Download or read book Application and Development of Mass Spectrometry Technologies to Enable Biological Investigations written by Gary M. Wilson and published by . This book was released on 2020 with total page 313 pages. Available in PDF, EPUB and Kindle. Book excerpt: The research described in this dissertation showcases the utility and versatility of mass spectrometry for biological investigations and presents avenues for its continued improvement. Background on mass spectrometry-based proteomics and ancillary fields is provided in Chapter 1. Each subsequent chapter also includes a focused introduction to its respective contents. Chapters 2-4 were carried out in collaboration with members of the UW-Madison research community. We performed the proteomic sample preparation, analytical analysis, and data interpretation to advance the biological investigation. The manuscripts selected for these chapters highlight different proteomic techniques. The value of offline fractionation to increase analytical depth is presented in Chapter 2 to identify and quantify the protein regulators of zinc homeostasis during red blood cell development. In Chapter 3, global phosphoproteomics with tandem mass tags (TMT) is used to identify the role of an orphaned mitochondrial protein, Pptc7, and its importance in protein transport into mitochondria. The technique of transcriptomics-informed proteomics (proteogenomics) is featured in Chapter 4, in which novel proteins were identified in the lesser-studied life cycle of Toxoplasma gondii. Subsequent chapters delve into the enabling technologies developed \textit{en route} towards a robust, quantitative glycoproteomic pipeline. The study of the plasma glycoproteome in Chapter 5 highlights the benefits of using orthogonal enrichment methods and the optimization of MS parameters for intact glycopeptide profiling. Similarly, the design of a software environment, coined GlycoTools, to organize, inspect, and explore glycoproteomic data, with an emphasis on quality control, is presented in Chapter 6. Lastly, a large-scale glycoproteomic comparison of cell lines transformed with 6 different driving proliferative oncogenes is presented in Chapter 7, which was enabled by the concepts presented in Chapters 5 and 6.

Download or read book Mass Spectrometry Developmental Approaches to Answer Biological Questions written by Gwenael Pottiez and published by Springer. This book was released on 2015-02-05 with total page 77 pages. Available in PDF, EPUB and Kindle. Book excerpt: The understanding of the events taking place in a cell, a biological fluid or in any biological system is the main goal of biology research. Many fields of research use different technology to assess those events. Mass spectrometry is one of those techniques and this undergoes constant evolution and adaptation to always enhance the accuracy of the information provided. Proteomics provides a large panel of data on protein identity and protein expression that were made possible by mass spectrometry. For several years now mass spectrometry has become central to performing proteomic research, however this powerful tool is under constant evolution to be more sensitive and more resolute. More importantly mass spectrometry became a field of research focusing on new applications. Indeed, the complexity in biological systems relies on the changes of expression of transcription of proteins but also on the post-translational modification of proteins, the structure of proteins and the interaction between proteins, amongst others. As of now, several investigations tried to improve the quantification of proteins by mass spectrometry, the determination of post-translational modifications, the protein-protein and protein-nucleic acids interaction or the proteins structures. This book is structured as follows: after a brief introduction of the usual and most popular applications for mass spectrometry in proteomics, the most recent research and developments in mass spectrometry-based methodologies will be explored.

Download or read book Mass Spectrometry in Chemical Biology written by Norberto Peporine Lopes and published by Royal Society of Chemistry. This book was released on 2017-11-16 with total page 312 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mass spectrometry is one of the most widespread technologies in chemistry and has been increasingly used in biology with the rise of omics sciences. This book summarizes some important methodological approaches in mass spectrometry and applications in the field of chemical biology. The core chapters build on basic concepts introduced in the opening chapter and explore established fields such as high throughput screening, proteomics and metabolomics. Emerging applications of mass spectrometry in elucidating biosynthetic pathways, enzyme mechanisms and protein-protein interactions are then presented. Connections between these diverse research fields are highlighted throughout. The book concludes with a discussion of databases and future perspectives. This book will be a useful tool to early chemical biology researchers wishing to incorporate mass spectrometry as a tool in their research.

