Mass Spectrometry Reviews最新文献

{"title":"Rapid, Sensitive, and Versatile: A 5-Year Perspective on Applications of Ambient Ionization Mass Spectrometry in Bioanalytical Science","authors":"Muhammad Irfan,&nbsp;Hafiza Arslan Shagufta,&nbsp;Muhammad Usman Rasheed,&nbsp;Samreen Gul Khan,&nbsp;Muhammad Mahran Aslam,&nbsp;Huanwen Chen","doi":"10.1002/mas.70004","DOIUrl":"10.1002/mas.70004","url":null,"abstract":"<div>\u0000 \u0000 <p>Mass spectrometry (MS) is a widely recognized analytical technique that can be applied to both large and small molecules and is a potent analytical tool that advances both basic science and practical applications in and out of the lab. MS has become a desirable analytical technique in clinical and bioanalytical labs with its high sensitivity, broad applicability, and throughput benefits. Numerous MS approaches, combined with various separation methods including gas and liquid chromatography, have been proposed to examine intricate matrices. Nevertheless, this technique could be limited by the labor-intensive and drawn-out sample preparation needed before MS analysis. By enabling the direct MS analysis of complex materials under ambient settings with little to no sample pretreatment, AIMS has cut down on both analysis time and expense. Nonetheless, these methods' speed and simplicity make them appropriate for use in critical care and point-of-care testing. Because of this, ambient ionization mass spectrometry (AIMS) has inevitably appealed to a wide range of scientists. The field of AIMS has grown tremendously since its foundation in the mid-2000s, marked by the emergence of numerous new ion sources, a plethora of fascinating applications, and a discernible increase in interest from various fields of study. Around the world, ambient ionization techniques are becoming more and more widespread in laboratories as the science advances yearly. This review focuses on the recent bioanalytical applications of AIMS in fields such as clinics, drugs, forensics, food, and environment, with a specific emphasis on the research reported in manuscripts published during the last 5 years. Although certain methodological developments are mentioned in this review, its primary goal is to demonstrate the practical applications of AIMS in bioanalytical fields. A timely overview of AIMS-based procedures and their application in various sample situations is what this endeavor seeks to give bioanalytical researchers. Moreover, several cutting-edge biological applications have been highlighted to explain how the AIMS area can develop in the future. In this chapter, readers will be provided with a quick overview of the main AIMS methodologies and their recent applied use cases.</p>\u0000 </div>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":"45 5","pages":"969-1024"},"PeriodicalIF":6.0,"publicationDate":"2026-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144881799","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":"Software Design and Analytical Challenges for Confident Glycopeptide Identification With Data-Independent Acquisition","authors":"Mary Rachel Nalehua,&nbsp;Joseph Zaia","doi":"10.1002/mas.70000","DOIUrl":"10.1002/mas.70000","url":null,"abstract":"<div>\u0000 \u0000 <p>Glycosylation is an abundant post-translational modification that impacts a wide variety of functions, including protein regulation, cell adhesion, and structural integrity. The application of proteomics methods to glycopeptide assignment faces unique challenges due to high heterogeneity, which results in complex populations with low overall abundance per glycopeptide. In addition, glycans dissociate at a lower collision energy compared to their attached peptide component. The resulting mass spectral data require specialized assignment software, which has caused glycoproteomics to lag traditional proteomics. Existing software primarily focuses on data-dependent acquisition (DDA), but manual validation is frequently required, and experiments are necessarily limited by the stochastic nature of DDA ion-selection. Data-independent acquisition (DIA) allows for a more complete and robust analysis of glycopeptide samples, but analysis software is still sparse. In this review, we discuss the current state of DDA analysis software, the limitations, and how it can inform our forays into DIA glycoproteomics.</p>\u0000 </div>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":"45 5","pages":"959-968"},"PeriodicalIF":6.0,"publicationDate":"2026-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144525636","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":"A Comprehensive Review of Instrumentation and Applications in Post-Column and In-Source Derivatization for LC-MS","authors":"Nadeem Muhammad,&nbsp;Irshad Hussain,&nbsp;Xiao-An Fu,&nbsp;Amjad Ali,&nbsp;Dandan Guo,&nbsp;Laila Noureen,&nbsp;Qamar Subhani,&nbsp;Naushad Ahmad,&nbsp;Quan-Fei Zhu,&nbsp;Hairong Cui,&nbsp;Yu-Qi Feng","doi":"10.1002/mas.21930","DOIUrl":"10.1002/mas.21930","url":null,"abstract":"<div>\u0000 \u0000 <p>Liquid chromatography-mass spectrometry (LC-MS) has become an indispensable tool for elucidating molecular structures and quantifying diverse compounds within complex mixtures. Despite its versatility, it faces various challenges such as ion suppression, low sensitivity, analyte instability, and matrix effects, which are being overcome by different kinds of offline and online derivatization techniques to improve specificity and reduce potential interferences. In this context, considerable advancements have been made in reviewing and critically evaluating a wide range of developed methods and techniques; however, little attention has been given to post-column derivatization (PCD) in LC-MS. Therefore, this comprehensive review highlights state-of-the-art advancements in LC-MS with a specific focus on various types of chemical and physical PCD, and in-source derivatization. It also examines the latest instrumentation developments, highlights methods and influencing factors, and explores applications in food, proteomics, biology, pharmaceuticals, and environmental analysis from the past four decades. Besides, this review critically examines the role of PCD in LC-MS along with outlining its advantages and disadvantages. Furthermore, special emphasis is also made on prospects and insights for developing more versatile LC-PCD-MS techniques and in-source methodologies, to address ongoing challenges and aim to open new research avenues for analysts.