Journal of the American Society for Mass Spectrometry最新文献

{"title":"Multistage Linear Frequency Scanning Mass Analysis Processed by Fractional Fourier Transform.","authors":"Haoqiang Yan, Liangshun Hu, Shi Zhang, Dayu Li, Wei Xu","doi":"10.1021/jasms.5c00012","DOIUrl":"10.1021/jasms.5c00012","url":null,"abstract":"<p><p>The common method of mass analysis in a linear ion trap mass spectrometer is to eject ions with different mass-to-charge ratios (<i>m</i>/<i>z</i>) at different times by resonance excitation. Ions are ejected onto an electron multiplier (EM), generating pulsed signals called the ejection signal. Typically, the ejection signal consisting of multiple pulses is smoothed into a wider Gaussian-like pulse due to the limited bandwidth of the electronic system. For different scan rates and different samples, this bandwidth-limited electronic system and signal smoothing process will differentially increase the peak width and thus decrease the mass resolution. In this study, experiments at different scan rates were performed on a \"Brick\" miniature linear ion trap mass spectrometer. We propose a multistage linear frequency scanning mode that achieves improved mass resolution and extended mass range, in which fractional Fourier transform is applied to process the ejection signals. The proposed signal processing method improves the mass resolution and mitigates the impact of ghost peaks attributed to scattered ion ejection. A peak width of 0.84 Da at a <i>m</i>/<i>z</i> value of 242 and a scan rate of 8000 Da/s was achieved in experiments.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"1093-1099"},"PeriodicalIF":3.1,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143762582","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}

{"title":"Maximizing Data Coverage through Eight Sequential Mass Spectrometry Images of a Single Tissue Section.","authors":"Erin H Seeley","doi":"10.1021/jasms.5c00032","DOIUrl":"https://doi.org/10.1021/jasms.5c00032","url":null,"abstract":"<p><p>Typical mass spectrometry imaging (MSI) experiments involve the collection of data from only one class of molecules per section. However, it is often necessary to collect data from different classes of analytes from the same biopsy, and generally, serial sections are used for additional analyte classes. However, differences will be observed between the cells present in each section, especially if the sections are not immediately serial with each other. In this study, a method is presented that allows for 8 mass spectrometry images to be collected sequentially from the same tissue section, including metabolites in positive and negative mode, lipids in positive and negative mode, N-linked glycans, O-linked <i>N</i>-acetylglucosamine, small intact proteins, and tryptic peptides. The order of data collection allows for washing to be used that removes analytes already detected and enhances the signal of subsequently imaged analytes. The collection of multiple images from the same tissue section enables facile coregistration of multiple data sets for evaluation of co- and differential localization across molecular classes.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 5","pages":"1148-1157"},"PeriodicalIF":3.1,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143957010","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}

{"title":"Efficient, Zero Scrambling Fragmentation of Deuterium Labeled Peptides on the ZenoToF 7600 Electron Activated Dissociation Platform.","authors":"Joseph Anacleto, Ebadullah Kabir, Madeline Blanco, Yves Leblanc, Cristina Lento, Derek J Wilson","doi":"10.1021/jasms.5c00041","DOIUrl":"https://doi.org/10.1021/jasms.5c00041","url":null,"abstract":"<p><p>Hydrogen-deuterium exchange (HDX) mass spectrometry (MS) has become an increasingly important tool in protein research, with large-scale applications in biopharmaceutical development and manufacturing. One of the limitations of classical bottom-up HDX is that it usually provides a \"peptide-averaged\" picture of structure and dynamics, rather than site-specific (i.e., individual amino acid-level) information. A major challenge for site-specific HDX-MS analyses has been that classical fragmentation techniques such as CAD invariably cause random redistribution of the deuterium labels across the peptide backbone, known as deuterium scrambling. Several groups have demonstrated that this problem can be overcome using nonergodic fragmentation and \"cool\" ion flight conditions. A major hurdle to widespread adoption of this approach, however, is that the exceedingly low fragmentation efficiency of electron capture dissociation (ECD) combined with the lower transmission efficiency of \"cool\" ion flight conditions impose a very strong attenuation on sensitivity, to the point where this method becomes impractical for many \"real-world\" applications. Here, we introduce a workflow and instrument conditions on the Sciex 7600 ZenoToF electron activated dissociation (EAD) platform that allow for zero scrambling ECD fragmentation with limited (and in some cases no) sensitivity loss. We expect that this workflow will be ideal for broadly applicable, site-specific HDX-MS analyses using a middle-down workflow.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 5","pages":"1175-1181"},"PeriodicalIF":3.1,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12063609/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143955458","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}

