Journal of the American Society for Mass Spectrometry最新文献

{"title":"Attracting Computational Researchers to Proteomics.","authors":"Alyssa A Nitz, Ansima R Mongane, Luke Squires, Samuel H Payne","doi":"10.1021/jasms.4c00185","DOIUrl":"10.1021/jasms.4c00185","url":null,"abstract":"","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11457304/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103237","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":"Performance Comparison of Ambient Ionization Techniques Using a Single Quadrupole Mass Spectrometer for the Analysis of Amino Acids, Drugs, and Explosives.","authors":"Simone Mathias, Marius Amerio-Cox, Toni Jackson, David Douce, Bryan McCullough, Ashley Sage, Peter Luke, Carol Crean, Patrick Sears","doi":"10.1021/jasms.4c00277","DOIUrl":"10.1021/jasms.4c00277","url":null,"abstract":"<p><p>The utilization of ambient ionization (AI) techniques for mass spectrometry (MS) has significantly grown due to their ability to facilitate rapid and direct sample analysis with minimal sample preparation. This study investigates the performance of various AI techniques, including atmospheric solids analysis probe (ASAP), thermal desorption corona discharge (TDCD), direct analysis in real time (DART), and paper spray coupled to a Waters QDa mass spectrometer. The focus is on evaluating the linearity, repeatability, and limit of detection (LOD) of these techniques across a range of analytes, including amino acids, drugs, and explosives. The results show that each AI technique exhibits distinct advantages and limitations. ASAP and DART cover high concentration ranges, which may make them suitable for semiquantitative analysis. TDCD demonstrates exceptional linearity and repeatability for most analytes, while paper spray offers surprising LODs despite its complex setup (between 80 and 400 pg for most analytes). The comparison with electrospray ionization (ESI) as a standard method shows that ambient ionization techniques can achieve competitive LODs for various compounds such as PETN (80 pg ESI vs 100 pg ASAP), TNT (9 pg ESI vs 4 pg ASAP), and RDX (4 pg ESI vs 10 pg ASAP). This study underscores the importance of selecting the appropriate ambient ionization technique based on the specific analytical requirements. This comprehensive evaluation contributes valuable insights into the selection and optimization of AI techniques for diverse analytical applications.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11457451/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103241","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":"Investigating Protein-Nucleic Acid Binding Interactions with Diethylpyrocarbonate Covalent Labeling-Mass Spectrometry.","authors":"Zachary J Kirsch, Jonathan Ashby, Richard W Vachet","doi":"10.1021/jasms.4c00285","DOIUrl":"10.1021/jasms.4c00285","url":null,"abstract":"<p><p>Nucleic acids are important biomolecules that facilitate numerous cellular functions and have in recent years become promising candidates for treating disease. Consequently, there is a need for methods to characterize protein interactions with these molecules. Here, we demonstrate that diethylpyrocarbonate (DEPC) covalent labeling-mass spectrometry (CL-MS) can provide structural information for protein-nucleic acid binding by characterizing the binding sites of two DNA aptamers specific to thrombin. Reductions in thrombin labeling are observed at the pair's binding interfaces. Furthermore, we find that binding of the aptamers causes changes in labeling at residues in the thrombin active site and known exosites for each aptamer, showcasing the sensitivity of DEPC CL-MS to significant allosteric changes.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11497156/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103239","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":"Automated Assignment of ¹⁵N And ¹³C Enrichment Levels in Doubly-Labeled Proteins.","authors":"Elijah T Roberts, Alexander R Davis, Jeremy T Risher, Adam W Barb, I Jonathan Amster","doi":"10.1021/jasms.4c00218","DOIUrl":"10.1021/jasms.4c00218","url":null,"abstract":"<p><p>Uniform enrichment of ¹⁵N and ¹³C in proteins is commonly employed for 2D heteronuclear NMR measurements of the three-dimensional protein structure. Achieving a high degree of enrichment of both elements is important for obtaining high quality data. Uniform labeling of proteins and glycoproteins expressed in higher organisms (yeast or mammalian cell lines) is more challenging than expression in <i>Escherichia coli</i>, a prokaryote that grows on simple, chemically defined media but does not provide appropriate eukaryotic modifications. It is difficult to achieve complete incorporation of both heavy isotopes, and quality control measures are important for quantitating the level of their enrichment. Mass spectrometry measurements of the isotopic distribution of the intact protein or its proteolytic fragments provide the means to assess the enrichment level. A mass accuracy of 1 ppm or better is shown to be required to distinguish the correct combination of ¹³C and ¹⁵N enrichment due to subtle shifts in peak centroids with differences in the underlying, but unresolved, isotopic fine structure. A simple computer program was developed to optimize the fitting of experimental isotope patterns to statistically derived distributions. This method can determine the isotopic abundance from isotope patterns and isotopologue masses in conventional MS data for peptides, intact proteins, and glycans. For this purpose, MATLAB's isotope simulator, isotopicdist, has been modified to permit the variation of ¹⁵N and ¹³C enrichment levels and to perform a two-dimensional grid search of enrichment levels of both isotopes. We also incorporated an alternate isotope simulator, js-emass, into MATLAB for use in the same fitting program. Herein we benchmark this technique on natural abundance ubiquitin and uniformly [¹⁵N,¹³C]-labeled ubiquitin at both the intact and peptide level, outline considerations for data quality and mass accuracy, and report several improvements we have made to the previously reported analysis of the [¹⁵N,¹³C]-enriched human IgG Fc domain, a glycoprotein that has been expressed in <i>Saccharomyces cerevisiae</i>.