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Author: Zihui Li Publisher: ISBN: Category : Languages : en Pages : 0
Book Description
Proteins are important molecules that are involved in numerous critical biological processes. Consequently, understanding the functional roles and dysregulation of proteins constitutes a vital task in both basic and clinical research. However, it is very challenging to define the full complement of proteins due to their large degree of variations, especially considering that many proteins can undergo numerous post-translational modifications (PTMs) which dramatically affect protein conformations and functions. Recently, mass spectrometry (MS) has evolved as a powerful tool to characterize proteins and their PTMs benefiting from its high speed, sensitivity and the ability to monitor thousands of analytes simultaneously. This dissertation is devoted to the development and application of various MS-based strategies to facilitate the detection of proteins and their PTMs qualitatively and quantitatively. A portion of this dissertation describes the investigation of proteome-wide alterations with the development and maturation of human pancreas using custom-developed isobaric tags. This study focuses on the extracellular matrix proteins and provides information on the localization changes of selected proteins in islet or acinar compartments as well. The normal baseline data across the lifespan of human pancreas will become a valuable resource and benefit future studies into the pancreatic pathologies. Switching gear to protein PTMs, this dissertation documents the design and development of a novel biotin thiol tag to greatly improve the in-depth profiling of two important PTMs, citrullination and homocitrullination, from complex biological samples. The utility of the approach is demonstrated by providing the first tissue-specific citrullination and homocitrullination atlas in mice. The first high-throughput quantitative analysis pipeline of protein citrullination is subsequently developed by the integration with isobaric labeling strategy. We also further improve the protein citrullination detection by using a combination of various digestion and fragmentation techniques. Citrullination alteration during the progression of Alzheimer's disease is further explored using human cerebrospinal fluid to shed light on the disease pathogenesis. This dissertation also highlights the application of a novel sub-atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry platform for the in situ imaging of N-glycans. Spatial distribution of N-glycans in ovarian cancer tissue section may indicate potential association of this modification with tumor progression. Collectively, we expect the biological insights and technological advancements presented in this work will lead to improved understanding of microenvironment in both healthy and disease conditions, and the new knowledge gained from these studies will inspire and benefit future research effort in related fields.
Author: Zihui Li Publisher: ISBN: Category : Languages : en Pages : 0
Book Description
Proteins are important molecules that are involved in numerous critical biological processes. Consequently, understanding the functional roles and dysregulation of proteins constitutes a vital task in both basic and clinical research. However, it is very challenging to define the full complement of proteins due to their large degree of variations, especially considering that many proteins can undergo numerous post-translational modifications (PTMs) which dramatically affect protein conformations and functions. Recently, mass spectrometry (MS) has evolved as a powerful tool to characterize proteins and their PTMs benefiting from its high speed, sensitivity and the ability to monitor thousands of analytes simultaneously. This dissertation is devoted to the development and application of various MS-based strategies to facilitate the detection of proteins and their PTMs qualitatively and quantitatively. A portion of this dissertation describes the investigation of proteome-wide alterations with the development and maturation of human pancreas using custom-developed isobaric tags. This study focuses on the extracellular matrix proteins and provides information on the localization changes of selected proteins in islet or acinar compartments as well. The normal baseline data across the lifespan of human pancreas will become a valuable resource and benefit future studies into the pancreatic pathologies. Switching gear to protein PTMs, this dissertation documents the design and development of a novel biotin thiol tag to greatly improve the in-depth profiling of two important PTMs, citrullination and homocitrullination, from complex biological samples. The utility of the approach is demonstrated by providing the first tissue-specific citrullination and homocitrullination atlas in mice. The first high-throughput quantitative analysis pipeline of protein citrullination is subsequently developed by the integration with isobaric labeling strategy. We also further improve the protein citrullination detection by using a combination of various digestion and fragmentation techniques. Citrullination alteration during the progression of Alzheimer's disease is further explored using human cerebrospinal fluid to shed light on the disease pathogenesis. This dissertation also highlights the application of a novel sub-atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry platform for the in situ imaging of N-glycans. Spatial distribution of N-glycans in ovarian cancer tissue section may indicate potential association of this modification with tumor progression. Collectively, we expect the biological insights and technological advancements presented in this work will lead to improved understanding of microenvironment in both healthy and disease conditions, and the new knowledge gained from these studies will inspire and benefit future research effort in related fields.
Author: Oscar Alzate Publisher: CRC Press ISBN: 1420076264 Category : Medical Languages : en Pages : 356
Book Description
In this, the post-genomic age, our knowledge of biological systems continues to expand and progress. As the research becomes more focused, so too does the data. Genomic research progresses to proteomics and brings us to a deeper understanding of the behavior and function of protein clusters. And now proteomics gives way to neuroproteomics as we beg
Author: John R. Griffiths Publisher: John Wiley & Sons ISBN: 1119250897 Category : Science Languages : en Pages : 377
Book Description
Covers all major modifications, including phosphorylation, glycosylation, acetylation, ubiquitination, sulfonation and and glycation Discussion of the chemistry behind each modification, along with key methods and references Contributions from some of the leading researchers in the field A valuable reference source for all laboratories undertaking proteomics, mass spectrometry and post-translational modification research
Author: Salvatore Sechi Publisher: Springer Science & Business Media ISBN: 1597452556 Category : Science Languages : en Pages : 223
Book Description
This volume is a compendium of cutting-edge protocols for quantitative proteomics, and presents the most significant methods used in the field today. The focus on mass spectrometry (MS) is integral. Attention is given to state-of-the-art techniques for the characterization of the phosphoproteome and tandem MS for detection of inborn errors of metabolism. This volume is an indispensable resource in the search for novel biomarkers.
