Mass Spectrometry Applications for Comparative Proteomics and Peptidomic Discovery PDF Download

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Languages : en
Pages : 0

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In this thesis, multiple biological samples from various diseases models or treatments are investigated using shotgun proteomics and improved methods are developed to enable extended characterization and detection of neuropeptides. In general, this thesis aims to expand upon the rapidly evolving field of mass spectrometry (MS)-based proteomics and peptidomics by primarily enhancing small scale sample analysis. A review of the current status and progress in the field of biomarker discovery in peptidomics and proteomics is presented. To this rapidly expanding body of literature, our critical review offers new insights into MS-based biomarker studies investigating numerous biological samples, methods for post-translational modifications, quantitative proteomics, and biomarker validation. Methods are developed and presented, including immunodepletion for small volume cerebrospinal fluid (CSF) samples, for comparison of the CSF proteomes between an Alexander disease transgenic mouse model with overexpression of the glial fibrillary acidic protein and a control animal. This thesis also covers the application of the small scale immunodepletion of CSF for comparative proteomic analysis of a novel rat adapted scrapie (RAS) model for prion disease and compares the RAS CSF proteome to control rat CSF using MS. Large scale phosphoproteomics of starved vs. glucose fed yeast is presented to better understand the phosphoproteome changes that occur during glucose feeding. Method development for neuropeptide analysis is expanded upon using electron transfer dissociation (ETD) fragmentation to successfully sequence, for the first time, the crustacean hyperglycemic hormone precursor-related peptide (CPRP) from the blue crab Callinectes sapidus. In addition, a method for ETD sequencing of sulfonated neuropeptides using a magnesium salt adduct in an ion trap mass spectrometer is reported. This thesis also reports on a method for sub-ìg peptide isolation when using a molecular weight cut-off filtration device to improve sample recovery by over 2 orders of magnitude. All the protocols used throughout the work are provided in an easy to use step-by-step format in the Appendix. Collectively, this body of work extends the capabilities of mass spectrometry as a bioanalytical tool for shotgun proteomics and expands upon methods for neuropeptide discovery and analysis.

Author: Mikhail Soloviev
Publisher: John Wiley & Sons
ISBN: 0470196491
Category : Science
Languages : en
Pages : 432

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The definitive guide to peptidomics- a hands-on lab reference The first truly comprehensive book about peptidomics for protein and peptide analysis, this reference provides a detailed description of the hows and whys of peptidomics and how the techniques have evolved. With chapters contributed by leading experts, it covers naturally occurring peptides, peptidomics methods and new developments, and the peptidomics approach to biomarker discovery. Explaining both the principles and the applications, Peptidomics: Methods and Applications: * Features examples of applications in diverse fields, including pharmaceutical science, toxicity biomarkers, and neuroscience * Details the successful peptidomic analyses of biological material ranging from plants to mammals * Describes a cross section of analytical techniques, including traditional methodologies, emerging trends, and new techniques for high throughput approaches An enlightening reference for experienced professionals, this book is sufficiently detailed to serve as a step-by-step guide for beginning researchers and an excellent resource for students taking biotechnology and proteomics courses. It is an invaluable reference for protein chemists and biochemists, professionals and researchers in drug and biopharmaceutical development, analytical and bioanalytical chemists, toxicologists, and others.

Author: Michael L. Gross
Publisher: John Wiley & Sons
ISBN: 1118116542
Category : Medical
Languages : en
Pages : 484

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Book Description
The book that highlights mass spectrometry and its application in characterizing proteins and peptides in drug discovery An instrumental analytical method for quantifying the mass and characterization of various samples from small molecules to large proteins, mass spectrometry (MS) has become one of the most widely used techniques for studying proteins and peptides over the last decade. Bringing together the work of experts in academia and industry, Protein and Peptide Mass Spectrometry in Drug Discovery highlights current analytical approaches, industry practices, and modern strategies for the characterization of both peptides and proteins in drug discovery. Illustrating the critical role MS technology plays in characterizing target proteins and protein products, the methods used, ion mobility, and the use of microwave radiation to speed proteolysis, the book also covers important emerging applications for neuroproteomics and antigenic peptides. Placing an emphasis on the pharmaceutical industry, the book stresses practice and applications, presenting real-world examples covering the most recent advances in mass spectrometry, and providing an invaluable resource for pharmaceutical scientists in industry and academia, analytical and bioanalytical chemists, and researchers in protein science and proteomics.

