Journal of the American Society for Mass Spectrometry最新文献

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Profiling Multiple Steroid Subclasses Enabled by Rounded Turn SLIM Ion Mobility. 通过圆转弯SLIM离子迁移率分析多个类固醇子类。
IF 2.7 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2025-09-01 DOI: 10.1021/jasms.5c00218
Cole L Frank, Breland M Jones, Emmaleigh Efird, Makenna Hoover, Selena Kingsley, Heidi M Sabatini, Christopher D Chouinard
{"title":"Profiling Multiple Steroid Subclasses Enabled by Rounded Turn SLIM Ion Mobility.","authors":"Cole L Frank, Breland M Jones, Emmaleigh Efird, Makenna Hoover, Selena Kingsley, Heidi M Sabatini, Christopher D Chouinard","doi":"10.1021/jasms.5c00218","DOIUrl":"https://doi.org/10.1021/jasms.5c00218","url":null,"abstract":"<p><p>Ion mobility-mass spectrometry has shown tremendous potential for improving the analysis of various subclasses of steroids. Its speed and ability to separate isobaric and isomeric species makes it ideal for biomedical, clinical, food, environmental, and antidoping analyses. But while other high-resolution ion mobility (HRIM) techniques have begun to see increased use in steroidomics, Structures for Lossless Ion Manipulations (SLIM) is a relative newcomer to the field. HRIM methods are generally challenged with low molecular weight (MW < 400) analysis, but a recently developed SLIM platform has incorporated rounded turns, helium buffer gas, and increased SLIM RF frequency to enable improved low mass transmission. In the present work, we investigate this low mass-tailored SLIM system for the analysis of anabolic androgens, bile acids, endocrine hormones, and ketosteroids. Linear regression-corrected <sup>SLIM</sup>CCS<sub>He</sub> (CCS = collision cross section) values show excellent agreement with values obtained via direct measurement with a drift tube instrument but also underlie the importance of using class- and adduct-specific correction factors. Next, separation performance was evaluated for a range of challenging isomers and demonstrated good resolution for species with ΔCCS of <1%. Finally, the new rounded turn system was compared quantitatively with the traditional 90° (square turn) system in both nitrogen and helium buffer gases and revealed significantly improved signal across the board for rounded turn analyses with helium. Overall, this low mass-tailored system has remarkable promise for development of rapid, targeted steroid analysis in a range of applications.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144938354","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Relational Graph Convolutional Network for Robust Mass Spectrum Classification 鲁棒质谱分类的关系图卷积网络。
IF 2.7 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2025-09-01 DOI: 10.1021/jasms.5c00055
Raphaël La Rocca, , , Anthony Cioppa, , , Enrico Ferrarini, , , Monica Höfte, , , Marc Van Droogenbroeck, , , Edwin De Pauw, , , Gauthier Eppe, , and , Loïc Quinton*, 
{"title":"Relational Graph Convolutional Network for Robust Mass Spectrum Classification","authors":"Raphaël La Rocca,&nbsp;, ,&nbsp;Anthony Cioppa,&nbsp;, ,&nbsp;Enrico Ferrarini,&nbsp;, ,&nbsp;Monica Höfte,&nbsp;, ,&nbsp;Marc Van Droogenbroeck,&nbsp;, ,&nbsp;Edwin De Pauw,&nbsp;, ,&nbsp;Gauthier Eppe,&nbsp;, and ,&nbsp;Loïc Quinton*,&nbsp;","doi":"10.1021/jasms.5c00055","DOIUrl":"10.1021/jasms.5c00055","url":null,"abstract":"<p >Supervised machine learning methods have shown impressive performance in interpreting mass signals and automatically segmenting spatially meaningful regions in Mass Spectrometry Imaging (MSI). Such segmentation generates maps that provide researchers with valuable insights into sample composition and serve as a foundation for downstream statistical analyses. However, these models often require data set-specific preprocessing and do not fully exploit the rich mass features available in high-resolution mass spectrometry (HRMS). Unlike low-resolution mass spectrometry, HRMS reveals additional features such as mass defects and repeated mass differences that carry important chemical information. In this work, we propose a novel deep learning