Download or read book Mass Spectrometry for Drug Discovery and Drug Development written by Walter A. Korfmacher and published by John Wiley & Sons. This book was released on 2012-12-12 with total page 686 pages. Available in PDF, EPUB and Kindle. Book excerpt: Facilitates the discovery and development of new, effective therapeutics With coverage of the latest mass spectrometry technology, this book explains how mass spectrometry can be used to enhance almost all phases of drug discovery and drug development, including new and emerging applications. The book's fifteen chapters have been written by leading pharmaceutical and analytical scientists. Their contributions are based on a thorough review of the current literature as well as their own experience developing new mass spectrometry techniques to improve the ability to discover and develop new and effective therapeutics. Mass Spectrometry for Drug Discovery and Drug Development begins with an overview of the types of mass spectrometers that facilitate drug discovery and development. Next it covers: HPLC high-resolution mass spectrometry for quantitative assays Mass spectrometry for siRNA Quantitative analysis of peptides Mass spectrometry analysis of biological drugs Applications that support medicinal chemistry investigations Mass spectrometry imaging and profiling Throughout the book, detailed examples underscore the growing role of mass spectrometry throughout the drug discovery and development process. In addition, images of mass spectra are provided to explain how results are interpreted. Extensive references at the end of each chapter guide readers to the primary literature in the field. Mass Spectrometry for Drug Discovery and Drug Development is recommended for readers in pharmaceutics, including medicinal chemists, analytical chemists, and drug metabolism scientists. All readers will discover how mass spectrometry can streamline and advance new drug discovery and development efforts.

Download or read book Mass Spectrometry Handbook written by Mike S. Lee and published by John Wiley & Sons. This book was released on 2012-04-16 with total page 1362 pages. Available in PDF, EPUB and Kindle. Book excerpt: Due to its enormous sensitivity and ease of use, mass spectrometry has grown into the analytical tool of choice in most industries and areas of research. This unique reference provides an extensive library of methods used in mass spectrometry, covering applications of mass spectrometry in fields as diverse as drug discovery, environmental science, forensic science, clinical analysis, polymers, oil composition, doping, cellular research, semiconductor, ceramics, metals and alloys, and homeland security. The book provides the reader with a protocol for the technique described (including sampling methods) and explains why to use a particular method and not others. Essential for MS specialists working in industrial, environmental, and clinical fields.

Download or read book Advancements of Mass Spectrometry in Biomedical Research written by Alisa G. Woods and published by Springer. This book was released on 2019-07-25 with total page 813 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume explores the use of mass spectrometry for biomedical applications. Chapters focus on specific therapeutic areas such as oncology, infectious disease, and psychiatry. Additional chapters focus on methodology, technologies and instrumentation, as well as on analysis of protein-protein interactions, protein quantitation, and protein post-translational modifications. Various omics fields such as proteomics, metabolomics, glycomics, lipidomics, and adductomics are also covered. Applications of mass spectrometry in biotechnological and pharmaceutical industry are also discussed. This volume provides readers with a comprehensive and informative manual that will allow them to appreciate mass spectrometry and proteomic research, but also to initiate and improve their own work. This book acts as a technical guide as well as a conceptual guide to the newest information in this exciting field.

Download or read book Sample Preparation in Biological Mass Spectrometry written by Alexander R. Ivanov and published by Springer Science & Business Media. This book was released on 2011-06-15 with total page 1081 pages. Available in PDF, EPUB and Kindle. Book excerpt: The aim of this book is to provide the researcher with important sample preparation strategies in a wide variety of analyte molecules, specimens, methods, and biological applications requiring mass spectrometric analysis as a detection end-point. In this volume we have compiled the contributions from several laboratories which are employing mass spectrometry for biological analysis. With the latest inventions and introduction of highly sophisticated mass spectrometry equipment sample preparation becomes an extremely important bottleneck of biomedical analysis. We have a goal of giving the reader several successful examples of sample preparation, development and optimization, leading to the success in analytical steps and proper conclusions made at the end of the day. This book is structured as a compilation of contributed chapters ranging from protocols to research articles and reviews. The main philosophy of this volume is that sample preparation methods have to be optimized and validated for every project, for every sample type and for every downstream analytical technique.

