Rapid Communications in Mass Spectrometry最新文献

{"title":"Automated Multienzyme Digestion Workflows for Confident Characterization of Challenging Posttranslational Modifications in Therapeutic Antibodies by LC–MS/MS","authors":"Nanna Sofie Eskesen,&nbsp;Yann Leblanc,&nbsp;Justine Lempereur,&nbsp;Martin Ørgaard,&nbsp;Elizabeta Madzharova,&nbsp;Trine M. Sloth,&nbsp;Simon Krabbe,&nbsp;Alexandra K. Rebak,&nbsp;Magali André,&nbsp;Pernille F. Jensen,&nbsp;Dan B. Kristensen","doi":"10.1002/rcm.70165","DOIUrl":"10.1002/rcm.70165","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Rationale</h3>\u0000 \u0000 <p>Non-reduced trypsin digestion of therapeutic antibodies can generate large disulfide-linked peptide complexes that exhibit poor chromatographic and mass spectrometric performance. This limits the confident characterization of posttranslational modifications (PTMs) in specific antibody regions, such as the heavy-chain constant region 1 (CH1) domain, where conventional digestion produces 8-kDa complexes with poor fragmentation.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We developed automated multistep and multienzyme digestion workflows using immobilized trypsin, chymotrypsin, and proteinase K on magnetic beads. These workflows were implemented on a robotic platform and evaluated for their ability to characterize engineered cysteine residues in the CH1 domain of antibody–drug conjugate (ADC) intermediates. Analysis was performed using liquid chromatography–tandem mass spectrometry (LC–MS/MS).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The multienzyme workflows generated highly orthogonal peptide pools; for instance, selected workflows using trypsin only, trypsin combined with chymotrypsin, and trypsin combined with proteinase K yielded 13%, 14%, and 34% unique peptide identifications, respectively. In the challenging CH1 region, the multienzyme approach identified six distinct cysteine adducts at engineered Cys152. These included cysteinylation, homocysteinylation, and an unexpected, putative process-related impurity, thioglycolic acid capping, which was validated with unambiguous MS and MS/MS evidence using selected multienzyme workflows. Relative extracted-ion current-based levels of these cappings were observed and found to be similar across selected workflows; for instance, relative levels of thioglycolic acid capping from 12% to 15% were observed across selected workflows.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>The presented automated multienzyme workflows serve as complementary tools in an analytical toolbox, which can be strategically deployed for targeting challenging regions of biopharmaceutical products. We demonstrate significantly improved precursor signal quality and MS/MS sequence coverage compared to trypsin-only protocols. The presented workflows are fast (36–92 min total runtime) and utilize commercially available reagents and instrumentation, making them suitable for direct implementation in biopharmaceutical analytical development and quality control laboratories.</p>\u0000 </section>\u0000 </div>","PeriodicalId":225,"journal":{"name":"Rapid Communications in Mass Spectrometry","volume":"40 21","pages":""},"PeriodicalIF":1.8,"publicationDate":"2026-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13501424/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148807973","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":"Complexation of Divalent Metals by Natural Furoquinoline Alkaloids: An Electrospray Mass Spectrometry and DFT Study","authors":"María Belén Valdez,&nbsp;Jorge Alejandro Palermo,&nbsp;Fernanda D'Jonsiles,&nbsp;Gabriela M. Cabrera,&nbsp;Gastón E. Siless","doi":"10.1002/rcm.70162","DOIUrl":"10.1002/rcm.70162","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Rationale</h3>\u0000 \u0000 <p>Despite the well-established metal-chelating properties of 8-hydroxyquinoline and related compounds, little is known about the interaction of furoquinoline alkaloids with biologically relevant metal ions. This study highlights the value of combining ESI-MS, energy-resolved mass spectrometry breakdown experiments, and DFT approaches to characterize metal-binding properties of methoxy-substituted furoquinoline alkaloids, enabling the differentiation of positional isomers through characteristic metal-adduct formation and ion fragmentation.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>The complexation behavior of the studied alkaloids toward Mg²⁺, Ca²⁺, Co²⁺, Cu²⁺, and Zn²⁺ was studied by electrospray ionization mass spectrometry in a micrOTOF Q II mass spectrometer. Energy-resolved mass spectrometry breakdown experiments were performed to assess the relative stability of the observed adducts. Adduct profiles were graphically compared by PCA of the ESI/MS dataset. Binding modes were evaluated by DFT calculations by B3LYP 6-311+G(2d,3p).