architecture based on a Relational Graph Convolutional Network (R-GCN) that captures and leverages those HRMS mass features. Our model explicitly encodes structural features such as mass defects and known mass differences to represent each spectrum as a graph, enabling the learning of associations between chemically related ion families. To the best of our knowledge, no existing deep learning models for MSI classification incorporate this level of chemically informed mass structure. Most existing methods treat spectra as flat vectors or image-like inputs, thereby ignoring the underlying mass relationships. We evaluate our R-GCN approach against several conventional machine learning and deep learning baselines across diverse MSI data sets, demonstrating its robustness to common signal variations (e.g., mass shift, ion loss). Finally, we integrate Class Activation Mapping (CAM) to enhance model interpretability, enabling the identification of ion families that are relevant to specific biological or spatial regions.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 10","pages":"2036–2047"},"PeriodicalIF":2.7,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144938374","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Effect of pH on the Kinetics of Cysteine-to-Cystine Conversion in Thin Films Formed by ESI Microdroplet Deposition pH对ESI微滴沉积薄膜中半胱氨酸到胱氨酸转化动力学的影响。
IF 2.7 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2025-08-29 DOI: 10.1021/jasms.5c00195
Marta Managò, , , Chiara Salvitti, , , Anna Troiani, , , Alessia Di Noi, , , Andreina Ricci, , and , Federico Pepi*, 
{"title":"Effect of pH on the Kinetics of Cysteine-to-Cystine Conversion in Thin Films Formed by ESI Microdroplet Deposition","authors":"Marta Managò,&nbsp;, ,&nbsp;Chiara Salvitti,&nbsp;, ,&nbsp;Anna Troiani,&nbsp;, ,&nbsp;Alessia Di Noi,&nbsp;, ,&nbsp;Andreina Ricci,&nbsp;, and ,&nbsp;Federico Pepi*,&nbsp;","doi":"10.1021/jasms.5c00195","DOIUrl":"10.1021/jasms.5c00195","url":null,"abstract":"<p >The oxidation of cysteine to cystine was investigated in aqueous thin films generated by the deposition of electrospray ionization (ESI) microdroplets. The confined volume of the thin film promotes the reaction, resulting in up to 80% conversion of cysteine to cystine at a thin film temperature of 40 °C. The pH of the solution is a critical parameter, influencing both the yield and the kinetics of the reaction. Strong reaction acceleration factors in thin film with respect to the bulk were measured.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 10","pages":"2189–2196"},"PeriodicalIF":2.7,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/jasms.5c00195","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144938301","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Simulating Collision-Induced Dissociation Tandem Mass Spectrometry (CID-MS/MS) for the Blood Exposome Database Using Quantum Chemistry Methods - A Pilot Study 使用量子化学方法模拟碰撞诱导解离串联质谱(CID-MS/MS)用于血液暴露体数据库-一项试点研究。
IF 2.7 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2025-08-28 DOI: 10.1021/jasms.5c00179
Jesi Lee,  and , Dinesh Barupal*, 
{"title":"Simulating Collision-Induced Dissociation Tandem Mass Spectrometry (CID-MS/MS) for the Blood Exposome Database Using Quantum Chemistry Methods - A Pilot Study","authors":"Jesi Lee,&nbsp; and ,&nbsp;Dinesh Barupal*,&nbsp;","doi":"10.1021/jasms.5c00179","DOIUrl":"10.1021/jasms.5c00179","url":null,"abstract":"<p >A significant number of compounds in exposome databases and chemical inventories lack mass spectral data due to the nonavailability of reference standards. To address this limitation, computational chemistry methods can be utilized to extend mass spectral libraries for a set of chemicals. In this pilot study, we employed quantum-chemistry-based software QCxMS to generate collision-induced dissociation mass spectra for 121 compounds from the Blood Exposome Database. We developed a scalable computational framework that integrates QCxMS and additional tools, utilizing a grid-based parameter selection strategy and defined coverage criteria. Our approach systematically