Read Books Online and Download eBooks, EPub, PDF, Mobi, Kindle, Text Full Free.
Improvements To Stable Isotope And Label Free Quantitative Proteomic Methods
Download Improvements To Stable Isotope And Label Free Quantitative Proteomic Methods full books in PDF, epub, and Kindle. Read online Improvements To Stable Isotope And Label Free Quantitative Proteomic Methods ebook anywhere anytime directly on your device. Fast Download speed and no annoying ads. We cannot guarantee that every ebooks is available!
Book Synopsis Improvements to Stable Isotope and Label-free Quantitative Proteomic Methods by :
Download or read book Improvements to Stable Isotope and Label-free Quantitative Proteomic Methods written by and published by . This book was released on 2013 with total page 181 pages. Available in PDF, EPUB and Kindle. Book excerpt: The following thesis presents strategies for improving throughput and accuracy of mass spectrometry based proteomic methods and the application of these methods to study biological systems. A brief description of qualitative and quantitative proteomics is presented in Chapter 1. In Chapter 2, I report the first description of using mass defects for stable isotope labeling with amino acids in cell culture (SILAC). Using amino acid isotopologues with sub dalton mass differences permits increased multiplexing without concomitant increase in spectral complexity that occurs with SILAC based methods. Chapter 3 introduces quantitative amine reactive mass defect labels. These labels offer quantitation similar to mass defect SILAC but are compatible with tissue sample analysis. Chapter 4 describes a gas phase purification method that improves the accuracy and dynamic range of isobaric labeling by reducing measurement interference derived from precursor co-isolatation. Gas phase purification is accomplished by reacting selected peptide precursors with a proton transfer reagent, followed by re-isolation, fragmentation, and analysis of the charge reduced peptide. This method is then applied to measure changes in the mouse liver mitochondrial acetylome in Chapters 5 and 6. Dramatic changes associated with SIRT3 knockout and calorie restriction are described in Chapter 5. More subtle effects of obesity and fasting are presented in Chapter 6. Finally, a high-throughput workflow to comprehensively sequence a yeast proteome is reported in Chapter 7. This workflow offers a path toward high-throughput label-free proteomics experiments.
Book Synopsis Quantitative Proteomics by : Claire E Eyers
Download or read book Quantitative Proteomics written by Claire E Eyers and published by Royal Society of Chemistry. This book was released on 2014-01-10 with total page 391 pages. Available in PDF, EPUB and Kindle. Book excerpt: As a component of post-genome science, the field of proteomics has assumed great prominence in recent years. Whereas quantitative analyses focussed initially on relative quantification, a greater emphasis is now placed on absolute quantification and consideration of proteome dynamics. Coverage of the topic of quantitative proteomics requires consideration both of the analytical fundamentals of quantitative mass spectrometry and the specific demands of the problem being addressed. Quantitative Proteomics aims to outline the state of the art in mass spectrometry-based quantitative proteomics, describing recent advances and current limitations in the instrumentation used, together with the various methods employed for generating high quality data. Details on both strategies describing how stable isotope labelling can be applied and methods for performing quantitative analysis of proteins in a label-free manner are given. The utility of these strategies to understanding cellular protein dynamics are then exemplified with chapters looking at spatial proteomics, dynamics of protein function as determined by quantifying changes in protein post-translational modification and protein turnover. Finally, a key application of these techniques to biomarker discovery and validation is presented, together with the rapidly developing area of quantitative analysis of protein-based foodstuffs. This exemplary book is essential reading for analytical and biological mass spectrometrists working in proteomics research, as well as those undertaking either fundamental or clinical-based investigations with an interest in understanding protein dynamics and/or biomarker assessment.
Book Synopsis Cell-Free Translation Systems by : A.S. Spirin
Download or read book Cell-Free Translation Systems written by A.S. Spirin and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 254 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is a unique book that describes the most recent achievements in the methodology of protein biosynthesis under cell-free conditions. Various versions of cell-free protein-synthesizing systems and their applications to production of individual proteins on a preparative scale are reviewed. The most recent, advanced methodologies, such as continuous-exchange and continuous-flow cell-free systems and novel effecting batch-format cell-free procedures, are considered. Special attention is drawn to the possibilities of structural (NMR; X-ray) analysis of various gene expression products with the use of a new generation of cell-free systems.
