Journal of the American Society for Mass Spectrometry最新文献_第6页

Multipass CCS Refiner: A Web Application for Accurate Collision Cross Section Calibration in Cyclic Ion Mobility-Mass Spectrometry 多通道CCS精炼厂：循环离子迁移-质谱法中精确碰撞截面校准的Web应用程序。

IF 2.7 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2025-08-19 DOI: 10.1021/jasms.5c00199

Eric C. Gier, Dmitry Leontyev and Facundo M. Fernández*,

{"title":"Multipass CCS Refiner: A Web Application for Accurate Collision Cross Section Calibration in Cyclic Ion Mobility-Mass Spectrometry","authors":"Eric C. Gier, Dmitry Leontyev and Facundo M. Fernández*, ","doi":"10.1021/jasms.5c00199","DOIUrl":"10.1021/jasms.5c00199","url":null,"abstract":"In this paper, we present the Multipass CCS Refiner, an R application for calibrating multipass collision cross section (CCS) measurements with cyclic ion mobility spectrometry (cIMS). The Multipass CCS Refiner combines the necessary tools for calculating accurate CCS measurements from multipass cIMS experiments into a user-friendly web-based Shiny interface accessible regardless of programming knowledge. The application provides a suite of functions for calculating accurate arrival times, automated pass counting approximation, correction of arrival time perturbations during separation, constructing calibration curves unique to specific instrument settings, separating fine mobility features, and a variety of visualization tools. Code for the application is structured to be easily modified to meet the user’s needs. The Multipass CCS Refiner implements the calibration approach described by Lin and Costello to reduce the need for carefully selected separation times while accounting for artifacts underlying fluctuations in measured ion arrival times. The application is showcased with downloadable data files of commonly used standards, which can be run in the app directly or edited with user experimental data.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 9","pages":"2000–2004"},"PeriodicalIF":2.7,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/jasms.5c00199","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144881774","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

Faces of Mass Spectrometry/Kylie Bemis 质谱分析的面孔/Kylie Bemis。

IF 2.7 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2025-08-18 DOI: 10.1021/jasms.5c00225

Anne Brenner, J.D. Brookbank and Kylie Bemis,

引用次数: 0

The Protective Effects of CO2 on Fragile Ions in Differential Mobility Spectrometry 差分迁移率光谱法研究CO2对脆弱离子的保护作用。

IF 2.7 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2025-08-18 DOI: 10.1021/jasms.5c00098

Andrew L. Finlay, Wojciech Gabryelski and W. Scott Hopkins*,

{"title":"The Protective Effects of CO2 on Fragile Ions in Differential Mobility Spectrometry","authors":"Andrew L. Finlay, Wojciech Gabryelski and W. Scott Hopkins*, ","doi":"10.1021/jasms.5c00098","DOIUrl":"10.1021/jasms.5c00098","url":null,"abstract":"We explore the protective effects of adding CO2 to the N2 carrier gas when we conduct differential mobility spectrometry (DMS) analysis of fragile ions. A selection of fragile analytes of varying chemistries were chosen from our lab inventory and include protonated glycine, methylbenzyl ammonium, methoxybenzylpyridinium, the protonated 2-pentanone dimer, deprotonated GenX (a perfluoroalkyl substance; PFAS), and deprotonated trifluoroacetic acid. By raising the separation voltage or the carrier gas temperature, conditions were set to induce fragmentation of the analyte ions within the DMS collision cell. Subsequently introducing CO2 into the N2 carrier gas at concentrations ranging from 10 – 70% mitigated ion fragmentation and resulted in signal intensity gains of multiple orders of magnitude. Interestingly, stabilization of the fragile ions sometimes occurred without introducing significant ionogram peak shifts (i.e., shifts of less than 1 V), indicating that these ions exhibit relatively weak interactions with the CO2 modifier. Electronic structure calculations yield Gibbs binding energies of ca. – 1 kJ mol–1 under the DMS conditions employed, further supporting the hypothesis that dynamic ion-CO2 clustering is not the root cause of the observed protective effect. The addition of CO2 was also found to stabilize noncovalently bound dimers, presumably generated at the ionization source. These results indicate that, in these examples, CO2 cools the ions in the energetic DMS environment via momentum transfer and energy partitioning, and that introducing CO2 into DMS gas mixtures could enable the stabilization, separation, and analysis of fragile analytes.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 9","pages":"1860–1868"},"PeriodicalIF":2.7,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144870789","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

Dissecting Interactions between RNA and Coronavirus Nucleocapsid Proteins Using Native Mass Spectrometry 利用天然质谱分析RNA与冠状病毒核衣壳蛋白之间的相互作用。