explored protomeric isomers and applied predefined parameter combination sets sequentially based on molecular structures. This workflow produced high-quality <i>in silico</i> spectra for 81 compounds that achieved entropy similarity scores ≥700 and at least two matching fragment ions against the NIST23 library, yielding 71% spectral coverage. These results highlight the importance of optimizing simulation parameters and accounting for protomeric diversity to enhance the spectral quality and computational efficiency. This workflow provides a practical strategy to add mass spectral data for most compounds in the Blood Exposome Database at reasonable computational cost, supporting the spectral library expansion for improved compound annotation in exposomics.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 10","pages":"2171–2180"},"PeriodicalIF":2.7,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144938326","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Electron Capture Dissociation for Discovery Top-Down Proteomics of Peptides and Small Proteins on Chromatographic Time Scales 电子捕获解离在色谱时间尺度上发现多肽和小蛋白自上而下的蛋白质组学。
IF 2.7 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2025-08-28 DOI: 10.1021/jasms.5c00116
Lester S. Manly, , , Anne M. Roberts, , , Joseph S. Beckman, , and , Blaine R. Roberts*, 
{"title":"Electron Capture Dissociation for Discovery Top-Down Proteomics of Peptides and Small Proteins on Chromatographic Time Scales","authors":"Lester S. Manly,&nbsp;, ,&nbsp;Anne M. Roberts,&nbsp;, ,&nbsp;Joseph S. Beckman,&nbsp;, and ,&nbsp;Blaine R. Roberts*,&nbsp;","doi":"10.1021/jasms.5c00116","DOIUrl":"10.1021/jasms.5c00116","url":null,"abstract":"<p >Bottom-up proteomics introduces proteoform ambiguity due to the loss of connectivity between peptides and their original proteoforms. Top-down proteomics (TDP) removes the ambiguity through the direct identification and characterization of intact proteoforms and their respective post-translational modifications (PTM). Electron capture dissociation (ECD) is an efficient and gentle peptide and protein fragmentation strategy that can be used for both bottom-up and top-down approaches. Here, we used an Agilent 6550 Q-TOF mass spectrometer retrofitted with an e-MSion ECD cell. Top-down sequencing capabilities of the cell were evaluated by sequencing of intact peptides and proteins on high-performance liquid chromatography (HPLC) time scales. Amyloid beta 1-40 (Aβ40) was first tested due to its pathophysiological role in Alzheimer’s disease and served as our large peptide standard. We sequenced Aβ40 via reverse-phase HPLC-MS and achieved 95% sequence coverage on chromatographic time scales utilizing a data-dependent acquisition (DDA)-based method. Acetone-precipitated protein extracts from human brain were then separated by HPLC and analyzed with a DDA method, which identified 16 proteoforms between 2 and 17 kDa with sequence coverage ranging from 7 to 90% based on proteoform size and composition. In addition to proteoform identification, ECD fragmentation distinguished multiple isoaspartate modifications from aspartate, as well as accurately differentiating leucine from isoleucine residues directly from the human brain sample. Here, we observed isoaspartate within a thymosin beta-4 proteoform. Additionally, we demonstrated the differentiation of leucine and isoleucine within a subunit of ubiquitin. This study advances the application of LC-Q-TOF instrumentation for discovery-based top-down proteomics utilizing ECD as enabled by the e-MSion ECD cell.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 10","pages":"2079–2093"},"PeriodicalIF":2.7,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/jasms.5c00116","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144938376","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Capturing Current Practices and Characterizing Measurement Reproducibility for Seized Drug Analysis Using Ambient Ionization Mass Spectrometry: An Interlaboratory Study 利用环境电离质谱法捕获当前实践和表征扣押药物分析的测量再现性:一项实验室间研究。
IF 2.7 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2025-08-27 DOI: 10.1021/jasms.5c00213