{"title":"Improving MALDI Mass Spectrometry Imaging Performance: Low-Temperature Thermal Evaporation for Controlled Matrix Deposition and Improved Image Quality.","authors":"Toufik Mahamdi, Cristina Gomez Serna, Roger Giné, Jordi Rofes, Shad Arif Mohammed, Pere Ràfols, Xavier Correig, María García-Altares, Carsten Hopf, Stefania-Alexandra Iakab, Oscar Yanes","doi":"10.1021/jasms.5c00015","DOIUrl":"https://doi.org/10.1021/jasms.5c00015","url":null,"abstract":"<p><p>The deposition of matrix compounds significantly influences the effectiveness of matrix-assisted laser desorption/ionization (MALDI) Mass Spectrometry Imaging (MSI) experiments, impacting sensitivity, spatial resolution, and reproducibility. Dry deposition methods offer advantages by producing homogeneous matrix layers and minimizing analyte delocalization without the use of solvents. However, refining these techniques to precisely control matrix thickness, minimize heating temperatures, and ensure high-purity matrix layers is crucial for optimizing MALDI-MSI performance. Here, we present a novel approach utilizing low-temperature thermal evaporation (LTE) for organic matrix deposition under reduced vacuum pressure. Our method allows for reproducible control of matrix layer thickness, as demonstrated by linear calibration for two organic matrices, 2,5-dihydroxybenzoic acid (DHB) and 1,5-diaminonaphthalene (DAN). The environmental scanning electron microscopy images reveal a uniform distribution of small-sized matrix crystals, consistently on the sub-micrometer scale, across tissue slides following LTE deposition. Remarkably, LTE serves as an additional purification step for organic matrices, producing very pure layers irrespective of initial matrix purity. Furthermore, stability assessment of MALDI-MSI data from mouse brain sections coated with LTE-deposited DHB or DAN matrix indicates minimal impact on ionization efficiency, signal intensity, and image quality even after storage at -80 °C for 2 weeks, underscoring the robustness of LTE-deposited matrices for MSI applications. Comparative analysis with the spray-coating method highlights several advantages of LTE deposition, including enhanced ionization, reduced analyte diffusion, and improved MSI image quality.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 5","pages":"1100-1110"},"PeriodicalIF":3.1,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12063169/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143957006","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}

{"title":"Faces of Mass Spectrometry/Amanda Hummon.","authors":"Anne Brenner, J D Brookbank","doi":"10.1021/jasms.5c00052","DOIUrl":"10.1021/jasms.5c00052","url":null,"abstract":"","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"923-925"},"PeriodicalIF":3.1,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143539913","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}

{"title":"Multispectrum ModiFinder Site Localization Performance.","authors":"Mohammad Reza Zare Shahneh, James Pyke, Emma E Rennie, Mingxun Wang","doi":"10.1021/jasms.4c00464","DOIUrl":"10.1021/jasms.4c00464","url":null,"abstract":"<p><p>Tandem mass spectrometry (MS/MS) is a powerful technique for structural identification of small molecules, yet a significant portion of MS/MS spectra from untargeted experiments remain unidentifiable through spectrum library matching. ModiFinder, a computational tool, tackles this issue by predicting the site of chemical modifications on known analogs of the unidentified compounds using MS/MS data. However, ModiFinder's performance is limited by insufficient peak data and fragmentation annotation ambiguities. In this study, we investigate how incorporating MS/MS spectra from multiple collision energies and mass spectrometry adducts can enhance ModiFinder's localization accuracy. Using a data set from Agilent Technologies comprising 2150 data-rich compounds (five times larger than previously available data sets), we evaluated the impact of complementary spectral information. Our results show that combining spectra from different adducts and collision energies expands ModiFinder's localization abilities to more compounds and improves the overall performance.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"999-1007"},"PeriodicalIF":3.1,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143810034","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}

{"title":"Internal Standard Utilization Strategies for Quantitative Paper Spray Mass Spectrometry.","authors":"Lucas R Abruzzi, John-Clare Laxton, Taelor M Zarkovic, Chris G Gill","doi":"10.1021/jasms.5c00036","DOIUrl":"10.1021/jasms.5c00036","url":null,"abstract":"<p><p>Premixing internal standards (ISTD) with liquid samples prior to paper spray mass spectrometry (PS-MS) analysis consumes unnecessary amounts of ISTD and is not feasible for all sample types and applications. Depositing ISTD directly on the paper independently from sample has been successfully employed in the literature but can negatively affect quantitative performance. We evaluated different ISTD utilization strategies using drugs of misuse as test analytes to investigate the sources of irreproducibility and bias. Performance was assessed using both pre- and postdeposited ISTD (relative to sample loading) at different volumes with a constant final mass loading of 1 ng of each ISTD compound. Precision and accuracy were lower when using independently deposited ISTD compared to premixed ISTD (average CV = 18% vs 1% and average |bias| = 61% vs 5% for independently deposited ISTD and premixed ISTD, respectively). The use of a robotic liquid sample handling system to deposit ISTD was compared with results obtained via manually pipetting. Predeposited ISTD performed best at lower deposition volumes when a robotic liquid handler was used (average CV = 8% and 11% for 2 and 10 μL, respectively), but manual pipetting of low volume ISTD depositions performed poorly. Postdeposited ISTD was inferior to predeposited ISTD strategies, favoring larger deposition volumes regardless of deposition method (average CV = 22% and 16% for 2 and 10 μL, respectively). Systematic biases associated with each ISTD utilization strategy were effectively corrected for using strategy-matched calibrations, and AAFS (American Academy of Forensic Sciences) accuracy and precision requirements were achieved in almost all cases.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"1167-1174"},"PeriodicalIF":3.1,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143787402","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}

