Kseniya Dryahina, Miroslav Polášek, Juraj Jašík, Kristýna Sovová, Patrik Španěl
{"title":"Ion Chemistry in Dielectric Barrier Discharge Ionization: Recent Advances in Direct Gas Phase Analyses.","authors":"Kseniya Dryahina, Miroslav Polášek, Juraj Jašík, Kristýna Sovová, Patrik Španěl","doi":"10.1002/mas.21914","DOIUrl":"10.1002/mas.21914","url":null,"abstract":"<p><p>Dielectric barrier discharge ionization (DBDI) sources, employing low-temperature plasma, have emerged as sensitive and efficient ionization tools with various atmospheric pressure ionization processes. In this review, we summarize a historical overview of the development of DBDI, highlighting key principles of gas-phase ion chemistry and the mechanisms underlying the ionization processes within the DBDI source. These processes start with the formation of reagent ions or metastable atoms from the discharge gas, which depends on the nature of the gas (helium, nitrogen, air) and on the presence of water vapor or other compounds or dopants. The processes of ionizing the analyte molecules are summarized, including Penning ionization, electron transfer, proton transfer and ligand switching from secondary hydrated hydronium ions. Presently, the DBDI-MS methods face a challenge in the accurate quantification of gaseous analytes, limiting its broader application in biological, environmental, and medical realms where relative quantification using standards is inherently complex for gaseous matrices. Finally, we propose future avenues of research to enhance the analytical capabilities of DBDI-MS.</p>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":" ","pages":""},"PeriodicalIF":6.9,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142589942","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":"Mass Spectrometry-Based Proteomics for Assessing Epitranscriptomic Regulations.","authors":"Yen-Yu Yang, Zhongwen Cao, Yinsheng Wang","doi":"10.1002/mas.21911","DOIUrl":"https://doi.org/10.1002/mas.21911","url":null,"abstract":"<p><p>Epitranscriptomics is a rapidly evolving field that explores chemical modifications in RNA and how they contribute to dynamic and reversible regulations of gene expression. These modifications, for example, N<sup>6</sup>-methyladenosine (m<sup>6</sup>A), are crucial in various RNA metabolic processes, including splicing, stability, subcellular localization, and translation efficiency of mRNAs. Mass spectrometry-based proteomics has become an indispensable tool in unraveling the complexities of epitranscriptomics, offering high-throughput, precise protein identification, and accurate quantification of differential protein expression. Over the past two decades, advances in mass spectrometry, including the improvement of high-resolution mass spectrometers and innovative sample preparation methods, have allowed researchers to perform in-depth analyses of epitranscriptomic regulations. This review focuses on the applications of bottom-up proteomics in the field of epitranscriptomics, particularly in identifying and quantifying epitranscriptomic reader, writer, and eraser (RWE) proteins and in characterizing their functions, posttranslational modifications, and interactions with other proteins. Together, by leveraging modern proteomics, researchers can gain deep insights into the intricate regulatory networks of RNA modifications, advancing fundamental biology, and fostering potential therapeutic applications.</p>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":" ","pages":""},"PeriodicalIF":6.9,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142454325","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}
Charlotte Mase, Maxime Sueur, Hélène Lavanant, Christopher Paul Rüger, Pierre Giusti, Carlos Afonso
{"title":"Ion Source Complementarity for Characterization of Complex Organic Mixtures Using Fourier Transform Mass Spectrometry: A Review.","authors":"Charlotte Mase, Maxime Sueur, Hélène Lavanant, Christopher Paul Rüger, Pierre Giusti, Carlos Afonso","doi":"10.1002/mas.21910","DOIUrl":"https://doi.org/10.1002/mas.21910","url":null,"abstract":"<p><p>Complex organic mixtures are found in many areas of research, such as energy, environment, health, planetology, and cultural heritage, to name but a few. However, due to their complex chemical composition, which holds an extensive potential of information at the molecular level, their molecular characterization is challenging. In mass spectrometry, the ionization step is the key step, as it determines which species will be detected. This review presents an overview of the main ionization sources employed to characterize these kinds of samples in Fourier transform mass spectrometry (FT-MS), namely electrospray (ESI), atmospheric pressure photoionization (APPI), atmospheric pressure chemical ionization (APCI), atmospheric pressure laser ionization (APLI), and (matrix-assisted) laser desorption ionization ((MA)LDI), and their complementarity in the characterization of complex organic mixtures. First, the ionization techniques are examined in the common direct introduction (DI) usage. Second, these approaches are discussed in the context of coupling chromatographic techniques such as gas chromatography, liquid chromatography, and supercritical fluid chromatography.</p>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":" ","pages":""},"PeriodicalIF":6.9,"publicationDate":"2024-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142454324","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}
Yixuan Xie, Carolina Brás-Costa, Zongtao Lin, Benjamin A Garcia