Download or read book Mass Spectrometry in Structural Biology and Biophysics written by Igor A. Kaltashov and published by John Wiley & Sons. This book was released on 2012-04-03 with total page 312 pages. Available in PDF, EPUB and Kindle. Book excerpt: The definitive guide to mass spectrometry techniques in biology and biophysics The use of mass spectrometry (MS) to study the architecture and dynamics of proteins is increasingly common within the biophysical community, and Mass Spectrometry in Structural Biology and Biophysics: Architecture, Dynamics, and Interaction of Biomolecules, Second Edition provides readers with detailed, systematic coverage of the current state of the art. Offering an unrivalled overview of modern MS-based armamentarium that can be used to solve the most challenging problems in biophysics, structural biology, and biopharmaceuticals, the book is a practical guide to understanding the role of MS techniques in biophysical research. Designed to meet the needs of both academic and industrial researchers, it makes mass spectrometry accessible to professionals in a range of fields, including biopharmaceuticals. This new edition has been significantly expanded and updated to include the most recent experimental methodologies and techniques, MS applications in biophysics and structural biology, methods for studying higher order structure and dynamics of proteins, an examination of other biopolymers and synthetic polymers, such as nucleic acids and oligosaccharides, and much more. Featuring high-quality illustrations that illuminate the concepts described in the text, as well as extensive references that enable the reader to pursue further study, Mass Spectrometry in Structural Biology and Biophysics is an indispensable resource for researchers and graduate students working in biophysics, structural biology, protein chemistry, and related fields.

Download or read book Mass Spectrometry Application in Biology written by Greg Gorman and published by MDPI. This book was released on 2018-10-08 with total page 1 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is a printed edition of the Special Issue "Mass Spectrometry Application in Biology" that was published in IJMS

Download or read book Quantitative Biological and Clinical Mass Spectrometry written by Anthony I. Mallet and published by John Wiley & Sons. This book was released on 2018-04-27 with total page 224 pages. Available in PDF, EPUB and Kindle. Book excerpt: A basic overview of mass spectrometry relevant to life and health science applications, illustrated throughout with relevant case studies This introductory text provides information and assistance to new users of mass spectrometry (MS) working in clinical or biochemical fields who are faced with implementing and designing quantitative mass spectrometric assays for a variety of classes of molecules of biological interest. It presents a detailed discussion on how to optimize measurement parameters for a candidate reference quantitative analysis, including calibration procedures, sensitivity, reproducibility, speed of assay and compliance with regulatory authorities. Quantitative Biological and Clinical Mass Spectrometry uses examples where development has not been immediately successful but where unforeseen problems have arisen and describes the strategies used to solve these. Advances in addressing the very large numbers of clinical samples that arise on routine screening programs such as those involved in inborn errors of metabolism studies are discussed. Direct mass spectrometric based analyses applicable to point of care testing (POCT) situations are also covered. The book concludes with a short section on possible novel developments, bibliography, references, and a glossary of terms. Shows how the presence of false results can be detected and understood Describes the ‘parts’ of modern instruments from sample introduction through ionization, mass analysis and detection, and the variety of techniques of tandem mass spectrometry Discusses the requirement for specificity in an assay method Fully illustrated throughout Highly relevant to all key areas of mass spectrometric analysis Quantitative Biological and Clinical Mass Spectrometry appeals to those newly exposed to the use of combined chromatography and mass spectrometry for analysis of biological material and to scientists experienced in automated clinical analysis using immunoassays or who are new to mass spectrometry.

Download or read book Mass Spectrometry of Proteins written by Caroline A. Evans and published by Humana. This book was released on 2020-08-14 with total page 264 pages. Available in PDF, EPUB and Kindle. Book excerpt: New insights into modern medicine and systems biology are enabled by innovative protocols and advanced technologies in mass spectrometry-based proteomics. This volume details new pipelines, workflows, and ways to process data that allow for new frontiers in proteomics to be pushed forward. With applications to biomarker discovery, interactions between proteins, between biological systems, dynamics of post-translational modifications among others, new protocols have been developed and iteratively refined to probe the endless complexity of the proteome in ever greater details. This volume deals with methods for data dependent and data independent mass spectrometry analyses. Valuable, first-hand information is provided from designing experiments, sample preparation and analysis, exploitation of public datasets and carrying out reproducible data pipelines, using modern computational tools such as Galaxy or Jupyter. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Mass Spectrometry of Proteins: Methods and Protocols aims to ensure successful results in the further study of this vital field.