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11450805/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103238","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":"Sequencing of Phosphorodiamidate Morpholino Oligomers by Hydrophilic Interaction Chromatography Coupled to Tandem Mass Spectrometry.","authors":"Mingming Wang, Brian O'Day, Brian Michaels, Jurjus Jurayj, Bao Zhong Cai, Tao Wei","doi":"10.1021/jasms.4c00281","DOIUrl":"10.1021/jasms.4c00281","url":null,"abstract":"<p><p>Sequencing of phosphorodiamidate morpholino oligomers (PMOs) by hydrophilic interaction chromatography (HILIC) coupled to tandem mass spectrometry (MS/MS) is reported. The MS/MS analysis was performed using a quadrupole/time-of-flight (Q-ToF) mass analyzer and collision induced dissociation (CID) in negative ion mode. To improve MS sensitivity in negative ion mode, HILIC conditions, including the separation column, mobile phases, and MS parameters, were optimized. Using the developed HILIC-CID-MS/MS method, 100% sequence coverage was achieved for PMOs ranging from 18-mer to 25-mer. Additionally, the method was successfully applied to identifying positional isomers of <i>n</i> - 1 deletion impurities present in PMO drug substances.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11450806/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103242","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":"Self-Organizing Maps for Secondary Ion Mass Spectrometry.","authors":"Sarah E Bamford, Wil Gardner, David A Winkler, Benjamin W Muir, Damminda Alahakoon, Paul J Pigram","doi":"10.1021/jasms.4c00318","DOIUrl":"10.1021/jasms.4c00318","url":null,"abstract":"<p><p>Secondary ion mass spectrometry (SIMS) is a powerful analytical technique for characterizing the molecular and elemental composition of surfaces. Individual mass spectra can provide information about the mean surface composition, while spatial mapping can elucidate the spatial distributions of molecular species in 2D and 3D with no prior labeling of molecular targets. The data sets produced by SIMS techniques are large and inherently complex, often containing subtle relationships between spatial and molecular features. Machine learning algorithms are well suited to exploring this complexity, making them ideal for data analysis, interpretation, and visualization of SIMS data sets. One such algorithm, the self-organizing map (SOM), is particularly well suited to clustering similar samples and reducing the dimensionality of hyperspectral data sets. Here, we present an introduction to the SOM, a concise mathematical description, and recent examples of its use in SIMS and other related mass spectrometry techniques. These examples demonstrate how SOMs may be used to interpret high volumes of individual mass spectra, imaging, or depth profiling data sets. This review will be useful for specialists in SIMS and other mass spectral techniques seeking to explore self-organizing maps for data analysis.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142278576","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":"Design and Implementation of a Desorption Electro-flow Focusing Sprayer on an Orbitrap Mass Spectrometer for DESI Mass Spectrometry Imaging at High Spatial Resolution and at High Speed.","authors":"Carl Frederik Marc Hansen, Lukas Dobrovolskis, Christian Janfelt","doi":"10.1021/jasms.4c00341","DOIUrl":"https://doi.org/10.1021/jasms.4c00341","url":null,"abstract":"<p><p>Since desorption electrospray ionization mass spectrometry (DESI-MS) was first presented in 2004, the fundamental design of the sprayer has undergone relatively minor modifications. This changed in 2022 when Takats and co-workers implemented the desorption electro-flow focusing (DEFFI) sprayer design by modifying the sprayer from a commercial DESI system, leading to significantly improved spatial resolution and robustness compared with the traditional DESI-MSI sprayer design. Here, we present the design of a new DEFFI sprayer that can be built from standard fittings and connectors in combination with an aluminum spray head that can be machined in most mechanic workshops. The new design represents a cost-efficient approach to improved DESI-MSI on mass spectrometers from all vendors, including high-resolution instruments such as Orbitraps and FT-ICR. The new DEFFI sprayer is demonstrated on a QExactive Orbitrap mass spectrometer, resulting in a massively improved ion yield compared with the classic DESI sprayer. The improved ion yield enables DESI-MSI at ion injection times down to 5 ms, allowing for DESI-MSI at a potentially very high speed. More importantly, the DEFFI sprayer delivers a more robust and focused spray, which is easier to use and requires less optimization. It provides high spatial resolution with limited effort compared with previous modifications of the traditional DESI design. Imaging of rat testis was performed at pixel sizes down to 12 μm, suggesting a spatial resolution of approximately 30 μm, which may have potential for further improvement.