Author: Claire E Eyers Publisher: Royal Society of Chemistry ISBN: 1782621091 Category : Science Languages : en Pages : 391
Book Description
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.
Author: Bin Wang Publisher: ISBN: Category : Languages : en Pages : 0
Book Description
Proteins are among the most abundant organic molecules in living systems and the basic building blocks of an organism. Therefore, understanding the functional roles and abnormalities of proteins is a crucial undertaking in both fundamental scientific inquiry and clinical investigation. However, the task of comprehensively defining the complete repertoire of proteins is fraught with significant difficulties, primarily coming from their molecular diversity, extensive variabilities, including post-translational modifications (PTMs), which pose substantial challenges to accurate and comprehensive characterization. The extensive PTMs and their dynamic regulation dramatically increase the potential number of functional proteins, or proteoforms. Mass spectrometry (MS) has emerged as a robust and indispensable analytical tool for studying biomolecules, particularly in proteomics and investigations of PTMs with its rapid analysis speed, remarkable sensitivity, high resolution, and the ability to simultaneously detect numerous analytes in a single analytical run.This dissertation is devoted to the development and application of MS-based strategies to facilitate the detection of PTMs and structural proteomics. A large portion of this dissertation documents the design and development of a novel biotin thiol tag to significantly improve the in-depth profiling of two important PTMs, citrullination and homocitrullination, from complex biological samples. Further enhancements to the detection of protein citrullination are achieved through the combined utilization of diverse digestions and fragmentation techniques. The effectiveness and utility of this approach are illustrated through the creation of the tissue-specific citrullination and homocitrullination atlas in mice. Additionally, a high-throughput quantitative analysis pipeline for protein citrullination is developed by integrating an isobaric labeling strategy. We then describe the method combining novel biotin-derivative tag with a histone limited digestion method for direct identification of citrullination sites on histones in human cells. Moreover, citrullination alteration during the progression of Alzheimer's disease (AD) and type 1 diabetes are further explored using human cerebrospinal fluid and human pancreas to shed light on this important yet understudied PTM in disease pathogenesis. This dissertation also highlights recent advancements of citrullination-specific MS approaches and integration of the potential methodology for improved citrullination identification and characterization. Besides PTMs analysis, this dissertation also documents research efforts in structural proteomics. As additional misfolded proteins presumably exist distinctly in AD disease states, which would serve as rich source of AD biomarkers, we used limited proteolysis coupled with mass spectrometry (LiP-MS) to probe protein structural changes qualitatively and quantitatively. These newly discovered conformational biomarker candidates establish valuable future directions for exploring the molecular mechanism and designing therapeutic targets for AD. Collectively, we expect that the biological discoveries and technological breakthroughs presented in this PhD dissertation will contribute to a deeper understanding of human physiological and pathological pathways. The novel insights obtained from these investigations are expected to serve as a catalyst for further research in related areas, inspiring future efforts to advance our understanding of significant biological questions. The implications of this work have the potential to benefit a wide range of scientific fields, paving the way for new discoveries and applications that could ultimately improve human health and well-being.
Author: W. Andy Tao Publisher: John Wiley & Sons ISBN: 1118970217 Category : Science Languages : en Pages : 448
Book Description
PROVIDES STRATEGIES AND CONCEPTS FOR UNDERSTANDING CHEMICAL PROTEOMICS, AND ANALYZING PROTEIN FUNCTIONS, MODIFICATIONS, AND INTERACTIONS—EMPHASIZING MASS SPECTROMETRY THROUGHOUT Covering mass spectrometry for chemical proteomics, this book helps readers understand analytical strategies behind protein functions, their modifications and interactions, and applications in drug discovery. It provides a basic overview and presents concepts in chemical proteomics through three angles: Strategies, Technical Advances, and Applications. Chapters cover those many technical advances and applications in drug discovery, from target identification to validation and potential treatments. The first section of Mass Spectrometry-Based Chemical Proteomics starts by reviewing basic methods and recent advances in mass spectrometry for proteomics, including shotgun proteomics, quantitative proteomics, and data analyses. The next section covers a variety of techniques and strategies coupling chemical probes to MS-based proteomics to provide functional insights into the proteome. In the last section, it focuses on using chemical strategies to study protein post-translational modifications and high-order structures. Summarizes chemical proteomics, up-to-date concepts, analysis, and target validation Covers fundamentals and strategies, including the profiling of enzyme activities and protein-drug interactions Explains technical advances in the field and describes on shotgun proteomics, quantitative proteomics, and corresponding methods of software and database usage for proteomics Includes a wide variety of applications in drug discovery, from kinase inhibitors and intracellular drug targets to the chemoproteomics analysis of natural products Addresses an important tool in small molecule drug discovery, appealing to both academia and the pharmaceutical industry Mass Spectrometry-Based Chemical Proteomics is an excellent source of information for readers in both academia and industry in a variety of fields, including pharmaceutical sciences, drug discovery, molecular biology, bioinformatics, and analytical sciences.
Author: Xiaofang Zhong (Ph.D.) Publisher: ISBN: Category : Languages : en Pages : 0
Book Description
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.
Author: Kazuhiro Imai Publisher: CRC Press ISBN: 9814316989 Category : Science Languages : en Pages : 304
Book Description
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. T
Author: Katrin Marcus Publisher: Humana Press ISBN: 9781617798863 Category : Science Languages : en Pages : 539
Book Description
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.
Author: Zihui Li
Author: Zihui Li
Author: Oscar Alzate
Author: John R. Griffiths
Author: Salvatore Sechi
Author: Claire E Eyers
Author: Bin Wang
Author: W. Andy Tao
Author: Xiaofang Zhong (Ph.D.)
Author: Kazuhiro Imai
Author: Katrin Marcus