Edward Sisco*, , , Dennis D. Leber, , and , Arun S. Moorthy, 
{"title":"Capturing Current Practices and Characterizing Measurement Reproducibility for Seized Drug Analysis Using Ambient Ionization Mass Spectrometry: An Interlaboratory Study","authors":"Edward Sisco*,&nbsp;, ,&nbsp;Dennis D. Leber,&nbsp;, and ,&nbsp;Arun S. Moorthy,&nbsp;","doi":"10.1021/jasms.5c00213","DOIUrl":"10.1021/jasms.5c00213","url":null,"abstract":"<p >The use of ambient ionization mass spectrometry (AI-MS) to aid in the preliminary screening of seized drug evidence has steadily increased over the past two decades. Unlike gas chromatography–mass spectrometry (GC-MS), where electron ionization using a single quadrupole analyzer is commonplace, a wide range of ionization sources and mass spectrometers can be used in AI-MS. Differences in instrument configuration can lead to substantial variability in the mass spectral data obtained. An interlaboratory study, consisting of 35 participants from 17 laboratories, was conducted to begin to understand the landscape and the differences in the data that are produced. Laboratories analyzed a series of 21 solutions across multiple days using their own instrumental methods. Mass spectra were extracted and compared to understand operator, within-lab, and between-lab reproducibility for common compounds and mixtures observed in seized drug analysis. In addition, five participants analyzed the 21 solutions using prescribed method parameters to measure reproducibility improvements when using identical instrumental conditions. Mass spectral reproducibility, measured through pairwise cosine similarity, was found to be generally quite high, regardless of sample type, instrument type, method, or operator. Low-fragmentation spectra showed the lowest variability, as they were dominated by intact protonated molecule peaks. Several potential issues that increased variability were identified, including carryover from mass calibrants, poor sample introduction, and mass spectrometer inlets that required cleaning. The use of uniform method parameters was shown to increase the reproducibility of mass spectra across laboratories, most notably at higher in-source collision-induced dissociation energies. This study provides initial insights into the current landscape of AI-MS in seized drug analysis and lays the foundation for future studies that can provide needed data for the development of documentary standards, standard methods, and possibly the establishment of error rates.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 10","pages":"2239–2252"},"PeriodicalIF":2.7,"publicationDate":"2025-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/jasms.5c00213","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144938196","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Optimization of q Value for Sensitive Detection of Uridine and Thymidine Nucleosides by MS3 MS3灵敏检测尿苷和胸腺苷核苷q值的优化
IF 2.7 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2025-08-27 DOI: 10.1021/jasms.5c00245
Zheng Duan, , , Chen Wang, , and , Yinsheng Wang*, 
{"title":"Optimization of q Value for Sensitive Detection of Uridine and Thymidine Nucleosides by MS3","authors":"Zheng Duan,&nbsp;, ,&nbsp;Chen Wang,&nbsp;, and ,&nbsp;Yinsheng Wang*,&nbsp;","doi":"10.1021/jasms.5c00245","DOIUrl":"10.1021/jasms.5c00245","url":null,"abstract":"<p >Liquid chromatography-tandem mass spectrometry has been widely used to quantify modified nucleosides enzymatically released from RNA and DNA. Compared to MS/MS, MS<sup>3</sup> offers higher specificity for analytes in complex sample matrices because coeluting chemical interferences can be more effectively filtered out. To date, the detection of uracil- and thymine-containing nucleosides and their modified derivatives still suffers from poor sensitivity, owing, in part, to their relatively low proton affinities. In this study, we explored various settings of <i>q</i> values in the MS<sup>3</sup> analysis of unmodified and chemically modified uridine and thymidine nucleosides on a linear ion trap mass spectrometer. Our results showed that increasing the <i>q</i> value led to markedly improved sensitivities for detecting some of these nucleosides using MS<sup>3</sup>. Our work suggests that optimizing the <i>q</i> value constitutes a useful approach for the highly sensitive detection of modified nucleosides and other types of analytes by MS<sup>3</sup>.