Mass Spectrometry Reviews最新文献

{"title":"Using mass spectrometry-based methods to understand amyloid formation and inhibition of alpha-synuclein and amyloid beta","authors":"Wesley J. Wagner,&nbsp;Michael L. Gross","doi":"10.1002/mas.21814","DOIUrl":"10.1002/mas.21814","url":null,"abstract":"<p>Amyloid fibrils, insoluble β-sheets structures that arise from protein misfolding, are associated with several neurodegenerative disorders. Many small molecules have been investigated to prevent amyloid fibrils from forming; however, there are currently no therapeutics to combat these diseases. Mass spectrometry (MS) is proving to be effective for studying the high order structure (HOS) of aggregating proteins and for determining structural changes accompanying protein–inhibitor interactions. When combined with native MS (nMS), gas-phase ion mobility, protein footprinting, and chemical cross-linking, MS can afford regional and sometimes amino acid spatial resolution of the aggregating protein. The spatial resolution is greater than typical low-resolution spectroscopic, calorimetric, and the traditional ThT fluorescence methods used in amyloid research today. High-resolution approaches can struggle when investigating protein aggregation, as the proteins exist as complex oligomeric mixtures of many sizes and several conformations or polymorphs. Thus, MS is positioned to complement both high- and low-resolution approaches to studying amyloid fibril formation and protein–inhibitor interactions. This review covers basics in MS paired with ion mobility, continuous hydrogen-deuterium exchange (continuous HDX), pulsed hydrogen-deuterium exchange (pulsed HDX), fast photochemical oxidation of proteins (FPOP) and other irreversible labeling methods, and chemical cross-linking. We then review the applications of these approaches to studying amyloid-prone proteins with a focus on amyloid beta and alpha-synuclein. Another focus is the determination of protein–inhibitor interactions. The expectation is that MS will bring new insights to amyloid formation and thereby play an important role to prevent their formation.</p>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":"43 4","pages":"782-825"},"PeriodicalIF":6.6,"publicationDate":"2022-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9427217","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":"Adventures with peaks","authors":"Martin Sadilek,&nbsp;Michael Volny,&nbsp;Victor Ryzhov","doi":"10.1002/mas.21816","DOIUrl":"10.1002/mas.21816","url":null,"abstract":"","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":"43 3","pages":"413-419"},"PeriodicalIF":6.6,"publicationDate":"2022-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33521490","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":"How I have learnt to ignore bibliometrics","authors":"František Tureček","doi":"10.1002/mas.21815","DOIUrl":"10.1002/mas.21815","url":null,"abstract":"","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":"43 3","pages":"422-426"},"PeriodicalIF":6.6,"publicationDate":"2022-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33521491","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":"Reminiscence on Frantisek Tureček","authors":"Ivan K. Chu","doi":"10.1002/mas.21817","DOIUrl":"10.1002/mas.21817","url":null,"abstract":"","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":"43 3","pages":"420-421"},"PeriodicalIF":6.6,"publicationDate":"2022-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33499557","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":"Proteomics-based mass spectrometry profiling of SARS-CoV-2 infection from human nasopharyngeal samples","authors":"Sayantani Chatterjee,&nbsp;Joseph Zaia","doi":"10.1002/mas.21813","DOIUrl":"10.1002/mas.21813","url":null,"abstract":"<p>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the on-going global pandemic of coronavirus disease 2019 (COVID-19) that continues to pose a significant threat to public health worldwide. SARS-CoV-2 encodes four structural proteins namely membrane, nucleocapsid, spike, and envelope proteins that play essential roles in viral entry, fusion, and attachment to the host cell. Extensively glycosylated spike protein efficiently binds to the host angiotensin-converting enzyme 2 initiating viral entry and pathogenesis. Reverse transcriptase polymerase chain reaction on nasopharyngeal swab is the preferred method of sample collection and viral detection because it is a rapid, specific, and high-throughput technique. Alternate strategies such as proteomics and glycoproteomics-based mass spectrometry enable a more detailed and holistic view of the viral proteins and host–pathogen interactions and help in detection of potential disease markers. In this review, we highlight the use of mass spectrometry methods to profile the SARS-CoV-2 proteome from clinical nasopharyngeal swab samples. We also highlight the necessity for a comprehensive glycoproteomics mapping of SARS-CoV-2 from biological complex matrices to identify potential COVID-19 markers.