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Quinolines <b>1</b>-<b>5</b> yielded stable metal adducts with distinct profiles. Ligand oxidation to [M]^+. and Cu(I) adduct formation occurred mainly for furoquinolines <b>1-3</b>. Methyl-loss fragmentation characterized compounds with an 8-methoxyquinoline motif. Isomeric furoquinolines showed markedly different metal-binding adduct profiles. Flindersiamine <b>1</b> showed the strongest metal-binding affinity, yielding intense [3M+Me]²⁺ and [2M+Me]²⁺ adducts, and DFT calculations support its ability to act as an N,O-bidentate ligand.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Metal-adduct profiles obtained by ESI-MS, supported by PCA analysis, provide a robust analytical framework for differentiating positional isomers of methoxy-substituted furoquinoline alkaloids. ESI-MS and DFT studies identified the 8-methoxy substituent as a key determinant of metal complexation in furoquinoline alkaloids, revealing flindersiamine <b>1</b> as the strongest Cu²⁺-binding ligand and providing a basis for future studies on the biological properties of these compounds.</p>\u0000 </section>\u0000 </div>","PeriodicalId":225,"journal":{"name":"Rapid Communications in Mass Spectrometry","volume":"40 21","pages":""},"PeriodicalIF":1.8,"publicationDate":"2026-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148807944","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":"Convenient Determination of Trace Methylcyclosiloxanes in Water by Vortex-Assisted Small-Scale Liquid–Liquid Extraction and GC–MS Analysis","authors":"Jiale Fang,&nbsp;Zhijun Yuan,&nbsp;Yunfei Zhao,&nbsp;Lingling Teng,&nbsp;Lingxia An,&nbsp;Kezhi Jiang","doi":"10.1002/rcm.70164","DOIUrl":"https://doi.org/10.1002/rcm.70164","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Rationale</h3>\u0000 \u0000 <p>Volatile methylcyclosiloxanes, particularly octamethylcyclotetrasiloxane (D4), decamethylcyclopentasiloxane (D5), and dodecamethylcyclohexasiloxane (D6), are commonly found in the environment and have gained significant attention as emerging contaminants. However, their accurate quantification at trace levels can be challenging because of complex environmental matrices and background interferences.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Method</h3>\u0000 \u0000 <p>VMCSs were extracted from water using vortex-assisted small-scale liquid–liquid extraction (LLE) with <i>n</i>-hexane as the extractant. Both the VMCS standards and the extracts were analyzed using gas chromatography–mass spectrometry (GC–MS). The mechanistic fragmentation of D4, D5, and D6 in EI-MS was studied through ¹³C-labeling experiments.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>In EI-MS, the molecular ion readily eliminates a methyl radical to form the ion [M–CH₃]⁺ for D4, D5, and D6. For D4, the ion [M–CH₃]⁺ subsequently loses CH₄, while the ions corresponding to D5 and D6 tend to undergo cyclization and methyl-shift, resulting in the characteristic ions of (CH₃)₃Si⁺ (<i>m/z</i> 73) and [M–CH₃–CH₄]⁺. These characteristic ions were used as the quantitative or qualitative indicators in the developed GC–MS method for determining D4, D5, and D6, achieving limits of quantification of 0.72–0.99 ng/mL. Efficient extraction of VMCSs in water was achieved within 12 min at room temperature, using only 0.40 mL of <i>n</i>-hexane for each extraction operation. Isotope-spiked experiments demonstrated satisfactory recoveries: 107.9% ± 8.0% for D4, 97.2% ± 5.8% for D5, and 84.7% ± 5.6% for D6. Analysis of real water samples revealed concentrations of D4, D5, and D6 in surface water ranging from 0.05 to 0.09 ng/mL, 0.07 to 0.27 ng/mL, and 0.07 to 0.25 ng/mL, respectively.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusion</h3>\u0000 \u0000 <p>We developed a convenient and accurate method for the determination of trace level of D4, D5, and D6 in water, which addresses the limitations of traditional LLME, and offers a simple and environmentally friendly detection protocol for quantifying trace VMCSs in water.</p>\u0000 </section>\u0000 </div>","PeriodicalId":225,"journal":{"name":"Rapid Communications in Mass Spectrometry","volume":"40 21","pages":""},"PeriodicalIF":1.8,"publicationDate":"2026-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148785203","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":"Automated Tissue Classification and Candidate Biomarker Feature Extraction in Mass Spectrometry Imaging Based on Interpretable Deep Learning Algorithm","authors":"Guang Xu,&nbsp;Shengfeng Gan,&nbsp;Bo Guo,&nbsp;Li Yang","doi":"10.1002/rcm.70168","DOIUrl":"https://doi.org/10.1002/rcm.70168","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Rationale</h3>\u0000 \u0000 <p>Mass spectrometry imaging (MSI) generates high-dimensional spatial-spectral data that requires efficient computational methods for tissue classification and candidate biomarker feature extraction. Deep learning offers a promising approach, yet the interpretability of model predictions and identification of biologically relevant spectral features remain challenging.