Download or read book Evolution of Translational Omics written by Institute of Medicine and published by National Academies Press. This book was released on 2012-09-13 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt: Technologies collectively called omics enable simultaneous measurement of an enormous number of biomolecules; for example, genomics investigates thousands of DNA sequences, and proteomics examines large numbers of proteins. Scientists are using these technologies to develop innovative tests to detect disease and to predict a patient's likelihood of responding to specific drugs. Following a recent case involving premature use of omics-based tests in cancer clinical trials at Duke University, the NCI requested that the IOM establish a committee to recommend ways to strengthen omics-based test development and evaluation. This report identifies best practices to enhance development, evaluation, and translation of omics-based tests while simultaneously reinforcing steps to ensure that these tests are appropriately assessed for scientific validity before they are used to guide patient treatment in clinical trials.

Download or read book Methods Development in Biological Mass Spectrometry written by Taufika Islam Williams and published by . This book was released on 2005 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Mass Spectrometry for the Novice written by John Greaves and published by CRC Press. This book was released on 2013-10-16 with total page 312 pages. Available in PDF, EPUB and Kindle. Book excerpt: With usage of mass spectrometry continually expanding, an increasing number of scientists, technicians, students, and physicians are coming into contact with this valuable technique. Mass spectrometry has many uses, both qualitative and quantitative, from analyzing simple gases to environmental contaminants, pharmaceuticals, and complex biopolymers. The extraordinary versatility can make mass spectrometers daunting to novices. Consequently, new users would benefit greatly from an understanding of the basic concepts as well as the processes that occur in these instruments. Mass Spectrometry for the Novice provides exactly that, with detailed, straightforward descriptions and clear illustrations of principles of operations and techniques. The book begins with an overview that includes essential definitions and then provides information on the components of and the strategies used in the most common instruments. The authors discuss the methodologies available, classes of compounds analyzed, and the types of data that can be generated. A group of representative applications from published articles is summarized, demonstrating the diversity of mass spectrometry. The authors also condense the essentials of the topic into one invaluable chapter that provides a set of concise take-home messages on all aspects of mass spectrometry. The final section provides a collection of resources including books, reviews, and useful websites. Using simple language, new color figures, clever cartoons, and assuming no prior knowledge, this book provides a readily understandable entrée to mass spectrometry. A CD-ROM with selected figures and cartoons is included.

Download or read book Mass Spectrometry written by Marek Smoluch and published by John Wiley & Sons. This book was released on 2019-06-17 with total page 361 pages. Available in PDF, EPUB and Kindle. Book excerpt: Provides a comprehensive description of mass spectrometry basics, applications, and perspectives Mass spectrometry is a modern analytical technique, allowing for fast and ultrasensitive detection and identification of chemical species. It can serve for analysis of narcotics, counterfeit medicines, components of explosives, but also in clinical chemistry, forensic research and anti-doping analysis, for identification of clinically relevant molecules as biomarkers of various diseases. This book describes everything readers need to know about mass spectrometry—from the instrumentation to the theory and applications. It looks at all aspects of mass spectrometry, including inorganic, organic, forensic, and biological MS (paying special attention to various methodologies and data interpretation). It also contains a list of key terms for easier and faster understanding of the material by newcomers to the subject and test questions to assist lecturers. Knowing how crucial it is for young researchers to fully understand both the power of mass spectrometry and the importance of other complementary methodologies, Mass Spectrometry: An Applied Approach teaches that it should be used in conjunction with other techniques such as NMR, pharmacological tests, structural identification, molecular biology, in order to reveal the true function(s) of the identified molecule. Provides a description of mass spectrometry basics, applications and perspectives of the technique Oriented to a broad audience with limited or basic knowledge in mass spectrometry instrumentation, theory, and its applications in order to enhance their competence in this field Covers all aspects of mass spectrometry, including inorganic, organic, forensic, and biological MS with special attention to application of various methodologies and data interpretation Includes a list of key terms, and test questions, for easier and faster understanding of the material Mass Spectrometry: An Applied Approach is highly recommended for advanced students, young scientists, and anyone involved in a field that utilizes the technique.