{"title":"Mass Spectrometry Analysis of Nucleic Acid Modifications: From Beginning to Future.","authors":"Yixuan Xie, Carolina Brás-Costa, Zongtao Lin, Benjamin A Garcia","doi":"10.1002/mas.21907","DOIUrl":"10.1002/mas.21907","url":null,"abstract":"<p><p>Nucleic acids are fundamental biological molecules that encode and convey genetic information within living organisms. Over 150 modifications have been found in nucleic acids, which are involved in critical biological functions, including regulating gene expression, stabilizing nucleic acid structure, modulating protein translation, and so on. The dysregulation of nucleic acid modifications is correlated with many diseases such as cancers and neurological disorders. However, it is still challenging to simultaneously characterize and quantify diverse modifications using traditional genomic methods. Mass spectrometry (MS) has served as a crucial tool to solve this issue, and can directly identify the modified species through their distinct mass differences compared to the canonical ones and provide accurate quantitative information. This review surveys the history of nucleic acid modification discovery, advancements in MS-based methods, nucleic acid sample preparation, and applications in biological and medical research. We expect the high-throughput and valuable quantitative information from MS analysis will be more broadly applied to studying nucleic acid modification status in different pathological conditions, which is key to filling gaps in traditional genomics and transcriptomics research and enabling researchers to gain insights into epigenetics and epitranscriptomics.</p>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":" ","pages":""},"PeriodicalIF":6.9,"publicationDate":"2024-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142277683","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}
Haiyan Lu, Zexin Zhu, Lauren Fields, Hua Zhang, Lingjun Li
{"title":"Mass Spectrometry Structural Proteomics Enabled by Limited Proteolysis and Cross-Linking.","authors":"Haiyan Lu, Zexin Zhu, Lauren Fields, Hua Zhang, Lingjun Li","doi":"10.1002/mas.21908","DOIUrl":"https://doi.org/10.1002/mas.21908","url":null,"abstract":"<p><p>The exploration of protein structure and function stands at the forefront of life science and represents an ever-expanding focus in the development of proteomics. As mass spectrometry (MS) offers readout of protein conformational changes at both the protein and peptide levels, MS-based structural proteomics is making significant strides in the realms of structural and molecular biology, complementing traditional structural biology techniques. This review focuses on two powerful MS-based techniques for peptide-level readout, namely limited proteolysis-mass spectrometry (LiP-MS) and cross-linking mass spectrometry (XL-MS). First, we discuss the principles, features, and different workflows of these two methods. Subsequently, we delve into the bioinformatics strategies and software tools used for interpreting data associated with these protein conformation readouts and how the data can be integrated with other computational tools. Furthermore, we provide a comprehensive summary of the noteworthy applications of LiP-MS and XL-MS in diverse areas including neurodegenerative diseases, interactome studies, membrane proteins, and artificial intelligence-based structural analysis. Finally, we discuss the factors that modulate protein conformational changes. We also highlight the remaining challenges in understanding the intricacies of protein conformational changes by LiP-MS and XL-MS technologies.</p>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":" ","pages":""},"PeriodicalIF":6.9,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142277684","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":"Conjugation of primary amine groups in targeted proteomics.","authors":"Yang Cai","doi":"10.1002/mas.21906","DOIUrl":"https://doi.org/10.1002/mas.21906","url":null,"abstract":"<p><p>Primary amines, in the form of unmodified N-terminus of peptide/protein and unmodified lysine residue, are perhaps the most important functional groups that can serve as the starting points in proteomic analysis, especially via mass spectrometry-based approaches. A variety of multifunctional probes that conjugate primary amine groups through covalent bonds have been developed and employed to facilitate protein/protein complex characterization, including identification, quantification, structure and localization elucidation, protein-protein interaction investigation, and so forth. As an integral part of more accurate peptide quantification in targeted proteomics, isobaric stable isotope-coded primary amine labeling approaches eventually facilitated protein/peptide characterization at the single-cell level, paving the way for single-cell proteomics. The development and advances in the field can be reviewed in terms of key components of a multifunctional probe: functional groups and chemistry for primary amine conjugation; hetero-bifunctional moiety for separation/enrichment of conjugated protein/protein complex; and functionalized linker/spacer. Perspectives are primarily focused on optimizing primary amine conjugation under physiological conditions to improve characterization of native proteins, especially those associated with the surface of living cells/microorganisms.</p>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":" ","pages":""},"PeriodicalIF":6.9,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142124378","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}
Sophie Liuu, Annelaure Damont, Alain Perret, Olivier Firmesse, François Becher, Gwenaëlle Lavison-Bompard, Amandine Hueber, Amina S Woods, Ekaterina Darii, François Fenaille, Jean-Claude Tabet