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>A comprehensive computational pipeline was developed for automatic tissue layer classification of a public mouse urinary bladder MSI dataset. Building upon prior work that compared manual tissue layer labels with those automatically generated via spectral preprocessing, t-SNE, and hierarchical clustering, in this study we separately use each type of class label to train convolutional neural networks (CNNs) for supervised classification. Gradient-weighted Class Activation Mapping (Grad-CAM) and SHapley Additive exPlanations (SHAP) were employed to compute layer-specific summed importance scores to evaluate each mass spectral feature and extract class-discriminative features.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>On the mouse urinary bladder MSI dataset, both manual labels and cluster-derived labels (t-SNE + hierarchical clustering) enabled the CNN model to achieve training accuracies exceeding 0.9 for classifying three tissue layers. Interpretability methods successfully identified discriminative <i>m/z</i> features, including known lipids such as SM(34:1) (<i>m/z</i> 741.54) and PC(34:1) (<i>m/z</i> 798.54), consistent with previously reported biological markers. Compared to the intensity values, the importance scores of the top class-discriminative features generated by both interpretability methods exhibited a sharper contrast and superior ability to delineate tissue-layer-specific distributions in their ion images. Furthermore, evaluation on an independent colorectal cancer dataset yielded a test accuracy of 0.758, suggesting that cross-patient generalizability varied across different data sources.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>This study presented an effective deep learning framework for accurate and interpretable tissue classification in MSI data. The CNN modeling and deep learning interpretability provided a robust approach for both automated segmentation and biological discovery, facilitating the identification of spatially resolved metabolic features in tissue sections.</p>\u0000 </section>\u0000 </div>","PeriodicalId":225,"journal":{"name":"Rapid Communications in Mass Spectrometry","volume":"40 21","pages":""},"PeriodicalIF":1.8,"publicationDate":"2026-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148785031","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":"Chemical Characterization and Mechanism Analysis of Ganjianglingzhu Decoction in the Treatment of Low Back Pain Based on UPLC-Q-TOF-MS/MS and Network Pharmacology","authors":"Baoduan Chen,&nbsp;Ping Li,&nbsp;Jun Shi,&nbsp;Fei Xu,&nbsp;Sifan Sun","doi":"10.1002/rcm.70167","DOIUrl":"https://doi.org/10.1002/rcm.70167","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Rationale</h3>\u0000 \u0000 <p>Ganjianglingzhu decoction (GJLZD), a classical traditional Chinese medicine (TCM) formula, has been widely used in the treatment of low back pain. However, its chemical composition and underlying mechanisms remain insufficiently elucidated.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>The chemical profile of GJLZD was comprehensively characterized by UPLC-Q-TOF-MS/MS. Representative bioactive constituents were subsequently selected for target prediction using the PharmMapper and SwissTargetPrediction databases. Overlapping targets between compound-related targets and low back pain–related targets retrieved from the GeneCards database were subjected to protein–protein interaction (PPI) analysis, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses, as well as molecular docking and molecular dynamics (MD) simulation.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Based on MS/MS fragmentation patterns and literature comparison, a total of 58 constituents were tentatively characterized from GJLZD. These mainly included flavonoids, alkaloids, phenolic acids, and terpenoids. We identified 466 overlapping targets between the active components and low back pain. PPI analysis highlighted SRC, PIK3CA, and AKT1 as the major hub targets. GO and KEGG enrichment analyses suggested that these targets were primarily involved in signal transduction, inflammatory regulation, and metabolism. The enriched pathways included VEGF, FcεRI, and AGE-RAGE signaling. Molecular docking revealed that neoglycyrol showed the strongest binding affinity to AKT1, with a binding energy of −7.93 kcal/mol. MD simulation further confirmed the stability of the neoglycyrol–AKT1 complex over 100 ns.