</p>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":"43 1","pages":"193-229"},"PeriodicalIF":6.6,"publicationDate":"2022-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10112611","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":"Uncommon posttranslational modifications in proteomics: ADP-ribosylation, tyrosine nitration, and tyrosine sulfation","authors":"Aarti Bashyal,&nbsp;Jennifer S. Brodbelt","doi":"10.1002/mas.21811","DOIUrl":"10.1002/mas.21811","url":null,"abstract":"<p>Posttranslational modifications (PTMs) are covalent modifications of proteins that modulate the structure and functions of proteins and regulate biological processes. The development of various mass spectrometry-based proteomics workflows has facilitated the identification of hundreds of PTMs and aided the understanding of biological significance in a high throughput manner. Improvements in sample preparation and PTM enrichment techniques, instrumentation for liquid chromatography-tandem mass spectrometry (LC-MS/MS), and advanced data analysis tools enhance the specificity and sensitivity of PTM identification. Highly prevalent PTMs like phosphorylation, glycosylation, acetylation, ubiquitinylation, and methylation are extensively studied. However, the functions and impact of less abundant PTMs are not as well understood and underscore the need for analytical methods that aim to characterize these PTMs. This review focuses on the advancement and analytical challenges associated with the characterization of three less common but biologically relevant PTMs, specifically, adenosine diphosphate-ribosylation, tyrosine sulfation, and tyrosine nitration. The advantages and disadvantages of various enrichment, separation, and MS/MS techniques utilized to identify and localize these PTMs are described.</p>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":"43 2","pages":"289-326"},"PeriodicalIF":6.6,"publicationDate":"2022-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9182380","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":"Inferring kinase activity from phosphoproteomic data: Tool comparison and recent applications","authors":"Sander R. Piersma,&nbsp;Andrea Valles-Marti,&nbsp;Frank Rolfs,&nbsp;Thang V. Pham,&nbsp;Alex A. Henneman,&nbsp;Connie R. Jiménez","doi":"10.1002/mas.21808","DOIUrl":"10.1002/mas.21808","url":null,"abstract":"<p>Aberrant cellular signaling pathways are a hallmark of cancer and other diseases. One of the most important signaling mechanisms involves protein phosphorylation/dephosphorylation. Protein phosphorylation is catalyzed by protein kinases, and over 530 protein kinases have been identified in the human genome. Aberrant kinase activity is one of the drivers of tumorigenesis and cancer progression and results in altered phosphorylation abundance of downstream substrates. Upstream kinase activity can be inferred from the global collection of phosphorylated substrates. Mass spectrometry-based phosphoproteomic experiments nowadays routinely allow identification and quantitation of &gt;10k phosphosites per biological sample. This substrate phosphorylation footprint can be used to infer upstream kinase activities using tools like Kinase Substrate Enrichment Analysis (KSEA), Posttranslational Modification Substrate Enrichment Analysis (PTM-SEA), and Integrative Inferred Kinase Activity Analysis (INKA). Since the topic of kinase activity inference is very active with many new approaches reported in the past 3 years, we would like to give an overview of the field. In this review, an inventory of kinase activity inference tools, their underlying algorithms, statistical frameworks, kinase-substrate databases, and user-friendliness is presented. The most widely-used tools are compared in-depth. Subsequently, recent applications of the tools are described focusing on clinical tissues and hematological samples. Two main application areas for kinase activity inference tools can be discerned. (1) Maximal biological insights can be obtained from large data sets with group comparisons using multiple complementary tools (e.g., PTM-SEA and KSEA or INKA). (2) In the oncology context where personalized treatment requires analysis of single samples, INKA for example, has emerged as tool that can prioritize actionable kinases for targeted inhibition.</p>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":"43 4","pages":"725-751"},"PeriodicalIF":6.6,"publicationDate":"2022-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mas.21808","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33482751","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":"Development of mass spectrometric glycan characterization tags using acid-base chemistry and/or free radical chemistry","authors":"Rayan Murtada,&nbsp;Shane Finn,&nbsp;Jinshan Gao","doi":"10.1002/mas.21810","DOIUrl":"10.1002/mas.21810","url":null,"abstract":"<p>Despite recent advances in glycomics, glycan characterization still remains an analytical challenge. Accordingly, numerous glycan-tagging reagents with different chemistries were developed, including those involving acid-base chemistry and/or