Book Synopsis Quantitative Methods in Proteomics by : Katrin Marcus
Download or read book Quantitative Methods in Proteomics written by Katrin Marcus and published by Humana Press. This book was released on 2012-06-08 with total page 539 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein modifications and changes made to them, as well as the quantities of expressed proteins, can define the various functional stages of the cell. Accordingly, perturbations can lead to various diseases and disorders. As a result, it has become paramount to be able to detect and monitor post-translational modifications and to measure the abundance of proteins within the cell with extreme sensitivity. While protein identification is an almost routine requirement nowadays, reliable techniques for quantifying unmodified proteins (including those that escape detection under standard conditions, such as protein isoforms and membrane proteins) is not routine. Quantitative Methods in Proteomics gives a detailed survey of topics and methods on the principles underlying modern protein analysis, from statistical issues when planning proteomics experiments, to gel-based and mass spectrometry-based applications. The quantification of post-translational modifications is also addressed, followed by the “hot” topics of software and data analysis, as well as various overview chapters which provide a comprehensive overview of existing methods in quantitative proteomics. Written in the successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Quantitative Methods in Proteomics serves as a comprehensive and competent overview of the important and still growing field of quantitative proteomics.
Book Synopsis Proteomics for Biological Discovery by : Timothy D. Veenstra
Download or read book Proteomics for Biological Discovery written by Timothy D. Veenstra and published by John Wiley & Sons. This book was released on 2006-06-12 with total page 361 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by recognized experts in the study of proteins, Proteomics for Biological Discovery begins by discussing the emergence of proteomics from genome sequencing projects and a summary of potential answers to be gained from proteome-level research. The tools of proteomics, from conventional to novel techniques, are then dealt with in terms of underlying concepts, limitations and future directions. An invaluable source of information, this title also provides a thorough overview of the current developments in post-translational modification studies, structural proteomics, biochemical proteomics, microfabrication, applied proteomics, and bioinformatics relevant to proteomics. Presents a comprehensive and coherent review of the major issues faced in terms of technology development, bioinformatics, strategic approaches, and applications Chapters offer a rigorous overview with summary of limitations, emerging approaches, questions, and realistic future industry and basic science applications Discusses higher level integrative aspects, including technical challenges and applications for drug discovery Accessible to the novice while providing experienced investigators essential information Proteomics for Biological Discovery is an essential resource for students, postdoctoral fellows, and researchers across all fields of biomedical research, including biochemistry, protein chemistry, molecular genetics, cell/developmental biology, and bioinformatics.
Book Synopsis Quantification of Ribosomal Proteins by Mass Spectrometry by : Zubida Al-Majdoub
Download or read book Quantification of Ribosomal Proteins by Mass Spectrometry written by Zubida Al-Majdoub and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Absolute quantitative proteomics typically relies on the use of stable isotope labelled internal standards introduced in a known amount. Comparative signal intensities of the labelled and unlabelled peptides allow the inference of protein concentration. However, the availability of standard labelled signature peptides in accurately known amounts is a limitation to the widespread of this approach. Here, new approach termed ''QconCAT'' has been developed for absolute quantification and for the determination of 30S and 50S ribosomal proteins stoichiometry. These QconCAT proteins are concatamers of Lys C/tryptic peptides for 54 ribosomal proteins. Trypsin, the most widely used enzyme in proteomics, has a few caveats especially with ribosomal proteins as it does not perform well due to the presence of high numbers of small and basic residue and creates relatively short peptides. There is, thus, room for improvement using alternative proteases. Here, we evaluate the performance of such a sequential strategy (Lys-C/Trypsin). We show this strategy, is capable of increasing number of suitable signature peptides for designing ribosomal proteins QconCATs. Secondly, the method for multiplexed absolute quantification, 30S QconCAT, has been extended to enable the determination of stoichiometry of ribosomal proteins in control and gentamicin-treated