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>This study systematically characterized the chemical constituents of GJLZD and elucidated its potential mechanisms in treating low back pain. The results suggest a multicomponent and multi-target mode of action. The integrated strategy combining UPLC-Q-TOF-MS/MS with network pharmacology and molecular simulations proved valuable for investigating the pharmacological basis of TCM formulas. Further experimental validation is still needed to confirm these findings.</p>\u0000 </section>\u0000 </div>","PeriodicalId":225,"journal":{"name":"Rapid Communications in Mass Spectrometry","volume":"40 21","pages":""},"PeriodicalIF":1.8,"publicationDate":"2026-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148784420","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":"Sensitivity Enhancement by Dual Deflection Electrodes in an Electrospray Ionization Source","authors":"Motoki Date,&nbsp;Shun Kumano,&nbsp;Masuyuki Sugiyama,&nbsp;Hideki Hasegawa,&nbsp;Masaki Watanabe","doi":"10.1002/rcm.70159","DOIUrl":"https://doi.org/10.1002/rcm.70159","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Rationale</h3>\u0000 \u0000 <p>In electrospray ionization–mass spectrometry (ESI-MS), ESI configurations such as orthogonal spray arrangements are often used to suppress droplet introduction into the vacuum chamber, but they can also reduce the ion flux into the vacuum region. Previous methods that electrostatically deflected ions toward the vacuum inlet using a single electrode achieved signal enhancement but could not adequately control deflection position, limiting performance. Therefore, we investigated whether adding a second deflection electrode to create a more localized electric field could further increase ion flux into the vacuum region and enhance sensitivity.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Electrostatic analysis was performed using a two-dimensional cross-sectional model for three ion-source configurations: no electrode, single-plate electrode, and dual electrodes (plate and cylindrical rod). For experimental evaluation, direct-infusion experiments (100 μL min⁻¹) were performed using reserpine (<i>m</i>/<i>z</i> = 609.3) and a CsI/diethylamine mixture spanning <i>m</i>/<i>z</i> values of 74–912, and electrode voltages were stepped (E1, 0–5 kV; E2, 1–3 kV). Flow-injection analysis (FIA) of reserpine (0.5–20 ng mL⁻¹) was conducted to evaluate quantitative performance.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Electrostatic analysis showed that the dual-electrode configuration concentrated the inlet-directed field near the inlet and suppressed the unwanted field above it. Experimentally, the dual-electrode configuration increased the reserpine signal by 3.3-fold compared with the configuration without electrodes. Across five chemically diverse ions, signal enhancements were obtained. For singly charged species, the gain scaled inversely with collision cross-section, indicating a specific benefit for low-ion-mobility analytes. FIA yielded a 4.0-fold increase in the calibration curve slope and halved the lower limit of quantification without degrading linearity (<i>R</i>² = 0.998).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Localizing the electric field using two deflection electrodes enhances ion signal intensity, sensitivity, and quantitative limits in the ESI source configuration examined here. These results indicate that spatial control of the deflection field is an effective strategy for improving ion transmission in an orthogonal ESI source.</p>\u0000 </section>\u0000 </div>","PeriodicalId":225,"journal":{"name":"Rapid Communications in Mass Spectrometry","volume":"40 21","pages":""},"PeriodicalIF":1.8,"publicationDate":"2026-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148784165","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":"Integrated Metabolomic and Gut Microbiome Analyses Reveal the Therapeutic Effects of Xuanfei Heji in Rats With Chronic Obstructive Pulmonary Disease","authors":"Jianping Liu,&nbsp;Ningxing Duan,&nbsp;Tian Xin,&nbsp;Yang Cao,&nbsp;Haiyan Qian","doi":"10.1002/rcm.70166","DOIUrl":"https://doi.org/10.1002/rcm.70166","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Background</h3>\u0000 \u0000 <p>Chronic obstructive pulmonary disease (COPD) is a leading cause of death, underscoring the need for improved therapies. Xuanfei Heji (XFHJ), a hospital-prepared herbal formula, has been used clinically in the treatment of COPD. However, its mechanisms remain unclear.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>XFHJ constituents were profiled using UHPLC–HRMS. COPD was induced in rats by intratracheal lipopolysaccharide instillation and cigarette smoke exposure. Treatment effects were assessed using pulmonary function, lung histopathology, and proinflammatory cytokines. Untargeted serum metabolomics and fecal 16S rRNA gene sequencing were performed; associations among differential metabolites, microbial taxa, and inflammatory markers were evaluated using Spearman's rank correlation analysis.