Download or read book Development and Application of Mass Spectrometry based Strategies for Structural Elucidation of Heparin Isomers and Metabolic Investigations of Nutrition and Pluripotent Stem Cells written by John Kenji Meissen and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Mass spectrometry (MS) is a powerful analytical tool applied in modern biological sciences research. Its capacity for accurate quantitation of molecular structures, ability to determine molecular mass with millidalton accuracy, and capability to fragment ions into constituent structures provide scientists with the means necessary to effectively explore complex biological systems. The goals of my dissertation work were to develop and apply new MS-based strategies to enhance knowledge and understanding of biochemical phenotypes; in particular, my novel mass spectrometry methods were applied to differentiate pluripotent stem cell types, to understand the metabolic effects of fructose consumption, and to study the role of rare heparin and heparan sulfate structural features in mediating protein binding. Chapter 1 covers the development and application of methodology employing collision induced dissociation (CID) to effectively identify heparin and heparan sulfate disaccharide sulfation patterns, including forms containing the rare 3-O-sulfate moiety. Heparin and heparin sulfate possess a large number of structural isomers due to variable sulfation patterns spanning numerous positions within a repeating disaccharide subunit, and a single CID event was inadequate to generate fragment ions differentiating 3-O-sulfated species from other structural isomers. However, application of two successive CID events enabled cross-ring dissociation generating unique fragment ions for 3-O-sulfated structures. A method employing two successive CID events was developed and applied to an 11-sulfated heparin octasaccharide structure displaying affinity for chemokine ligand 2 (CCL2) revealing that, in contrast to several other heparin and heparan sulfate binding proteins, CCL2 does not preferentially bind a structure containing 3-O-sulfation. Following completion of the heparin/heparan sulfate project, the focus of the dissertation work shifted toward metabolomics. Metabolomics, the identification and quantification of all metabolites in a system under a given set of conditions, is a growing discipline in biological research and can enhance our understanding of biochemical response in complex biological systems to disease state, environmental stress, nutrition, and many other factors. Chapter 2 explores characterization of currently available instrumentation, chromatography methods, and software tools for construction of a liquid chromatography mass spectrometry (LCMS)-based metabolite profiling method maximizing the capabilities of current technologies. Six different chromatography columns with twelve different mobile phase combinations were evaluated with a series of standards to elucidate an effective chromatography method. The mass accuracy and isotope abundance error of the Agilent 6530 quadrupole time of flight (QTOF) and Leco Citius liquid chromatography high resolution time of flight mass spectrometers were determined with known plasma sample metabolites to identify the limitations of each platform. The capabilities and limitations of four untargeted data processing tools, including MZmine and Genedata Refiner MS, were evaluated based on their ability to accurately report intensity of known metabolites in plasma samples with data sets from both instruments. This series of characterization and evaluation experiments enabled selection and integration of individual components to construct a hydrophilic interaction chromatography (HILIC)-QTOF MS metabolite profiling workflow which maximizes the capabilities of tested technologies and possesses the potential to expand understanding of biological systems across many research projects. Chapter 3 investigates the metabolic relationships of induced pluripotent stem cells (iPSCs), iPSC parental embryonic fibroblasts, and embryonic stem cells (ESC). The HILIC-QTOF workflow developed in chapter 2 and an established gas chromatography time of flight (GC-TOF) method were used for metabolite profiling of all three cell types. GC-TOF data processing provided 111 identified metabolites including glycolysis, pentose phosphate pathway, and citric acid cycle metabolites as well as amino acids, free fatty acids, and sugar alcohols. HILIC-QTOF data processing yielded 55 annotated metabolites including many complex lipids, acylcarnitines, amino acids, and purine structures. Annotated structures were integrated into MetaMapp metabolite networks to facilitate identification of compound classes and metabolite pathways displaying statistically significant differences between cell lines. Results indicate that iPSCs display greater metabolic similarity to genuine ESCs than the iPSC parental embryonic fibroblasts. However, iPSCs possess clear differences from ESCs in complex lipid structures, essential and non-essential amino acids, and metabolites involved in polyamine biosynthesis. Chapter 4 explores the metabolic effects of fructose with a human HepG2 liver cell model. Targeted methodologies were applied to test the hypothesis that high fructose exposure would increase hexosamine generation, and that the increase in hexosamine generation would be associated with greater lipogenic gene expression in the HepG2 model system. Lipogenic enzyme abundance and expression levels were determined for HepG2 cells incubated in media containing 5.5 mM glucose, 5.5 mM glucose + 5.0 mM fructose, and 10.5 mM glucose. Hexosamine biosynthesis pathway (HBP) metabolite levels were determined with targeted LC-QTOF and GC-TOF strategies for each hexose condition. Application of the targeted metabolite analysis strategies in combination with lipogenic gene expression and enzyme abundance analysis revealed that fructose exposure does not result in increased levels of hexosamine biosynthesis pathway metabolites or, contrary to rodent models, cause increased expression of lipogenic enzymes in the HepG2 model system. Should this effect translate to the human liver in vivo, it would suggest that increased lipogenesis caused by high fructose consumption occurs primarily through means other than lipogenic gene expression. Similar to chapter 4, chapter 5 explores the metabolic effects of fructose with a human HepG2 liver cell model. However, untargeted metabolite profiling methods were applied to generate a more broad investigation of fructose effects on liver cell metabolism. The HILIC-QTOF workflow developed in chapter 2 and an established GC-TOF method were used for metabolite profiling of HepG2 metabolite extracts from cells incubated in media conditions identical to the previous targeted analysis. Analysis of cell extracts with the GC-TOF system enabled identification of 112 different metabolites, and analysis with the HILIC-QTOF system enabled annotation of 54 different metabolites. Integration of GC-TOF and HILIC-QTOF data sets yielded 156 unique annotations representing a wide array of structural classes and enzymatic pathways. Results indicate that metabolite profiles of HepG2 liver cells grown in all three media conditions are greatly similar. However, several distinct changes in metabolite abundance were observed based on both fructose addition and hexose concentration. Fructose dependent effects were observed in long-chain acylcarnitine structures and amino acids involved in folate metabolism. Carbohydrate concentration dependent effects were observed with acylcarnitine and complex lipid structures.