cultures in a single experiment using LTQ-Orbitrap. Ribosomal samples were isolated from the whole cell lysate by sucrose density centrifugation, and the relevant fractions were pooled and analyzed. Specifically we targeted ribosomes with sub-lethal concentrations of gentamicin and compared that with ribosome untreated samples. Our results showed that the stoichiometry of 30S ribosomal proteins and 3 others from large subunit was measured to be close to 1:1 copy number per ribosome along with some unique variations, such as ribosomal proteins S1 with low copy number and S2 with high copy number as established in the literature. Among these, ribosomal protein S4, S7 and S8 were selected for investigations as these proteins are early-assembly proteins and our result confirmed the stoichiometry of these proteins in untreated samples are very similar. We also found there is a variation in up-regulation of ribosomal proteins in treated cultures, result from the gentamicin cell injury. The last three chapters of this thesis dealing with the appearance of E.coli and S.epidermidis bacterial resistant to gentamicin and azithromycin, and this problem has inspired extensive searches towards the goal of obtaining novel drug targets that have a synergistic effect with these two anti-ribosomal drugs with improved antibacterial activity and reduced toxicity. We use label-free quantitative proteomic analysis coupled with mass spectrometry to investigate how E.coli and S.epidermidis adapts to the presence of sub-lethal concentrations of gentamicin and azithromycin in aerobic and oxygen-limited cultures as gentamicin effect on both conditions. We found that gentamicin caused the up-regulation of proteins involved in translation such as L1, L10, S2, S1, S8 , S10 and L9 in E.coli cultures. Three ribosomal proteins were up-regulated by gentamicin in both aerobic and oxygen-limited cultures: L1, L10 and S2. Similar expression for azithromycin on E.coli was observed, up-regulation of proteins involved in translation such as ribosomal proteins L6 and L11, whereas expression patterns of gentamicin-treated cells on S.epidermidis were un-expected as proteins necessary for pathogenesis were up-regulated by gentamicin. Our data provide several ribosomal proteins as drug targets that could produce a synergistic effect with gentamicin and azithromycin.
Book Synopsis Proteomic and Metabolomic Approaches to Biomarker Discovery by : Haleem J. Issaq
Download or read book Proteomic and Metabolomic Approaches to Biomarker Discovery written by Haleem J. Issaq and published by Academic Press. This book was released on 2019-10-24 with total page 504 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteomic and Metabolomic Approaches to Biomarker Discovery, Second Edition covers techniques from both proteomics and metabolomics and includes all steps involved in biomarker discovery, from study design to study execution. The book describes methods and presents a standard operating procedure for sample selection, preparation and storage, as well as data analysis and modeling. This new standard effectively eliminates the differing methodologies used in studies and creates a unified approach. Readers will learn the advantages and disadvantages of the various techniques discussed, as well as potential difficulties inherent to all steps in the biomarker discovery process. This second edition has been fully updated and revised to address recent advances in MS and NMR instrumentation, high-field NMR, proteomics and metabolomics for biomarker validation, clinical assays of biomarkers and clinical MS and NMR, identifying microRNAs and autoantibodies as biomarkers, MRM-MS assay development, top-down MS, glycosylation-based serum biomarkers, cell surface proteins in biomarker discovery, lipodomics for cancer biomarker discovery, and strategies to design studies to identify predictive biomarkers in cancer research. Addresses the full range of proteomic and metabolomic methods and technologies used for biomarker discovery and validation Covers all steps involved in biomarker discovery, from study design to study execution Serves as a vital resource for biochemists, biologists, analytical chemists, bioanalytical chemists, clinical and medical technicians, researchers in pharmaceuticals and graduate students
Download or read book Plant Proteomics written by Jozef Samaj and published by Springer Science & Business Media. This book was released on 2007-09-09 with total page 397 pages. Available in PDF, EPUB and Kindle. Book excerpt: Plant Proteomics highlights rapid progress in this field, with emphasis on recent work in model plant species, sub-cellular organelles, and specific aspects of the plant life cycle such as signaling, reproduction and stress physiology. Several chapters present a detailed look at diverse integrated approaches, including advanced proteomic techniques combined with functional genomics, bioinformatics, metabolomics and molecular cell biology, making this book a valuable resource for a broad spectrum of readers.