IF 2.7 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2025-08-17 DOI: 10.1021/jasms.5c00159

Virginia K. James, Olivia E. Dioli and Jennifer S. Brodbelt*,

{"title":"Dissecting Interactions between RNA and Coronavirus Nucleocapsid Proteins Using Native Mass Spectrometry","authors":"Virginia K. James, Olivia E. Dioli and Jennifer S. Brodbelt*, ","doi":"10.1021/jasms.5c00159","DOIUrl":"10.1021/jasms.5c00159","url":null,"abstract":"The nucleocapsid protein is the most abundant protein in the SARS-CoV virus and plays critical roles in RNA packaging and storage, yet the nature of the protein’s interactions with RNA remain elusive owing to the presence of multiple disordered regions of the protein. Here we evaluate the protein–RNA and protein–protein interactions of nucleocapsid proteins from the SARS-CoV-1 WT, SARS-CoV-2 WT, and SARS-CoV-1 omicron to better understand how the interactions are modulated by sequence variations. By using native mass spectrometry, we reveal that all three nucleocapsid proteins exist as both monomers and dimers that bind up to two RNA molecules per monomer, suggesting dual RNA binding sites. Ultraviolet photodissociation (UVPD) was used to localize the RNA binding sites found in the RNA binding domain and N-terminus of the nucleocapsid protein. The stabilities of the dimer complexes of the three nucleocapsid were monitored using energy-variable collision-induced dissociation, revealing that the dimer from SARS-CoV-1 is less stable than the dimers of the other two SARS-CoV variants in the gas phase. Furthermore, variable temperature electrospray ionization (ESI) experiments of the RNA-bound nucleocapsid proteins indicated that the protein–RNA interactions are stronger than the protein–protein interactions in solution as the dimeric protein–RNA complexes dissociate into monomeric protein–RNA complexes prior to the loss of RNA.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 9","pages":"1921–1928"},"PeriodicalIF":2.7,"publicationDate":"2025-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144870787","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

Faces of Mass Spectrometry/Tabiwang Arrey 质谱分析的面孔/Tabiwang Arrey。

IF 2.7 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2025-08-15 DOI: 10.1021/jasms.5c00262

Anne Brenner, and , J. D. Brookbank,

引用次数: 0

Positively Charged Water Microdroplets Ionize Surrounding Gas Molecules 带正电的水微滴电离周围的气体分子。

IF 2.7 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2025-08-14 DOI: 10.1021/jasms.5c00178

Yuanyi He, Yifan Meng and Richard N. Zare*,

引用次数: 0

Long-Term System Suitability Evaluation for Mass Accuracy in the Analysis of Small Molecules by High-Resolution Mass Spectrometry 高分辨率质谱法分析小分子质量精度的长期系统适用性评价。

IF 2.7 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2025-08-12 DOI: 10.1021/jasms.5c00128

Paul Löffler, Svante Rehnstam, Lutz Ahrens, Foon Yin Lai and Alberto Celma*,

{"title":"Long-Term System Suitability Evaluation for Mass Accuracy in the Analysis of Small Molecules by High-Resolution Mass Spectrometry","authors":"Paul Löffler, Svante Rehnstam, Lutz Ahrens, Foon Yin Lai and Alberto Celma*, ","doi":"10.1021/jasms.5c00128","DOIUrl":"10.1021/jasms.5c00128","url":null,"abstract":"High-resolution mass spectrometry (HRMS) is critical for the identification and characterization of (un)known organic chemicals. In this regard, ensuring high mass accuracy in HRMS instruments is essential for reliable results in nontarget and suspect screening. This study presents a practical approach for evaluating and maintaining mass accuracy over time using ultrahigh pressure liquid chromatography coupled with electrospray ionization Orbitrap HRMS. A set of 13 reference standards, encompassing a range of polarities and chemical families, was analyzed before and after sample analysis batches to assess the impact of various factors on the instrumental performance regarding mass accuracy. The aim is not to recalibrate the system but to provide a reliable snapshot of the mass accuracy over time. The study found that the positive ionization mode exhibited higher accuracy and precision compared with the negative mode. Factors affecting mass accuracy included calibration quality, the number of batch injections, and the time between calibrations, where the two latter factors were related to each other. Results suggest that performing system suitability tests for high-resolution accurate masses with two injections before and after sample analysis is adequate for ensuring acceptable mass spectrometric performance for robust and reliable HRMS data acquisition, but performing three injections is recommended. This protocol ensures that informed decisions can be made with regard to the mass accuracy, the calibration, and a potential recalibration before HRMS data acquisition is performed.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 9","pages":"2005–2012"},"PeriodicalIF":2.7,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/jasms.5c00128","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144833684","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