</p></div>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":"45 5","pages":"879-913"},"PeriodicalIF":6.0,"publicationDate":"2026-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143612708","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":"Progress in Characterization of Lipopolysaccharides and Lipid A by Mass Spectrometry","authors":"Amanda Helms,&nbsp;Jennifer S. Brodbelt","doi":"10.1002/mas.21934","DOIUrl":"10.1002/mas.21934","url":null,"abstract":"<div>\u0000 \u0000 <p>Lipopolysaccharides (LPS) are complex molecules embedded in the outer membrane of Gram-negative bacteria. LPS are highly heterogeneous across species and strains, posing a significant analytical challenge. This review article explores recent advances in the identification and characterization of LPS, with a particular focus on the role of mass spectrometry (MS) techniques. The review highlights how MS, in conjunction with various separation methods and spanning different ionization techniques and dissociation modes, has enabled more precise and sensitive determination of LPS composition, with a focus on lipid A structure. Finally, emerging trends in MS applications for LPS research are discussed and its potential to provide deeper insights into the development of antibiotic resistance among pathogenic bacteria.</p>\u0000 </div>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":"45 5","pages":"929-958"},"PeriodicalIF":6.0,"publicationDate":"2026-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143951726","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":"Defining Spectral Quality in Mass Spectrometry-Based Proteomics: A Retrospective Review","authors":"Vilenne Frédérique,&nbsp;Appeltans Simon,&nbsp;Askenazi Manor,&nbsp;Valkenborg Dirk","doi":"10.1002/mas.21933","DOIUrl":"10.1002/mas.21933","url":null,"abstract":"<div>\u0000 \u0000 <p>Mass spectrometry-based proteomics is essential for advancing preventive and personalised medicine. Technological advancements have greatly increased both the number and sensitivity of spectra generated in a single experiment. Traditionally, spectra are identified using database search engines that depend on large and continuously expanding databases. This expansion enlarges the search space, posing challenges for controlling the false discovery rate in peptide identification. While many bioinformatic workflows employ rescoring algorithms as a post-processing step to manage false discoveries, preprocessing spectra offers a promising alternative. One such method, spectral quality assessment, classifies spectra as “high” quality (likely containing a peptide) or “low” quality (predominantly consisting of noise). This review provides a comprehensive perspective on spectral quality assessment, examining existing tools and their underlying principles. We discuss key considerations such as the definition of spectral quality, normalisation, the use of experimental training data, and future research in the field. By highlighting the potential of spectral quality assessment to improve peptide identification and reduce false discoveries, we aim to elaborate on its potential for the proteomics community.</p>\u0000 </div>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":"45 5","pages":"914-928"},"PeriodicalIF":6.0,"publicationDate":"2026-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143961094","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 Extracellular Vesicle Proteomics for Biomarker Discovery.","authors":"Ya-Juan Liu, Juan Peng, Chao Kang","doi":"10.1002/mas.70040","DOIUrl":"https://doi.org/10.1002/mas.70040","url":null,"abstract":"<p><p>Extracellular vesicle (EV) proteomics has emerged as a powerful platform for decoding intercellular communication and advancing biomarker discovery across human diseases. EVs carry proteins that reflect their cells of origin, offering a minimally invasive window into physiological and pathological processes. Mass spectrometry (MS) now enables deep, high-resolution EV proteome profiling, aided by improved isolation and rigorous characterization that ensure sample purity and integrity. Advanced computational pipelines integrating quantitative modeling, spectral-library prediction, machine learning and multi-omics analysis extract meaningful biological signals, revealing subtle disease-associated EV signatures and establishing EV proteomics as a strong platform for biomarker discovery and precision medicine. This review provides an integrated framework linking EV isolation principles, characterization strategies, mass-spectrometric workflows, and computational analysis to the biological and clinical insights they generate. We also highlight key challenges and future directions, including the need for standardized reference materials, unified pre-analytical workflows, and EV proteome reference atlases. Together, these innovations are transforming EV proteomics into a next-generation tool for precision medicine.