Book Synopsis Proteomic Profiling and Analytical Chemistry by : Pawel Ciborowski
Download or read book Proteomic Profiling and Analytical Chemistry written by Pawel Ciborowski and published by Elsevier. This book was released on 2016-03-02 with total page 300 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteomic Profiling and Analytical Chemistry: The Crossroads, Second Edition helps scientists without a strong background in analytical chemistry to understand principles of the multistep proteomic experiment necessary for its successful completion. It also helps researchers who do have an analytical chemistry background to break into the proteomics field. Highlighting points of junction between proteomics and analytical chemistry, this resource links experimental design with analytical measurements, data analysis, and quality control. This targeted point of view will help both biologists and chemists to better understand all components of a complex proteomic study. The book provides detailed coverage of experimental aspects such as sample preparation, protein extraction and precipitation, gel electrophoresis, microarrays, dynamics of fluorescent dyes, and more. The key feature of this book is a direct link between multistep proteomic strategy and quality control routinely applied in analytical chemistry. This second edition features a new chapter on SWATH-MS, substantial updates to all chapters, including proteomic database search and analytical quantification, expanded discussion of post-hoc statistical tests, and additional content on validation in proteomics. Covers the analytical consequences of protein and peptide modifications that may have a profound effect on how and what researchers actually measure Includes practical examples illustrating the importance of problems in quantitation and validation of biomarkers Helps in designing and executing proteomic experiments with sound analytics
Book Synopsis Quantitative Proteome Analysis by : Kazuhiro Imai
Download or read book Quantitative Proteome Analysis written by Kazuhiro Imai and published by CRC Press. This book was released on 2013-08-05 with total page 314 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book focuses on the advantages and disadvantages of each of the commonly used quantitative proteomic methods in terms of accuracy, sensitivity, and reproducibility. It also concentrates on the effective applications of these methods that resulted in many discoveries of the role of the proteins expressed in living cells and biological fluids. The first part of the book focuses on the description of advantages and disadvantages of each of the commonly used quantitative proteomic methods in terms of accuracy, sensitivity, and, especially, reproducibility. The second part of the book focuses on providing concise descriptions of the effective applications of these methods to demonstrate how they have resulted in many important discoveries of the roles of the proteins expressed in living cells.
Book Synopsis An Integrated Experimental and Computational Approach to Proteomics: Scaling from High Resolution Qualitative Analysis to Quantitative Measurements with Confidence Evaluation by : Chongle Pan
Download or read book An Integrated Experimental and Computational Approach to Proteomics: Scaling from High Resolution Qualitative Analysis to Quantitative Measurements with Confidence Evaluation written by Chongle Pan and published by . This book was released on 2006 with total page 283 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the research described here, a substantial advancement in both qualitative and quantitative proteomic measurements was achieved using an integrated experiment and computational approach. The improved proteomic measurements can help elucidate a range of biological processes.
Book Synopsis Advancing Mass Spectrometry-based Discovery and Targeted Approaches for Disease Proteomic and Ptm Analyses by : Xiaofang Zhong (Ph.D.)
