Advancing Qualitative And Quantitative Proteomics Peptidomics Via Development Of Novel Mass Spectrometry Based Approaches

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Advancing Qualitative and Quantitative Proteomics/peptidomics Via Development of Novel Mass Spectrometry-based Approaches

Author : Qing Yu
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (17 download)

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Book Synopsis Advancing Qualitative and Quantitative Proteomics/peptidomics Via Development of Novel Mass Spectrometry-based Approaches by : Qing Yu

Download or read book Advancing Qualitative and Quantitative Proteomics/peptidomics Via Development of Novel Mass Spectrometry-based Approaches written by Qing Yu and published by . This book was released on 2017 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Computational and Statistical Methods for Protein Quantification by Mass Spectrometry

Author : Ingvar Eidhammer
Publisher : John Wiley & Sons
ISBN 13 : 111849377X
Total Pages : 290 pages
Book Rating : 4.1/5 (184 download)

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Book Synopsis Computational and Statistical Methods for Protein Quantification by Mass Spectrometry by : Ingvar Eidhammer

Download or read book Computational and Statistical Methods for Protein Quantification by Mass Spectrometry written by Ingvar Eidhammer and published by John Wiley & Sons. This book was released on 2012-12-10 with total page 290 pages. Available in PDF, EPUB and Kindle. Book excerpt: The definitive introduction to data analysis in quantitative proteomics This book provides all the necessary knowledge about mass spectrometry based proteomics methods and computational and statistical approaches to pursue the planning, design and analysis of quantitative proteomics experiments. The author’s carefully constructed approach allows readers to easily make the transition into the field of quantitative proteomics. Through detailed descriptions of wet-lab methods, computational approaches and statistical tools, this book covers the full scope of a quantitative experiment, allowing readers to acquire new knowledge as well as acting as a useful reference work for more advanced readers. Computational and Statistical Methods for Protein Quantification by Mass Spectrometry: Introduces the use of mass spectrometry in protein quantification and how the bioinformatics challenges in this field can be solved using statistical methods and various software programs. Is illustrated by a large number of figures and examples as well as numerous exercises. Provides both clear and rigorous descriptions of methods and approaches. Is thoroughly indexed and cross-referenced, combining the strengths of a text book with the utility of a reference work. Features detailed discussions of both wet-lab approaches and statistical and computational methods. With clear and thorough descriptions of the various methods and approaches, this book is accessible to biologists, informaticians, and statisticians alike and is aimed at readers across the academic spectrum, from advanced undergraduate students to post doctorates entering the field.

Mass Spectrometry-Based Chemical Proteomics

Author : W. Andy Tao
Publisher : John Wiley & Sons
ISBN 13 : 1118970217
Total Pages : 448 pages
Book Rating : 4.1/5 (189 download)

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Book Synopsis Mass Spectrometry-Based Chemical Proteomics by : W. Andy Tao

Download or read book Mass Spectrometry-Based Chemical Proteomics written by W. Andy Tao and published by John Wiley & Sons. This book was released on 2019-07-10 with total page 448 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Mass Spectrometry-based Approaches for Targeted Quantitative Proteomics in Biomarker Development

Author : Mary Joan Castillo
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (942 download)

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Book Synopsis Mass Spectrometry-based Approaches for Targeted Quantitative Proteomics in Biomarker Development by : Mary Joan Castillo

Download or read book Mass Spectrometry-based Approaches for Targeted Quantitative Proteomics in Biomarker Development written by Mary Joan Castillo and published by . This book was released on 2015 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Quantitative Proteomics

Author : Claire E Eyers
Publisher : Royal Society of Chemistry
ISBN 13 : 1782621091
Total Pages : 391 pages
Book Rating : 4.7/5 (826 download)

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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.

Advancing Bottom-up Proteomics and Ptm Characterization Via Development of Novel Mass Spectrometry-based Approaches

Author : Fengfei Ma (Ph.D.)
Publisher :
ISBN 13 :
Total Pages : 335 pages
Book Rating : 4.:/5 (131 download)

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Book Synopsis Advancing Bottom-up Proteomics and Ptm Characterization Via Development of Novel Mass Spectrometry-based Approaches by : Fengfei Ma (Ph.D.)