Download or read book Medical Applications of Mass Spectrometry written by Karoly Vekey and published by Elsevier. This book was released on 2011-08-11 with total page 607 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mass spectrometry is fast becoming an indispensable field for medical professionals. The mass spectrometric analysis of metabolites and proteins promises to revolutionize medical research and clinical diagnostics. As this technology rapidly enters the medical field, practicing professionals and students need to prepare to take full advantage of its capabilities. Medical Applications of Mass Spectrometry addresses the key issues in the medical applications of mass spectrometry at the level appropriate for the intended readership. It will go a long way to help the utilization of mass spectrometry in medicine.The book comprises five parts. A general overview is followed by a description of the basic sampling and separation methods in analytical chemistry. In the second part a solid foundation in mass spectrometry and modern techniques of data analysis is presented. The third part explains how mass spectrometry is used in exploring various classes of biomolecules, including proteins and lipids. In the fourth section mass spectrometry is introduced as a diagnostic tool in clinical treatment, infectious pathogen research, neonatal diagnostics, cancer, brain and allergy research, as well as in various fields of medicine: cardiology, pulmonology, neurology, psychiatric diseases, hemato-oncology, urologic diseases, gastrointestinal diseases, gynecology and pediatrics. The fifth part covers emerging applications in biomarker discovery and in mass spectrometric imaging. * Provides a broad look at how the medical field is benefiting from advances in mass spectrometry.* Guides the reader from basic principles and methods to cutting edge applications.* There is NO comparable book on the market to fill this fast growing field.