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142363834","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":"Text Mining and Computational Chemistry Reveal Trends in Applications of Laser Desorption/Ionization Techniques to Small Molecules.","authors":"Nina P Bergman, Jonas Bergquist, Mikael Hedeland, Magnus Palmblad","doi":"10.1021/jasms.4c00293","DOIUrl":"10.1021/jasms.4c00293","url":null,"abstract":"<p><p>Continued development of laser desorption/ionization (LDI) since its inception in the 1960s has produced an explosion of soft ionization techniques, where ionization is assisted by the physical or chemical properties of a structure or matrix. While many of these techniques have primarily been used to ionize large biomolecules, including proteins, some have recently seen increasing applications to small molecules such as pharmaceuticals. Small molecules pose particular challenges for LDI techniques, including interference from the matrix or support in the low mass range. To investigate trends in the application of soft LDI techniques to small molecules, we combined text mining and computational chemistry, looking specifically at matrix substances, analyte properties, and the research domain. In addition to making visible the history of LDI techniques, the results may inform the choice of method and suggest new avenues of method development. All software and collected data are freely available on GitHub (https://github.com/ReinV/SCOPE), VOSviewer (https://www.vosviewer.com), and OSF (https://osf.io/zkmua/).</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11457301/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142278577","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":"Identifying and Quantifying Relative Concentrations of Epimers in Mixtures via Cyclic Ion Mobility Mass Spectrometry: Dexamethasone and Betamethasone as a Case Study.","authors":"Sudam S Mane, David V Dearden, Kenneth W Lee","doi":"10.1021/jasms.4c00258","DOIUrl":"10.1021/jasms.4c00258","url":null,"abstract":"<p><p>Epimers can show different biological activities and different pharmacological behaviors; therefore, their separation and analysis are crucial in the drug development process. Due to their similar chemical and physical properties, separation of epimers is challenging. This study demonstrates the application of cyclic ion mobility-mass spectrometry to separate, identify, and quantify dexamethasone and betamethasone in a binary mixture. Cyclic IMS separation of the isolated protonated dimer resulted in three peaks: dexamethasone homodimer, betamethasone homodimer, and their heterodimer. Besides providing improved separation over the protonated monomer, the presence of a heterodimer peak provides additional confirmation of an isomeric mixture. We identified the dexamethasone and betamethasone homodimer peaks by infusing pure solutions of each epimer and measuring each pure homodimer's arrival time. The measured peak areas indicated that the heterodimer is formed at twice the rate of each homodimer and that dexamethasone and betamethasone contribute equally to the heterodimer signal. Using this observation, we could accurately calculate the relative concentrations of each epimer by adding half of the heterodimer peak area to each homodimer peak area. These findings enable the identification and quantification of dexamethasone and betamethasone based on the arrival time distributions of their protonated dimers. This is the first demonstration of accurate relative quantification of epimers by separating charged dimers in the gas phase.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142071708","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":"Covalent Labeling Automated Data Analysis Platform for High Throughput in R (coADAPTr): A Proteome-Wide Data Analysis Platform for Covalent Labeling Experiments.","authors":"Raquel L Shortt, Lindsay K Pino, Emily E Chea, Carolina Rojas Ramirez, Daniel A Polasky, Alexey I Nesvizhskii, Lisa M Jones","doi":"10.1021/jasms.4c00196","DOIUrl":"https://doi.org/10.1021/jasms.4c00196","url":null,"abstract":"<p><p>Covalent labeling methods coupled to mass spectrometry have emerged in recent years for studying the higher order structure of proteins. Quantifying the extent of modification of proteins in multiple states (i.e., ligand free vs ligand-bound) can provide information on protein interaction sites and regions of conformational change. Though there are several software platforms that are used to quantify the extent of modification, the process can still be time-consuming, particularly for proteome-wide studies. Here, we present an open-source software for quantitation called Covalent labeling Automated Data Analysis Platform for high Throughput in R (coADAPTr). coADAPTr tackles the need for more efficient data analysis in covalent labeling mass spectrometry for techniques such as hydroxyl radical protein footprinting (HRPF). Traditional methods like Excel's Power Pivot (PP) are cumbersome and time-intensive, posing challenges for large-scale analyses. coADAPTr simplifies analysis by mimicking the functions used in the previous quantitation platform using PowerPivot in Microsoft Excel but with fewer steps, offering proteome-wide insights with enhanced graphical interpretations. Several features have been added to improve the fidelity and throughput compared to those of PowerPivot. These include filters to remove any duplicate data and the use of the arithmetic mean rather than the geometric mean for quantitation of the extent of modification. Validation studies confirm coADAPTr's accuracy and efficiency while processing data up to 200 times faster than conventional methods. Its open-source design and user-friendly interface make it accessible for researchers exploring intricate biological phenomena via HRPF and other covalent labeling MS methods. coADAPTr marks a significant leap in structural proteomics, providing a versatile and efficient platform for data interpretation. Its potential to transform the field lies in its seamless handling of proteome-wide data analyses, empowering researchers with a robust tool for deciphering complex structural biology data.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":null,"pages":null},"PeriodicalIF":3.1,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142363933","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}