Download or read book Advancing Bottom-up Proteomics and Ptm Characterization Via Development of Novel Mass Spectrometry-based Approaches written by Fengfei Ma (Ph.D.) and published by . This book was released on 2018 with total page 335 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mass spectrometry (MS) has emerged as a central technology for biomedical research largely due to its capability to provide unprecedented insights into the compositions and structures of the proteome. Thousands of proteins and peptides can be characterized in a single experiment, shedding lights on the complex biological processes and enabling discovery of novel therapeutic targets. This dissertation is devoted to the development of novel liquid chromatography (LC)-MS based techniques to characterize proteins and decipher post-translational modifications (PTMs) qualitatively and quantitatively. Specifically, novel sample preparation strategy has been developed for improved sample recovery and unbiased extraction of different categories of proteins. State-of-the-art hybrid fragmentation methods have been established for large scale differentiation of 3- and 4- hydroxyproline isomers. Furthermore, an integrated pipeline for in-depth investigation of protein glycosylation has been developed and implemented. These innovative analytical methodologies have been successfully demonstrated and applied to comprehensive characterization of biological scaffolds and breast cancer cells, which provide valuable insights into multiple research areas including tissue engineering and cancer biology.

Proteomics for Biological Discovery

Author : Timothy D. Veenstra
Publisher : John Wiley & Sons
ISBN 13 : 1119081696
Total Pages : 348 pages
Book Rating : 4.1/5 (19 download)

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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 2019-04-26 with total page 348 pages. Available in PDF, EPUB and Kindle. Book excerpt: An update to the popular guide to proteomics technology applications in biomedical research Building on the strength of the original edition, this book presents the state of the art in the field of proteomics and offers students and scientists new tools and techniques to advance their own research. Written by leading experts in the field, it provides readers with an understanding of new and emerging directions for proteomics research and applications. Proteomics for Biological Discovery begins by discussing the emergence of proteomics technologies and summarizing the potential insights to be gained from proteome-level research. The tools of proteomics, from conventional to novel techniques, are thoroughly covered, from underlying concepts to limitations and future directions. Later chapters provide an overview of the current developments in post-translational modification studies, structural proteomics, biochemical proteomics, applied proteomics, and bioinformatics relevant to proteomics. Chapters cover: Quantitative Proteomics for Differential Protein Expression Profiling; Protein Microarrays; Protein Biomarker Discovery; Biomarker Discovery using Mass Spectrometry Imaging; Protein-Protein Interactions; Mass Spectrometry Of Intact Protein Complexes; Crosslinking Applications in Structural Proteomics; Functional Proteomics; High Resolution Interrogation of Biological Systems via Mass Cytometry; Characterization of Drug-Protein Interactions by Chemoproteomics; Phosphorylation; Large-Scale Phosphoproteomics; and Probing Glycoforms of Individual Proteins Using Antibody-Lectin Sandwich Arrays. Presents a comprehensive and coherent review of the major issues in proteomic 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 Features new coverage of mass spectrometry for high throughput proteomic measurements, and novel quantitation strategies such as spectral counting and stable isotope labeling Discusses higher level integrative aspects, including technical challenges and applications for drug discovery Offers new chapters on biomarker discovery, global phosphorylation analysis, proteomic profiling using antibodies, and single cell mass spectrometry Proteomics for Biological Discovery is an excellent advanced resource for graduate students, postdoctoral fellows, and scientists across all the major fields of biomedical science.