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Chemical profiling tentatively identified 374 constituents. XFHJ improved pulmonary function and attenuated lung histopathological injury and inflammation. Tryptophan and glycerophospholipid metabolism were the principal treatment-associated pathways. XFHJ also altered gut microbial diversity and composition, with enrichment of potentially beneficial taxa such as <i>Bifidobacterium</i>, <i>Roseburia</i>, and several <i>Clostridia</i>-related taxa. Treatment-responsive taxa correlated positively with indole-related metabolites, which correlated inversely with pulmonary inflammatory markers.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>XFHJ exhibited significant therapeutic effects on COPD rats, and its mechanism may be correlated with regulating the intestinal microbiota structure and metabolic profiles of COPD rats, thereby attenuating lung histopathological injury and pulmonary inflammation.</p>\u0000 </section>\u0000 </div>","PeriodicalId":225,"journal":{"name":"Rapid Communications in Mass Spectrometry","volume":"40 21","pages":""},"PeriodicalIF":1.8,"publicationDate":"2026-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148784364","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":"Authentication of the Botanical Origins of Curcumae Radix Based on DNA Barcoding and HS-GC-IMS","authors":"Qingsong Jiang,&nbsp;Jiaxin Yin,&nbsp;Xiao Han,&nbsp;Jie Yong,&nbsp;Run Sun,&nbsp;Minghui Liu,&nbsp;Wanjiao Wang,&nbsp;Yu Wang,&nbsp;Menglei Song,&nbsp;Beibei Xiang,&nbsp;Heshui Yu","doi":"10.1002/rcm.70160","DOIUrl":"https://doi.org/10.1002/rcm.70160","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Rationale</h3>\u0000 \u0000 <p>As a classic multiorigin herbal medicine, the precise authentication of <i>Curcumae Radix</i> (Yujin) is crucial for ensuring market standardization and clinical efficacy. Given the complexity of herbal materials, single-method identification often lacks the resolution required to distinguish between closely related species or handle degraded with significant DNA degradation.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>A two-dimensional analytical strategy was applied to 24 batches of <i>Curcumae Radix</i> samples. This approach combined ITS2 DNA barcoding for genetic identification with headspace gas chromatography–ion mobility spectrometry (HS-GC-IMS) to analyze volatile organic compound (VOC) profiles. The resulting HS-GC-IMS data were processed using chemometric tools, including principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA), to compare and differentiate the decoction pieces.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The results demonstrated that while ITS2 DNA barcoding effectively identified <i>Curcuma kwangsiensis</i> S. G. Lee et C. F. Liang, it failed to discriminate between the closely related species <i>Curcuma longa</i> L. and <i>Curcuma phaeocaulis</i> Val. and was ineffective for DNA-degraded samples of <i>Curcuma wenyujin</i> Y. H. Chen et C. Ling. Conversely, HS-GC-IMS successfully established distinct VOC fingerprints for each source. When coupled with chemometric analysis, this method pinpointed specific interspecific discriminatory biomarkers that allowed for clear differentiation where genetic barcoding fell short.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusion</h3>\u0000 \u0000 <p>By integrating stable genetic information with volatile chemical fingerprints, this study establishes a complementary two-dimensional identification system. This strategy provides an innovative and reliable solution for the botanical authentication and quality control of <i>Curcumae Radix</i>, offering a broadly applicable paradigm for the precise identification of other complex herbal materials.</p>\u0000 </section>\u0000 </div>","PeriodicalId":225,"journal":{"name":"Rapid Communications in Mass Spectrometry","volume":"40 21","pages":""},"PeriodicalIF":1.8,"publicationDate":"2026-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148784068","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":"Fragment Coverage: Unified Visualization and Quantitative Assessment of MS/MS Fragmentation Supports Metabolite Identification in Macromolecule Drug Metabolism Studies","authors":"Paula Cifuentes,&nbsp;Albert Garriga,&nbsp;Fabien Fontaine,&nbsp;Ismael Zamora","doi":"10.1002/rcm.70163","DOIUrl":"10.1002/rcm.70163","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Rationale</h3>\u0000 \u0000 <p>Peptides and oligonucleotides are increasingly used as therapeutic agents, making the identification and structural elucidation of their metabolites a critical step in drug development. Liquid chromatography–mass spectrometry (LC-MS/MS) is the primary analytical technique for this purpose; however, extensive backbone fragmentation generates highly complex MS/MS spectra, making spectral interpretation challenging and limiting the exploitation of the structural information contained in MS/MS fragmentation data.