Unusual Fragmentations of Silylated Polyfluoroalkyl Compounds Induced by Electron Ionization 电子电离诱导的硅基化多氟烷基化合物的异常碎片化。

IF 2.7 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2025-08-11 DOI: 10.1021/jasms.5c00185

Yufang Zheng*, Edward P. Erisman, Weihua Ji, Stephen E. Stein and William E. Wallace,

{"title":"Unusual Fragmentations of Silylated Polyfluoroalkyl Compounds Induced by Electron Ionization","authors":"Yufang Zheng*, Edward P. Erisman, Weihua Ji, Stephen E. Stein and William E. Wallace, ","doi":"10.1021/jasms.5c00185","DOIUrl":"10.1021/jasms.5c00185","url":null,"abstract":"Per- and polyfluoroalkyl substances (PFAS) are environmentally persistent compounds that present analytical challenges due to their stability and low concentrations. In this study, electron ionization (EI) mass spectra of trimethylsilyl (TMS) derivatized fluorinated alcohols and carboxylic acids were examined to improve PFAS identification in the NIST Mass Spectral Reference Library. In contrast with the spectra of unsubstituted alcohol TMS compounds featuring losses of hydrocarbons, fluorinated alcohol TMS derivatives are characterized by the losses of fluorinated silyl groups. For example, a previously unreported [M–111]+ ion was consistently observed in compounds containing three methylene groups between the hydroxyl group and the first CF2 unit. Detailed quality assurance analysis using a suite of NIST software tools along with high-resolution TOF-MS confirmed the origin and elemental composition of these ions. MS2 experiments and full scan of TMS derivatives of fluorinated alcohols with varying numbers of methylene groups investigations suggest the formation of a five-membered ring intermediate as a key feature in this unique fragmentation pathway. These findings improve our understanding of PFAS fragmentation and support more accurate compound identification in analytical workflows.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 9","pages":"1970–1978"},"PeriodicalIF":2.7,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/jasms.5c00185","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144820316","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

Boosting Quantification of N-Glycans by an Enhanced Isobaric Multiplex Reagents for Carbonyl-Containing Compound (SUGAR) Tagging Strategy 在含羰基化合物（糖）标记策略中，增强等压多重试剂促进n -聚糖的定量。

IF 2.7 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2025-08-11 DOI: 10.1021/jasms.5c00153

Jingwei Zhang, Zicong Wang, Yuan Liu, Henrik Zetterberg and Lingjun Li*,

引用次数: 0

Dynamic Quadrupole Selection to Associate Precursor Masses with MS/MS Products in Data-Independent Acquisition 数据独立采集中MS/MS产品前体质量的动态四极选择。

IF 2.7 2区化学

Journal of the American Society for Mass Spectrometry Pub Date : 2025-08-08 DOI: 10.1021/jasms.5c00110

Keaton L. Mertz, Lia R. Serrano, Pavel Sinitcyn* and Joshua J. Coon*,

{"title":"Dynamic Quadrupole Selection to Associate Precursor Masses with MS/MS Products in Data-Independent Acquisition","authors":"Keaton L. Mertz, Lia R. Serrano, Pavel Sinitcyn* and Joshua J. Coon*, ","doi":"10.1021/jasms.5c00110","DOIUrl":"10.1021/jasms.5c00110","url":null,"abstract":"Data-independent acquisition (DIA) mass spectrometry facilitates high-throughput, reproducible bottom-up proteomic analyses. Typically, DIA methods coselect multiple precursor ions within a wide selection window. These precursors are simultaneously fragmented, superimposing the product ion signals into a complex chimeric spectrum. A method for varying the quadrupole selection width over the ion accumulation period is described. This method couples the intensity of a product ion to the mass of its precursor ion. By overlapping consecutive selection windows, scan-to-scan product ion intensity profiles can be used to infer precursor mass. We assess the method’s sensitivity to quadrupole width, accumulation time, and mass-to-charge range using internal fluoranthene calibrant and FlexMix calibration solution with Q-Orbitrap configured mass analyzers. Additionally, we explore usability of the described technique on a tryptic-digest monoclonal antibody sample, including both direct infusion and liquid chromatography of the sample. With direct infusion, product ions from two precursors separated by 1 thomson (Th) are resolved with this method using 10 Th windows with 5 Th overlap. The product ions are associated within 0.3 Th of their respective precursor ion’s m/z. Therefore, product ion spectra have a precursor ion m/z resolving power of ∼33.","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 9","pages":"1869–1876"},"PeriodicalIF":2.7,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144803223","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