Download or read book Advancing Mass Spectrometry-based Discovery and Targeted Approaches for Disease Proteomic and Ptm Analyses written by Xiaofang Zhong (Ph.D.) and published by . This book was released on 2019 with total page 239 pages. Available in PDF, EPUB and Kindle. Book excerpt: Stable-isotope labeling coupled with mass spectrometry (MS) has emerged as the central technology for proteome quantification. Chemical stable isotope labels can be categorized into two major classes, namely mass difference labels and isobaric labels. Based on the various labeling approaches, we firstly develop a strategy for discovery and verification of candidate biomarkers in cerebrospinal fluid of preclinical Alzheimer's disease (AD), an asymptomatic phase with neuropathological abnormalities but no cognitive impairment. To further improve quantification accuracy, we develop 5-plex mass defect-based N,N-dimethyl leucine (mdDiLeu) tags for quantitative proteomics as an MS1-centric quantification method. The limitations of current quantification methods used for biomarker verification include low specificity in complex backgrounds, limited analytical throughput, and wide dynamic range, we developed a hybrid offset-triggered multiplex absolute quantification (HOTMAQ) strategy for targeted proteomics. HOTMAQ combines cost-effective mass difference and isobaric tags to address these issues simultaneously. Given the controversial discovery of protein biomarkers in AD and no reliable protein biomarkers for early detection are available in mild cognitive impairment (MCI, a symptomatic predementia phase) or AD so far, it is pivotal to define new players to aid in accurate diagnosis of this devastating disease. Protein glycosylation is one of the most common and complex post-translational modifications (PTMs), playing a fundamental role in many key biological processes. we develop large-scale comparative N-glycoproteomics of cerebrospinal fluid to elucidate glycoprotein microheterogeneity and relate the subtle changes in glycan structural repertoire to disease progression of AD. Phosphorylation, another common PTM, has been revealed to regulate cell dedifferentiation in restenosis. Transforming growth factor beta (TGF-[beta]) and its signaling protein Smad3 play important roles in vascular restenosis, but very little is yet known about the downstream regulation in response to elevated TGF-[beta]/Smad3 in smooth muscle cell (SMC). We develop a highly multiplexed quantitative proteomics and phosphoproteomics approach to assess dynamic protein expression and phosphorylation changes in SMC. Taken together, this work not only improves the quantification strategies for discovery and targeted proteomics and global PTM analyses, but also presents a useful platform to discover biomarkers and explore the underlying molecular mechanism of several diseases.
Book Synopsis Applications of Monolithic Column and Isotope Dimethylation Labeling in Shotgun Proteome Analysis by : Fangjun Wang
Download or read book Applications of Monolithic Column and Isotope Dimethylation Labeling in Shotgun Proteome Analysis written by Fangjun Wang and published by Springer Science & Business Media. This book was released on 2013-12-02 with total page 103 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this thesis, the author outlines the development of new monolithic columns and isotope dimethyl labeling strategies and their applications in high-performance proteome analyses. Though different types of monolithic columns have been widely developed for chromatography and electrophoresis separation, their application in proteomics for complex peptide mixtures separation is still a challenge. The author discusses the preparation of new monolithic columns and optimization of chromatography separation capability to improve coverage and accuracy of proteome analysis. Further, the author describes a novel online multidimensional chromatography system combined with automated online isotope labeling, which significantly improves the throughput, sensitivity and accuracy of quantitative proteomics. In addition to the development of new technologies, the author investigates the proteome and phosphoproteome expression changes of clinical hepatocellular carcinoma tissues and the hippocampi of mice with Alzheimer’s disease. The work in this thesis has led to several publications in high-profile journals in the fields of analytical chemistry and proteome research.
Book Synopsis Quantitative Proteomics by Mass Spectrometry by : Salvatore Sechi
Download or read book Quantitative Proteomics by Mass Spectrometry written by Salvatore Sechi and published by Methods in Molecular Biology. This book was released on 2018-04-15 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume describes prominent methodologies developed by laboratories that have been leading the field of quantitative proteomics by mass spectrometry. The procedures for performing the experiments are described in an easy-to-understand manner with many technical details that usually are not reported in typical research articles. This second edition of Quantitative Proteomics by Mass Spectrometry provides a broad perspective of the methodologies used for quantifying proteins and post-translational modifications in different types of biomedical specimens. 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 thorough, Quantitative Proteomics by Mass Spectrometry, Second Edition is a valuable resource to help researchers understand and learn about the latest tools used in the study of quantitative proteomics by mass spectrometry.