{"title":"Origin and characterization of cyclodepsipeptides: Comprehensive structural approaches with focus on mass spectrometry analysis of alkali-cationized molecular species.","authors":"Sophie Liuu, Annelaure Damont, Alain Perret, Olivier Firmesse, François Becher, Gwenaëlle Lavison-Bompard, Amandine Hueber, Amina S Woods, Ekaterina Darii, François Fenaille, Jean-Claude Tabet","doi":"10.1002/mas.21904","DOIUrl":"https://doi.org/10.1002/mas.21904","url":null,"abstract":"<p><p>Cyclodepsipeptides (CDPs) represent a huge family of chemically and structurally diverse molecules with a wide ability for molecular interactions. CDPs are cyclic peptide-related natural products made up of both proteinogenic and nonproteinogenic amino acids linked by amide and ester bonds. The combined use of different analytical methods is required to accurately determine their integral structures including stereochemistry, thus allowing deeper insights into their often-intriguing bioactivities and their possible usefulness. Our goal is to present the various methods developed to accurately characterize CDPs. Presently, Marfey's method and NMR (nuclear magnetic resonance) are still considered the best for characterizing CDP configuration. Nevertheless, electrospray-high resolution tandem mass spectrometry (ESI-HRMS/MS) is of great value for efficiently resolving CDP's composition and sequences. For instance, recent data shows that the fragmentation of cationized CDPs (e.g., [M + Li]<sup>+</sup> and [M + Na]<sup>+</sup>) leads to selective cleavage of ester bonds and specific cationized product ions (b series) useful to get unprecedented sequence information. Thus, after a brief presentation of their structure, biological functions, and biosynthesis, we also provide a historic overview of these various analytical approaches as well as their advantages and limitations with a special emphasis on the emergence of methods based on HRMS/MS through recent fundamental works and applications.</p>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":" ","pages":""},"PeriodicalIF":6.9,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142015806","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}
Daniel Flender, Frédérique Vilenne, Charlotte Adams, Kurt Boonen, Dirk Valkenborg, Geert Baggerman
{"title":"Exploring the dynamic landscape of immunopeptidomics: Unravelling posttranslational modifications and navigating bioinformatics terrain.","authors":"Daniel Flender, Frédérique Vilenne, Charlotte Adams, Kurt Boonen, Dirk Valkenborg, Geert Baggerman","doi":"10.1002/mas.21905","DOIUrl":"https://doi.org/10.1002/mas.21905","url":null,"abstract":"<p><p>Immunopeptidomics is becoming an increasingly important field of study. The capability to identify immunopeptides with pivotal roles in the human immune system is essential to shift the current curative medicine towards personalized medicine. Throughout the years, the field has matured, giving insight into the current pitfalls. Nowadays, it is commonly accepted that generalizing shotgun proteomics workflows is malpractice because immunopeptidomics faces numerous challenges. While many of these difficulties have been addressed, the road towards the ideal workflow remains complicated. Although the presence of Posttranslational modifications (PTMs) in the immunopeptidome has been demonstrated, their identification remains highly challenging despite their significance for immunotherapies. The large number of unpredictable modifications in the immunopeptidome plays a pivotal role in the functionality and these challenges. This review provides a comprehensive overview of the current advancements in immunopeptidomics. We delve into the challenges associated with identifying PTMs within the immunopeptidome, aiming to address the current state of the field.</p>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":" ","pages":""},"PeriodicalIF":6.9,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141994849","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":"Reminiscences of a career in mass spectrometry in the US and in Spain","authors":"Emilio Gelpí","doi":"10.1002/mas.21803","DOIUrl":"10.1002/mas.21803","url":null,"abstract":"","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":"43 5","pages":"915-935"},"PeriodicalIF":6.9,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141892460","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}
Thierry N J Fouquet, Robert B Cody, Laurence Charles
{"title":"Degradation strategies for structural characterization of insoluble synthetic polymers by mass spectrometry.","authors":"Thierry N J Fouquet, Robert B Cody, Laurence Charles","doi":"10.1002/mas.21903","DOIUrl":"https://doi.org/10.1002/mas.21903","url":null,"abstract":"<p><p>With the advent of soft ionization techniques such as electrospray (ESI) and matrix-assisted laser desorption/ionization (MALDI) to produce intact gas-phase ions from nonvolatile macromolecules, mass spectrometry has become an essential technique in the field of polymeric materials. However, (co)polymers of very high molecular weight or with reticulated architectures still escape ESI or MALDI, mainly due to solubility issues. Strategies developed to tackle such an analytical challenge all rely on sample degradation to produce low-mass species amenable to existing ionization methods. Yet, chain degradation needs to be partial and controlled to generate sufficiently large species that still contain topological or architectural information. The present article reviews the different analytical degradation strategies implemented to perform mass spectrometry of these challenging synthetic polymers, covering thermal degradation approaches in sources developed in the 2000s, off-line sample pre-treatments for controlled chemical degradation of polymeric substrates, and most recent achievements employing reactive ionization modes to perform chemolysis on-line with MS.</p>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":" ","pages":""},"PeriodicalIF":6.9,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141873697","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}