In general, stable zinc-coordinated hexamers formed most readily in the presence of excipients, and various oligomers formed under aggregation-inducing conditions, with a noticeable prevalence of heptamer formation. We further investigated the structure and stability of native hexamers and non-native heptamers using collision-induced dissociation and collision-induced unfolding experiments. Although the expected single-monomer ejection was the main dissociation pathway for both species, zinc-coordinated hexamers also dissociated into two zinc-adducted trimers, whereas heptamers dissociated into dimer/pentamer and trimer/tetramer pairs. Gas-phase unfolding indicated conservation of subunit tertiary structure in hexamers and no distinct folded structures in heptamer subunits. Overall, this work demonstrates the utility of IM–MS as a rapid, high-resolution platform for probing insulin aggregation pathways and evaluating current and future insulin analog formulations.</p>\u0000 </div>","PeriodicalId":16178,"journal":{"name":"Journal of Mass Spectrometry","volume":"61 8","pages":""},"PeriodicalIF":2.1,"publicationDate":"2026-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148647905","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":"Evaluating Stabilizers Effects on Aroma Release Dynamics in Ice Cream: A PTR-ToF-MS Analysis","authors":"Camila Cossettin Teixeira,&nbsp;Michele Pedrotti,&nbsp;Lorenzo Gennari,&nbsp;Andrea Cavallero,&nbsp;Flavia Gasperi,&nbsp;Iuliia Khomenko,&nbsp;Franco Biasioli","doi":"10.1002/jms.70092","DOIUrl":"https://doi.org/10.1002/jms.70092","url":null,"abstract":"<div>\u0000 \u0000 <p>Capturing the dynamic volatilome of frozen matrices during phase transitions remains an analytical challenge, typically requiring invasive sampling. This study employs proton transfer reaction time-of-flight mass spectrometry (PTR-ToF-MS) as a rapid, noninvasive technique that directly samples headspace volatiles without preconcentration to efficiently monitor four peach-related aroma compounds (isoamyl acetate, 3-hexenyl acetate, linalool, and furaneol) from frozen to melted ice cream. The samples vary in stabilizer composition, including a control (no stabilizer), single-gum, binary, and ternary blends. Monitoring occurred in the frozen state (incubation for 1 min at 4°C) and after melting (incubation for 20 min at 30°C). Results demonstrate that all stabilizer blends attenuated volatile release (average reduction in total aroma release of 40.39%) compared with the control, although statistically significant formulation effects were compound dependent and were not observed for furaneol. The magnitude of suppression was dependent on both stabilizer composition and the physicochemical properties of the aroma compounds. Notably, individual aroma compounds displayed differential release patterns across formulations; isoamyl acetate generally showed a more pronounced release than cis-3-hexenyl acetate in specific stabilized formulations (LGK and LAK). Stabilizers that consistently suppressed peach-related volatiles also demonstrated reduced total odor activity values. These results validate PTR-ToF-MS as an effective tool for monitoring the volatilome of frozen matrices and tracking aroma release during melting, illustrating how stabilizer selection can be optimized for aroma delivery in ice cream.</p>\u0000 </div>","PeriodicalId":16178,"journal":{"name":"Journal of Mass Spectrometry","volume":"61 8","pages":""},"PeriodicalIF":2.1,"publicationDate":"2026-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148616708","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":"Determination of Mathieu Stability Plot for Planar Trap With Circular Trapping Region","authors":"Appala Naidu Kotana,&nbsp;Atanu K. Mohanty","doi":"10.1002/jms.70095","DOIUrl":"https://doi.org/10.1002/jms.70095","url":null,"abstract":"<div>\u0000 \u0000 <p>Planar toroidal ion traps with circular trapping regions are investigated using a toroidal multipole representation of the electrostatic potential. The multipole expansion coefficients are calculated and employed to model the electric potential in the vicinity of the trapping region. The accuracy of the analytical representation is validated through comparison with potentials computed using the boundary element method (BEM), showing excellent agreement near the trapping circle. Ion trajectories are numerically simulated for various combinations of RF and DC voltages to identify stable and unstable operating regimes. These regimes are subsequently mapped onto the Mathieu parameter space to construct Mathieu stability diagrams. The resulting stability regions reveal localized instability zones within the broader stable regions, highlighting the influence of nonlinear electric field components on ion dynamics. The secular frequencies predicted using the Mathieu parameters are compared with those extracted directly from ion trajectory simulations using the <i>harminv</i> tool. Good agreement is obtained between the two approaches, with relative errors remaining below 3% over a wide range of operating conditions, thereby confirming the validity of the theoretical and numerical methods employed in this study.</p>\u0000 </div>","PeriodicalId":16178,"journal":{"name":"Journal of Mass Spectrometry","volume":"61 8","pages":""},"PeriodicalIF":2.1,"publicationDate":"2026-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148617277","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}