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 10","pages":"2017–2021"},"PeriodicalIF":2.7,"publicationDate":"2025-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144938332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Absolute Quantitation of Coeluting Impurities in Peptide Drugs Using High Resolution Mass Spectrometry: Glucagon a Case Study in Pharmaceutical Development 利用高分辨率质谱法对多肽药物中溶出杂质的绝对定量:胰高血糖素——药物开发中的一个案例研究。
IF 2.7 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2025-08-26 DOI: 10.1021/jasms.5c00105
Anusha Kodidasu, , , Koushik Acharyya*, , and , Vasanthakumar Ganga Ramu*, 
{"title":"Absolute Quantitation of Coeluting Impurities in Peptide Drugs Using High Resolution Mass Spectrometry: Glucagon a Case Study in Pharmaceutical Development","authors":"Anusha Kodidasu,&nbsp;, ,&nbsp;Koushik Acharyya*,&nbsp;, and ,&nbsp;Vasanthakumar Ganga Ramu*,&nbsp;","doi":"10.1021/jasms.5c00105","DOIUrl":"10.1021/jasms.5c00105","url":null,"abstract":"<p >Synthetic peptide-based drugs provide customized therapeutic solutions, but developing a peptide medicine presents various challenges, especially in terms of impurity management. This holds true when traditional techniques like RP-HPLC fail to separate low-abundance coeluting impurities. In this regard, liquid chromatography combined with high-resolution mass spectrometry (LC-HRMS) has proven to be effective for identifying and characterizing peptide impurities, although its application for accurate quantitation is still limited. This study developed and validated two quantitation strategies using UPLC-HRMS, employing full scan and pseudo-MRM (<i>p</i>-MRM) modes, to identify and accurately quantify two structurally similar coeluting peptide impurities (des-Gly<sup>4</sup> glucagon and des-Thr<sup>5</sup> glucagon) observed in synthetic glucagon. The methods exhibited high specificity and demonstrated good linearity (<i>R</i><sup>2</sup> &gt; 0.99) across a concentration range of 0.25–25 μg/mL. The limits of detection (LODs) for des-Gly<sup>4</sup>-glucagon and des-Thr<sup>5</sup>-glucagon were determined to be as low as 0.01% and 0.02%, with limits of quantitation (LOQs) at 0.02% and 0.04%, respectively. Precision (RSD%) was recorded at less than 10%, and recovery ranged from 100% to 120%. A comparative analysis of the results indicated that both quantifitation methods performed similarly in terms of accuracy, precision, and recovery, producing comparable impurity estimates in three glucagon API samples. However, <i>p</i>-MRM showed slightly better linearity and sensitivity compared to the full scan EIC-based quantitation method.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 10","pages":"2072–2078"},"PeriodicalIF":2.7,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144938193","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Side Chain Driven Mass Spectral Fragmentation of Lys Containing Peptides: Cα-CO Bond Cleavage in Xxx-Lys-Xxx Sequences 含赖氨酸肽的侧链驱动质谱碎片化:xxx -赖氨酸- xxx序列中的Cα-CO键断裂。
IF 2.7 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2025-08-26 DOI: 10.1021/jasms.5c00154
Sanjeev Kumar, , , Marimuthu Vijayasarathy, , , Venkatesha M. Achanna, , and , Padmanabhan Balaram*, 