Author: Gyorgy Marko-Varga
Publisher: Elsevier
ISBN: 044451810X
Category : Language Arts & Disciplines
Languages : en
Pages : 663

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Book Description
Proteomics and peptidomics is the detailed understanding of the role that proteins and peptides play in health and disease and is a necessary compliment to genetic analysis. The functional expression analysis of both proteins and peptides plays a central role in modern drug discovery as well as drug development, and is also a key research area in systems biology. Proteomics and Peptidomics captures the width as well as the depth within the area and exemplifies the variety as well as the traditional basis of analytical chemistry that is needed in order to move forward in expression analysis studies. As a fast emerging field, it gives and overview of parts within the field combined with highly specialized and dedicated topics that are intended to compliment each other.

Author: Michael Schrader
Publisher: Humana
ISBN: 9781493985142
Category : Science
Languages : en
Pages : 423

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Book Description
This volume describes protocols for basic state-of-the-art approaches in the field of peptidomics. Most of these approaches are independent of the instruments used for analysis and can easily be adapted for equipment that is available in a typical proteomics facility. Chapters detail many of the basic techniques used to detect and identify peptides, methods for the relative quantitation of peptides between samples using isotopic labels or label-free approaches, and biological species as well as sample types. Written in the highly successful format of the Methods in Molecular Biology series, each chapter includes an introduction to the topic, a list of the necessary materials and reagents, reproducible step-by-step laboratory protocols, and tips on troubleshooting common problems and avoiding pitfalls. Authoritative and practical, Peptidomics: Methods and Strategies provides useful guidance for studies in the rapidly growing field of peptidomics.

Author: Qing Yu
Publisher:
ISBN:
Category :
Languages : en
Pages : 0

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Liquid chromatography mass spectrometry (LC-MS) has evolved as a powerful tool in protein and peptide identification and quantitation. It has the capability to monitor thousands of proteins and peptides simultaneously and therefore is a critical component in the study of underlying biological mechanisms and the discovery of novel therapeutic targets. This dissertation is devoted to the development and application of novel LC-MS based techniques to characterize proteomics and peptidomics qualitatively and quantitatively by incorporating various sample preparation strategies, novel MS methods and isobaric labeling technology. A portion of this dissertation describes the design and evaluation of several dimethylated amino acid tags and their potentials to be used as isobaric labeling reagents for protein and peptide quantitation. Their utilities are further demonstrated through their application in the study of global proteomic changes in models of restenosis. Although isobaric tags are originally designed for higher-energy collisional dissociation (HCD), we expand their use by enabling them to be coupled with electron-transfer/higher-energy collision dissociation (EThcD) fragmentation. The benefits of using such strategy in quantitative proteomics, especially phosphorylation studies, are recounted in this dissertation. Quantitative strategies presented in this dissertation are complemented by advances in MS-based protein and endogenous peptide sequencing methodologies. We established a workflow to sequence intact glycopeptides, enabling detailed investigation of complex protein glycosylation and its microheterogeneity. The application of this improved workflow revealed a hyperglycosylation trend from day 0 to day 7 post angioplasty along the progression of restenosis. Similarly, by employing a further modified strategy, this dissertation documented the discovery of O-linked glycosylation on endogenous signaling peptides, specifically insulin and its related peptide hormones. The significance of such discovery can be critical toward diabetes research and treatment. Meanwhile, this dissertation also describes the strategy to characterize large neuropeptides in a species with no genome information, which can be greatly useful for future neuropeptide research. Furthermore, we employ ion mobility MS (IM-MS) to study peptide structures and conformations, leading to discovery of D-amino acid containing peptides based on subtle changes in gas-phase conformations despite identical mass-to-charge ratio. The IM-MS strategy enables the study of this unique isobaric post-translational modification (PTM) in neuropeptides occurring via amino acid isomerization. Overall, this dissertation research not only improves upon isobaric labeling technique by exploring novel chemical tags and new fragmentation methods, but also presents a useful platform to enable in-depth investigation on complex PTMs and subtle conformational differences. Collectively, we expect that the technology advancements presented in this work will enable broad applications in various biological systems and lead to improved understanding of underlying molecular mechanisms.