{"title":"HDgraphiX: A Web-Based Tool for Visualization of Hydrogen/Deuterium Exchange Mass Spectrometry Data","authors":"Kent R. Vosper,&nbsp;Algirdas Velyvis* and Siavash Vahidi*,&nbsp;","doi":"10.1021/jasms.5c0000510.1021/jasms.5c00005","DOIUrl":"https://doi.org/10.1021/jasms.5c00005https://doi.org/10.1021/jasms.5c00005","url":null,"abstract":"<p >Hydrogen−deuterium exchange mass spectrometry (HDX-MS) investigates protein structural changes by measuring deuterium incorporation into the protein amide backbone. Due to the richness of information provided on protein conformational dynamics, HDX-MS data can be challenging to visualize effectively. To address this, we have developed HDgraphiX, a web-based tool that visualizes HDX-MS data by processing outputs from several popular analysis software packages including DynamX, HDExaminer, and HDX Workbench. HDgraphiX performs statistical analyses, filters data based on statistical significance, and presents the results as user-friendly publication-quality visualizations, including heatmaps (Chiclet plots), Woods plots, ladder plots, and volcano plots. Users can optionally generate PyMOL and ChimeraX coloring scripts to map deuterium uptake differences onto protein structures. Additionally, HDgraphiX offers numerous advanced options for customizing data processing and plotting without the need for manual data editing. To improve usability, users have the option to download a file containing all input settings, which can be reuploaded alongside HDX-MS data to avoid manual re-entry of custom settings.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":"36 5","pages":"1200–1203 1200–1203"},"PeriodicalIF":3.1,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143911194","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}

{"title":"Distinguishing Chiral Amino Acids Using Chiral Derivatization and Differential Ion Mobility Mass Spectrometry.","authors":"Simin Zhang, Xiangfeng Chen, T-Y Lui, Danna Hu, T-W Dominic Chan","doi":"10.1021/jasms.5c00054","DOIUrl":"https://doi.org/10.1021/jasms.5c00054","url":null,"abstract":"<p><p>The precise differentiation of chiral amino acids (AAs) holds significant potential for elucidating health and disease status. Herein, we developed an analytical strategy integrating chiral derivatization with differential ion mobility spectrometry (DMS)-mass spectrometry (MS) to achieve the enantiomeric separation of AAs. Utilizing <i>N</i>-(4-nitrophenoxycarbonyl)-l-phenylalanine 2-methoxyethyl ester (S-NIFE) as a chiral derivatization reagent, sodium-adducted S-NIFE-AA ions were generated and resolved via DMS-MS. By using the optimized carrier gas with 0.2% 1-propanol as a modifier, baseline separation of 11 enantiomeric AA pairs was successfully achieved. Compared with existing reports on DMS-based chiral AAs separation, the method proposed in this work exhibits a better separation efficiency for chiral AAs pairs. This further demonstrates the potential of DMS for chiral AAs and other metabolite analyses in the future.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143957274","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}

{"title":"Distinguishing the Metabolic Effect of Fetal and Adult Fibrinogen on Human Fibroblast Cell Culture by IR-MALDESI Mass Spectrometry Imaging.","authors":"Alena N Joignant, Anastasia Sheridan, Ashley C Brown, David C Muddiman","doi":"10.1021/jasms.5c00027","DOIUrl":"10.1021/jasms.5c00027","url":null,"abstract":"<p><p>Mass spectrometry imaging (MSI) of cells can elucidate metabolic changes with cellular and molecular specificity. Fibroblasts are mesenchymal cells that are important in tissue homeostasis and wound healing. During early wound healing, fibroblasts adhere to fibrinogen and migrate into fibrin clots, which are important interactions to stabilize early blood clots and promote subsequent tissue remodeling. It is understood that fibrinogen exists in distinct forms, fetal and adult, which have differing glycosylation and morphological effects on fibroblasts. Despite their importance to wound healing and the extracellular environment, fibroblasts are not commonly studied by MSI. While many MSI studies are conducted at the single-cell or subcellular level, there is still utility in accessing a broad view of the metabolic changes in a cell culture above single-cell spatial resolution. This enables imaging a wider area and larger number of cells directly from cell culture. In this work, dermal fibroblasts were imaged directly from cell culture chamber slides by infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI). This method enabled treating the chambers with adult or fetal fibrinogen prior to cell culture and reduced sample preparation prior to MSI. Many metabolic effects of serum and fibrinogen type were elucidated, with changes in many membrane lipids such as cholesterol and ceramides potentially contributing to the observed morphological effects of fibrinogen types on fibroblasts.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"1111-1119"},"PeriodicalIF":3.1,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143802149","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}