free radical chemistry. Acid-base chemistry excels at dissociating glycans into their constituent components in a systematic and predictable manner to generate cleavages at glycosidic bonds. Glycans are also highly susceptible to depolymerization by free radical processes, which is supported by results observed from electron-activated dissociation techniques. Therefore, the free radical activated glycan sequencing (FRAGS) reagent was developed so as to possess the characteristics of both acid-base and free radical chemistry, thus generating information-rich glycosidic bond and cross-ring cleavages. Alternatively, the free radical processes can be induced via photodissociation of the specific carbon-iodine bond which gives birth to similar fragmentation patterns as the FRAGS reagent. Furthermore, the methylated-FRAGS (Me-FRAGS) reagent was developed to eliminate glycan rearrangements by way of a fixed charged as opposed to a labile proton, which would otherwise yield additional, yet unpredictable, fragmentations including internal residue losses or multiple external residue losses. Lastly, to further enhance glycan enrichment and characterization, solid-support FRAGS was developed.</p>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":"43 2","pages":"269-288"},"PeriodicalIF":6.6,"publicationDate":"2022-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33485493","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 for the study of adipocyte cell secretome in cardiovascular diseases","authors":"Erica Gianazza,&nbsp;Maura Brioschi,&nbsp;Sonia Eligini,&nbsp;Cristina Banfi","doi":"10.1002/mas.21812","DOIUrl":"10.1002/mas.21812","url":null,"abstract":"<p>Adipose tissue is classically considered the primary site of lipid storage, but in recent years has garnered appreciation for its broad role as an endocrine organ, capable of remotely signaling to other tissues to alter their metabolic program. The adipose tissue is now recognized as a crucial regulator of cardiovascular health, mediated by the secretion of several bioactive products, with a wide range of endocrine and paracrine effects on the cardiovascular system. Thanks to the development and improvement of high-throughput mass spectrometry, the size and components of the human secretome have been characterized. In this review, we summarized the recent advances in mass spectrometry-based studies of the cell and tissue secretome for the understanding of adipose tissue biology, which may help to decipher the complex molecular mechanisms controlling the crosstalk between the adipose tissue and the cardiovascular system, and their possible clinical translation.</p>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":"43 4","pages":"752-781"},"PeriodicalIF":6.6,"publicationDate":"2022-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mas.21812","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33500716","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":"Advances in mass spectrometry imaging for toxicological analysis and safety evaluation of pharmaceuticals","authors":"Yilin Chen,&nbsp;Yanqiao Xie,&nbsp;Linnan Li,&nbsp;Zhengtao Wang,&nbsp;Li Yang","doi":"10.1002/mas.21807","DOIUrl":"10.1002/mas.21807","url":null,"abstract":"<p>Safety issues caused by pharmaceuticals have frequently occurred worldwide, posing a tremendous threat to human health. As an essential part of drug development, the toxicological analysis and safety evaluation is of great significance. In addition, the risk of pharmaceuticals accumulation in the environment and the monitoring of the toxicity from natural medicines have also received ongoing concerns. Due to a lack of spatial distribution information provided by common analytical methods, analyses that provide spatial dimensions could serve as complementary safety evaluation methods for better prediction and evaluation of drug toxicity. With advances in technical solutions and software algorithms, mass spectrometry imaging (MSI) has received increasing attention as a popular analytical tool that enables the simultaneous implementation of qualitative, quantitative, and localization without complex sample pretreatment and labeling steps. In recent years, MSI has become more attractive, powerful, and sensitive and has been applied in several scientific fields that can meet the safety assessment requirements. This review aims to cover a detailed summary of the various MSI technologies utilized in the biomedical and pharmaceutical area, including technical principles, advantages, current status, and future trends. Representative applications and developments in the safety-related issues of different pharmaceuticals and natural medicines are also described to provide a reference for pharmaceutical research, improve rational clinical medicine use, and ensure public safety.</p>","PeriodicalId":206,"journal":{"name":"Mass Spectrometry Reviews","volume":"42 5","pages":"2207-2233"},"PeriodicalIF":6.6,"publicationDate":"2022-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5767868","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}