Author:
Publisher:
ISBN:
Category :
Languages : en
Pages : 498

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Advances in mass spectrometry (MS) technology have made MS-based proteomics a promising tool for protein profiling and biomarker discovery. However, MS analyses of biological samples are challenging due to their vast complexity and large dynamic range. Because disease identifying biomarkers are likely low abundance proteins, it is imperative to remove high abundance proteins or apply enrichment techniques during sample preparation to detect and improve coverage of low abundance proteins. In addition, the complexity of the digested biological samples can be reduced by applying multiple orthogonal separations prior to LC-MS/MS such as multidimensional protein identification technology (MudPIT). In this dissertation, the major objectives include the following: (1) method development of sample preparation and chromatographic separation for MS-based quantitative proteomics, and (2) their applications in large-scale protein characterization in complex biological samples for differential expression analysis and biomarker discovery will be discussed. First, MudPIT combined with ESI-MS/MS was optimized for global proteome profiling in naïve and interleukin-2 (IL-2)-activated natural killer cells to identify IL-2 regulated proteins that elucidate new pathways associated with IL-2 signaling. A similar strategy was also applied to the comparative secretome analysis in rat vascular smooth muscle cells (VSMCs) stimulated by transforming growth factor-beta; (TGF-beta), which led to the identification of secreted proteins that may be associated with TGF-beta; signaling in VSMCs. In a third project, lectin affinity chromatography (LAC) was utilized in sample preparation of mouse plasma affected by prion disease to specifically enrich glycoproteins that may prove to be important biomarkers for prion diseases. The combination of LAC and MudPIT significantly reduced sample complexity and led to the discovery of a panel of potential biomarkers including the validation of serum amyloid P-component (SAP). Furthermore, PNGase F digestion analysis confirmed that the glycosylated form of SAP could be used as a potential diagnostic biomarker for prion diseases. Collectively, the work included in this thesis extends the capability of mass spectrometry as a powerful analytical tool for large-scale proteomic analysis in complex biological samples to identify disease biomarkers or biomolecules involved in critical cellular processes.

Author: Gwenael Pottiez
Publisher: Springer
ISBN: 9783319130880
Category : Science
Languages : en
Pages : 71

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Book Description
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.

Author: Susan E. Slade
Publisher:
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Category :
Languages : en
Pages : 0

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Author: Leo M.L. Nollet
Publisher: CRC Press
ISBN: 0429537506
Category : Business & Economics
Languages : en
Pages : 193

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Book Description
Consumers have the right to know what is in the food they are eating, and accordingly, a number of global food regulations require that the provenance of the food can be guaranteed from farm to fork. Many different instrumental techniques have been proposed for food authentication. Although traditional methods are still being used, new approaches such as genomics, proteomics, and metabolomics are helping to complement existing methodologies for verifying the claims made about certain food products. During the last decade, proteomics (the largescale analysis of proteins in a particular biological system at a particular time) has been applied to different research areas within food technology. Since proteins can be used as markers for many properties of a food, even indicating processes to which the food has been subjected, they can provide further evidence of the foods labeling claim. Proteomics for Food Authentication, a volume in the Food Analysis and Properties Series, is a comprehensive and updated overview of the applications, drawbacks, advantages, and challenges of proteomics for food authentication. Features: Provides a comprehensive and critical overview of the application of proteomics in food Helps food scientists determine the authenticity of several food products Provides applied techniques for both laboratory and industrial environments Describes workflows, technologies, and tools that are being assessed in proteomics-related studies Workflows, technologies, and tools that are being assessed in proteomics-related studies are described, followed by a review of the specific applications regarding food authenticity and, now and then, food quality. The book will provide a comprehensive and critical overview of the application of proteomics approaches to determine the authenticity of several food products updating the performances and current limitations of the applied techniques in both laboratory and industrial environments. As such it is well suited to food scientist, chemical engineers, food engineers, research labs, universities, governments, related food industries. Also available in the Food Analysis and Properties Series: Food Aroma Evolution: During Food Processing, Cooking, and Aging, edited by Matteo Bordiga and Leo M.L. Nollet (ISBN: 9781138338241) Ambient Mass Spectroscopy Techniques in Food and the Environment, edited by Leo M.L. Nollet and Basil K. Munjanja (ISBN: 9781138505568) Hyperspectral Imaging Analysis and Applications for Food Quality, edited by N.C. Basantia, Leo M.L. Nollet, and Mohammed Kamruzzaman (ISBN: 9781138630796) For a complete list of books in this series, please visit our website at: www.crcpress.com/Food-Analysis--Properties/book-series/CRCFOODANPRO