Book Synopsis Global Protein Quantification Using Neutron-encoded Mass Signatures and High-resolution Mass Spectrometry by :
Download or read book Global Protein Quantification Using Neutron-encoded Mass Signatures and High-resolution Mass Spectrometry written by and published by . This book was released on 2015 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The following chapters detail methodological and computational improvements to stable isotope labeling for mass spectrometry-based quantitative proteomics. The development of mass spectrometry for protein characterization and quantification is briefly reviewed in Chapter 1. Chapter 2 introduces the concept of neutron-encoded (NeuCode) mass signatures and demonstrates its potential for accurate and multiplexed protein quantification. The third chapter describes the design, synthesis, and use of new amino acid reagents that greatly expand the utility and scope of the NeuCode approach. In systematic and biological settings, NeuCode is benchmarked against current gold standard methods for quantitative accuracy and multiplexing. Chapter 4 examines the peculiar challenges associated with quantification of NeuCode features from high-resolution mass spectra and chronicles the computational algorithms developed to suit a variety of NeuCode labeling schemes. Conclusions and future directions inspired by the content of this thesis are discussed in Chapter 5.
Download or read book Comprehensive Biotechnology written by and published by Newnes. This book was released on 2011-08-26 with total page 5304 pages. Available in PDF, EPUB and Kindle. Book excerpt: The second edition of Comprehensive Biotechnology, Six Volume Set continues the tradition of the first inclusive work on this dynamic field with up-to-date and essential entries on the principles and practice of biotechnology. The integration of the latest relevant science and industry practice with fundamental biotechnology concepts is presented with entries from internationally recognized world leaders in their given fields. With two volumes covering basic fundamentals, and four volumes of applications, from environmental biotechnology and safety to medical biotechnology and healthcare, this work serves the needs of newcomers as well as established experts combining the latest relevant science and industry practice in a manageable format. It is a multi-authored work, written by experts and vetted by a prestigious advisory board and group of volume editors who are biotechnology innovators and educators with international influence. All six volumes are published at the same time, not as a series; this is not a conventional encyclopedia but a symbiotic integration of brief articles on established topics and longer chapters on new emerging areas. Hyperlinks provide sources of extensive additional related information; material authored and edited by world-renown experts in all aspects of the broad multidisciplinary field of biotechnology Scope and nature of the work are vetted by a prestigious International Advisory Board including three Nobel laureates Each article carries a glossary and a professional summary of the authors indicating their appropriate credentials An extensive index for the entire publication gives a complete list of the many topics treated in the increasingly expanding field
Book Synopsis Genomics, Proteomics, and Clinical Bacteriology by : Neil Woodford
Download or read book Genomics, Proteomics, and Clinical Bacteriology written by Neil Woodford and published by Springer Science & Business Media. This book was released on 2008-02-05 with total page 391 pages. Available in PDF, EPUB and Kindle. Book excerpt: Gazing into crystal balls is beyond the expertise of most scientists. Yet, as we look further into the 21st century, one does not have to be Nostradamus to predict that the current genomics and proteomics "revolution" will have an immense impact on medical bacteriology. This impact is already being re- ized in many academic departments, and although encroachment on routine diagnostic bacteriology, particularly in the hospital setting, is likely to occur at a slower pace, it remains nonetheless inevitable. Therefore, it is important that no one working in bacteriology should find themselves distanced from these fundamental developments. The involvement of all clinical bacteriologists is essential if the significant achievements of genome sequencing and analysis are to be turned into tangible advances, with resulting benefits for patient care and m- agement. It is our hope that Genomics, Proteomics, and Clinical Bacteriology: Methods and Reviews will play a part in bringing such a development to fruition. The advances in genomics and proteomics have already given us frequent opportunities to reassess our knowledge and understanding of established b- terial adversaries, and have provided us with the means to identify new foes. The new knowledge gained is enabling us to reconsider, for example, our c- cepts of bacterial pathogenicity, phylogeny and novel targets for antibacterial chemotherapy. These topics, and others, are considered in Genomics, Proteomics, and Clinical Bacteriology: Methods and Reviews.