{"title":"Side Chain Driven Mass Spectral Fragmentation of Lys Containing Peptides: Cα-CO Bond Cleavage in Xxx-Lys-Xxx Sequences","authors":"Sanjeev Kumar,&nbsp;, ,&nbsp;Marimuthu Vijayasarathy,&nbsp;, ,&nbsp;Venkatesha M. Achanna,&nbsp;, and ,&nbsp;Padmanabhan Balaram*,&nbsp;","doi":"10.1021/jasms.5c00154","DOIUrl":"10.1021/jasms.5c00154","url":null,"abstract":"<p >Mass spectral fragmentation of the tripeptide amide Ala-Lys-Ala-amide (AKA*) yields a product ion at <i>m</i>/<i>z</i> 228.1, which corresponds to a neutral loss of 43 Da from the <i>b</i><sub>3</sub> ion (<i>m</i>/<i>z</i> 271.1). Similar losses of 43 Da are observed from <i>b</i><sub>n</sub> ions in the hexapeptide AKAAKA* and tetrapeptide AKAA*. The role of the Lys2 residue, in mediating the neutral loss, is supported by the absence of the corresponding product ion in the MS<sup>2</sup> spectrum of AVA* and attenuation of the intensity in analogs containing ornithine/diaminobutyric acid residues at position 2. The role of the N-terminus amino group is suggested by the absence of this neutral loss when the residue Ala1 amino group is acetylated or dimethylated. In XKA* sequences, where X = Gly, Ala, Leu, Aib and Pro, the observed neutral losses from <i>b</i><sub>3</sub> are 29, 43, 85, 57, and 69 Da, respectively, indicative of C<sup>α</sup>-CO bond cleavage releasing the R-CH = NH fragment. Isotope labeling and comparison with mass spectral fragments generated from synthetic N<sup>α</sup>-formyl Lys-Ala-amide (fKA*) establish the identity of the ion at <i>m</i>/<i>z</i> 228 in the MS<sup>2</sup> spectrum of AKA* as the <i>b</i> ion [fKA]. A charge remote fragmentation pathway, involving proton abstraction from the terminal amino group, by the Lys2 ε amino group, followed by C<sup>α</sup>-CO bond cleavage, is proposed as a plausible mechanism for the observed noncanonical cleavage process.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 10","pages":"2134–2141"},"PeriodicalIF":2.7,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144938325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Interdomain Interactions Modulate Refolding Kinetics and Aggregation in a Monoclonal Antibody. 区域间相互作用调节单克隆抗体的折叠动力学和聚集。
IF 2.7 2区 化学
Journal of the American Society for Mass Spectrometry Pub Date : 2025-08-26 DOI: 10.1021/jasms.5c00166
Philipp Trolese, Andrea Pierangelini, Benedetta Fongaro, Patrizia Polverino de Laureto
{"title":"Interdomain Interactions Modulate Refolding Kinetics and Aggregation in a Monoclonal Antibody.","authors":"Philipp Trolese, Andrea Pierangelini, Benedetta Fongaro, Patrizia Polverino de Laureto","doi":"10.1021/jasms.5c00166","DOIUrl":"https://doi.org/10.1021/jasms.5c00166","url":null,"abstract":"<p><p>Understanding the structural determinants of antibody stability and aggregation is essential for therapeutic development. In this study, we investigated the unfolding and refolding behavior of bevacizumab under denaturing conditions using dynamic light scattering (DLS), circular dichroism (CD), and hydrogen-deuterium exchange mass spectrometry (HDX-MS). Unfolding was induced by incubating the antibody in 4 M guanidine hydrochloride (Gnd-HCl), followed by refolding through dilution with 1 M Gnd-HCl. Each domain exhibited distinct unfolding kinetics: the C<sub>H</sub>2 and V<sub>H</sub> domains unfolded rapidly, while the C<sub>H</sub>3 domain retained its structure until 45 min, consistent with its known thermodynamic stability. Aggregation, detected by DLS, was prevalent only after 120 min and overnight unfolding, coinciding with C<sub>H</sub>3 destabilization. Notably, aggregation-prone regions were identified in both the Fc and Fab portions of the antibody. Specifically, interactions at the C<sub>H</sub>2-C<sub>H</sub>3 and C<sub>H</sub>3-C<sub>H</sub>3 interfaces appear disrupted upon C<sub>H</sub>3 unfolding, leading to misfolded and aggregation-prone states in both domains. In parallel, the V<sub>H</sub> CDR H1 region exhibited aberrant protection after refolding, suggesting its involvement in aggregation. These findings highlight the cooperative nature of C<sub>H</sub>2-C<sub>H</sub>3 refolding and underscore the critical role of the C<sub>H</sub>3 stability in preventing aggregation. The involvement of both constant and variable domains emphasizes the complex, interdependent nature of monoclonal antibody aggregation. This work provides mechanistic insights into domain-specific contributions to folding and aggregation, offering guidance for the design of more stable therapeutic antibodies.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144938349","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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