</p>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":" ","pages":""},"PeriodicalIF":6.0,"publicationDate":"2026-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148662946","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":"Comprehensive Tutorial for Computational Methods of Protein Structure Prediction Incorporating Mass Spectrometry Data.","authors":"Zachary C Drake, Robert M Bolz, Elijah H Day, Steffen Lindert","doi":"10.1002/mas.70038","DOIUrl":"10.1002/mas.70038","url":null,"abstract":"<p><p>Here we present a series of tutorials demonstrating the use of various methods which integrate structural mass spectrometry (MS) data with computational protein structure prediction methods. We give usage examples of widely used modeling frameworks, including Rosetta-based approaches (ab initio modeling, comparative modeling, and protein-protein docking) and deep learning methods such as AlphaFold2. We then describe strategies for incorporating covalent labeling, ion mobility, and surface-induced dissociation MS data into these workflows through Rosetta scoring terms and specialized applications. Finally, we provide instructions on calculating structural metrics, such as solvent accessibility, collision cross sections, and energy-resolved MS data and comparing them to actual MS data. We also introduce new PyRosetta implementations of the PARCS algorithm and the SID_ERMS_Rescore application. Together, these tutorials provide a comprehensive framework for integrating computational modeling with structural MS to enhance protein structure prediction.</p>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":" ","pages":""},"PeriodicalIF":6.0,"publicationDate":"2026-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13413113/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148403007","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":"Mass Spectrometry Insights Into Post-Translational Modifications in Extracellular Vesicles.","authors":"Dávid Virág, Krisztián Márk Karvaly, Alexandra Molnár, Mirjam Balbisi, Júlia Németh, Lilla Turiák","doi":"10.1002/mas.70036","DOIUrl":"https://doi.org/10.1002/mas.70036","url":null,"abstract":"<p><p>Extracellular vesicles (EVs) are membrane-enclosed structures secreted by virtually all living cells, serving as essential mediators of intercellular communication in both physiological and pathological processes. There is growing interest in their potential applications as biomarkers, therapeutic targets, and drug delivery systems, which entails the need for a detailed understanding of their molecular composition. The functional cargo of EVs includes all types of biological macromolecules, among which proteins are of particular importance. As the vesicular proteome becomes increasingly mapped, research attention is gradually shifting toward post-translational modifications (PTMs), which fundamentally influence protein function and play key roles in all aspects of vesicular activity, including biogenesis, cargo sorting, recognition, and uptake. In this review, we outline recent advances in the application of mass spectrometry (MS)-based analysis of PTMs in EVs. In this context, we provide an overview of the roles of various PTMs in EV biology, discuss the impact of EV isolation methods on downstream PTM analyses, and address current challenges and approaches related to MS-based investigations. We further highlight key findings concerning specific PTMs, including glycosylation, phosphorylation, acetylation, methylation, lipidation, and small ubiquitin-like modifier (SUMOylation). Finally, we discuss studies focusing on the simultaneous analysis of multiple PTMs, as well as efforts toward multiomic data integration and single-EV characterization to resolve vesicular heterogeneity, highlighting these approaches as cutting-edge directions in the field.</p>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":" ","pages":""},"PeriodicalIF":6.0,"publicationDate":"2026-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148336946","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":"Standardization Challenges and Breakthroughs in Apolipoprotein B Detection: From Immunoassays to LC-MS/MS.","authors":"Anqi Pan, Haijian Zhao, Jing Wang, Jiangtao Zhang, Hao Zheng, Chuanbao Zhang, Wenxiang Chen, Tianjiao Zhang","doi":"10.1002/mas.70035","DOIUrl":"https://doi.org/10.1002/mas.70035","url":null,"abstract":"<p><p>Apolipoprotein B (apoB) is a key biomarker for risk assessment and treatment monitoring of atherosclerotic cardiovascular disease (ASCVD). Its clinical value has been validated by multiple studies, and its predictive performance for ASCVD risk is significantly superior to conventional lipid indicators in populations with complex lipid profiles. However, the standardization of apoB detection has long been a core bottleneck restricting its widespread clinical application, as discrepancies in results between different methods and laboratories can biases in clinical decision-making. In recent years, the development of Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) technology has provided a solution for optimizing apoB standardization. Currently, International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) is promoting the development of a primary reference measurement procedure based on mass spectrometry, aiming to achieve apoB standardization traceable to the International System of Units (SI). This review systematically outlines the clinical value of apoB, main detection methods, standardization challenges, and the application and prospects of LC-MS/MS in overcoming these challenges. We aim to provide insights for further optimizing apoB detection standardization.</p>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":" ","pages":""},"PeriodicalIF":6.0,"publicationDate":"2026-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148306333","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,&nbsp;Zhongwen Cao,&nbsp;Yinsheng Wang","doi":"10.1002/mas.21911","DOIUrl":"10.1002/mas.21911","url":null,"abstract":"<div>\u0000 \u0000 <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, <i>N</i>⁶-methyladenosine (m⁶A), 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>\u0000 </div>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":"45 4","pages":"672-690"},"PeriodicalIF":6.6,"publicationDate":"2026-06-07","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}