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>This study introduces two fragment-based metrics, fragment coverage and complete fragment coverage, to quantify structural coverage derived from MS/MS fragmentation at metabolite and parent compound levels. Their performance was evaluated across 33 LC-MS/MS experiments comprising peptide and oligonucleotide datasets. Ranking analysis based on mean average precision (MAP) assessed discrimination between true and false metabolite assignments. Additionally, a fragment viewer was developed to map MS/MS fragment ions onto structures, facilitating visualization and spectral interpretation.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>A total of 255 metabolites were identified, including 159 true metabolites and 96 false positives. True metabolites consistently exhibited higher fragment coverage and complete fragment coverage values than false positives. This trend was supported by ranking analysis using mean average precision (MAP), where complete fragment coverage achieved the highest performance (0.9737), followed by fragment coverage (0.9676), MassMetaSite score (MMS score) (0.9390), and isotopic similarity (0.9090). Two representative case studies demonstrated the applicability of the proposed metrics.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>The proposed fragment coverage metrics enable quantitative assessment of MS/MS fragmentation, providing complementary information to support manual interpretation of LC-MS/MS data in MetID workflows. Together with the fragment viewer tool, these approaches facilitate more efficient and interpretable analysis of complex MS/MS spectra in macromolecules.</p>\u0000 </section>\u0000 </div>","PeriodicalId":225,"journal":{"name":"Rapid Communications in Mass Spectrometry","volume":"40 21","pages":""},"PeriodicalIF":1.8,"publicationDate":"2026-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/rcm.70163","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148710833","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":"Revisiting the Fragmentation of Ketoconazole by Positive Electrospray Ionization Tandem Mass Spectrometry and Density Functional Theory Calculations","authors":"Fausto Carnevale Neto,&nbsp;Ricardo Vessecchi","doi":"10.1002/rcm.70156","DOIUrl":"10.1002/rcm.70156","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Rationale</h3>\u0000 \u0000 <p>Ketoconazole (KCZ) is a clinically essential antifungal and potent CYP3A4 inhibitor. Its gas-phase fragmentation under positive electrospray ionization tandem mass spectrometry (ESI-MS/MS) remains poorly characterized, undermining metabolite profiling and structural identification of related azoles.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We systematically mapped the fragmentation pathways of protonated KCZ using a dual-platform strategy combining quadrupole time-of-flight collision-induced dissociation (QTOF-CID) and Orbitrap higher-energy collisional dissociation (HCD) across a 10–60-eV collision energy range. Mechanistic assignments and protonation sites were supported by density functional theory (DFT) calculations at B3LYP/6-311++G(d,p) level in order to quantify thermodynamic barriers and dissociation energies.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Our study identified three distinct dissociation pathways: (1) piperazine ring opening driven by ketene loss (A1, <i>m/z</i> 489.1453) and alkylamine eliminations; (2) 1,3-dioxolane ring cleavages (e.g., C10, <i>m/z</i> 277.1547); and (3) radical-driven dissociation at the ether linker, yielding an imidazole radical cation (A28, <i>m/z</i> 82.0531, C₄H₆N₂^•+). DFT calculations established a clear thermodynamic hierarchy, where even-electron ions (e.g., A1, ΔG ≈ 19 kcal mol⁻¹) prevail at low energies, whereas the radical cation (A28, ΔG ≈ 86 kcal mol⁻¹) is only accessible at ≥ 40 eV. HCD conditions selectively promoted odd-electron ion formation, revealing platform-dependent fragmentation behavior.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>This work delivers the first comprehensive, computationally validated fragmentation map for KCZ, directly linking MS/MS observations to thermodynamic predictions and providing a robust reference for high-confidence identification of synthetic imidazole antifungals.</p>\u0000 </section>\u0000 </div>","PeriodicalId":225,"journal":{"name":"Rapid Communications in Mass Spectrometry","volume":"40 20","pages":""},"PeriodicalIF":1.8,"publicationDate":"2026-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148704962","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}