Quantitative Proteomics by Mass Spectrometry

Author : Salvatore Sechi
Publisher : Springer Science & Business Media
ISBN 13 : 1597452556
Total Pages : 223 pages
Book Rating : 4.5/5 (974 download)

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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 Springer Science & Business Media. This book was released on 2008-02-05 with total page 223 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Protein Analysis using Mass Spectrometry

Author : Mike S. Lee
Publisher : John Wiley & Sons
ISBN 13 : 1119359368
Total Pages : 282 pages
Book Rating : 4.1/5 (193 download)

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Book Synopsis Protein Analysis using Mass Spectrometry by : Mike S. Lee

Download or read book Protein Analysis using Mass Spectrometry written by Mike S. Lee and published by John Wiley & Sons. This book was released on 2017-05-26 with total page 282 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presents Practical Applications of Mass Spectrometry for Protein Analysis and Covers Their Impact on Accelerating Drug Discovery and Development Covers both qualitative and quantitative aspects of Mass Spectrometry protein analysis in drug discovery Principles, Instrumentation, Technologies topics include MS of peptides, proteins, and ADCs , instrumentation in protein analysis, nanospray technology in MS protein analysis, and automation in MS protein analysis Details emerging areas from drug monitoring to patient care such as Identification and validation of biomarkers for cancer, targeted MS approaches for biomarker validation, biomarker discovery, and regulatory perspectives Brings together the most current advances in the mass spectrometry technology and related method in protein analysis

Mass Spectrometry–Based Glycoproteomics and Its Clinic Application

Author : Haojie Lu
Publisher : CRC Press
ISBN 13 : 1000406601
Total Pages : 258 pages
Book Rating : 4.0/5 (4 download)

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Book Synopsis Mass Spectrometry–Based Glycoproteomics and Its Clinic Application by : Haojie Lu

Download or read book Mass Spectrometry–Based Glycoproteomics and Its Clinic Application written by Haojie Lu and published by CRC Press. This book was released on 2021-09-21 with total page 258 pages. Available in PDF, EPUB and Kindle. Book excerpt: As one of the most extensive and important protein post-translational modifications, glycosylation plays a vital role in regulating organisms and is associated with various physiological and pathological processes. Recently, researchers have focused on the need to characterize protein glycosylation sites, structures, and their degree of modification, to better understand their biological functions while also looking for potential biomarkers for diagnosis and treatment of disease. Mass spectrometry (MS) is one of the most powerful tools used to study biomolecules including glycoproteins and glycans. With the continuous development of glycoproteomics and glycomics based on MS analysis, more techniques have evolved and contribute to understanding the structure and function of glycoproteins and glycans. This book reviews advancements achieved in MS-based glycoproteomic analysis, including a wide range of analytical methodologies and strategies involved in selective enrichment; as well as qualitative, quantitative, and data analysis, together with their clinical applications. Significant examples are discussed to illustrate the principles, laboratory protocols, and advice for key implementation to ensure successful results. Mass Spectrometry–Based Glycoproteomics and Its Clinic Application will serve as a valuable resource to elucidate new techniques and their applications for students, postdocs, and researchers working in proteomics, glycoscience, analytical chemistry, biochemistry, and clinical medicine. Editor: Haojie Lu is a professor at Fudan University, specializing in proteomics based on mass spectrometry with particular emphasis on novel technologies for separation and identification of low-abundant proteins and post-translationally modified proteins (including glycosylation), as well as relative and absolute quantification methods for proteomics.

Advancing Mass Spectrometry-based Discovery and Targeted Approaches for Disease Proteomic and Ptm Analyses

Author : Xiaofang Zhong (Ph.D.)
Publisher :
ISBN 13 :
Total Pages : 239 pages
Book Rating : 4.:/5 (131 download)

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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.

The Development of Novel MALDI and Nanoelectrospray Mass Spectrometry Methods for the Improved Analysis of Proteins and Peptides

Author :
Publisher :
ISBN 13 :
Total Pages : 233 pages
Book Rating : 4.:/5 (623 download)

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Book Synopsis The Development of Novel MALDI and Nanoelectrospray Mass Spectrometry Methods for the Improved Analysis of Proteins and Peptides by :

Download or read book The Development of Novel MALDI and Nanoelectrospray Mass Spectrometry Methods for the Improved Analysis of Proteins and Peptides written by and published by . This book was released on 2005 with total page 233 pages. Available in PDF, EPUB and Kindle. Book excerpt: The development of matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) gave rise to the era of biological mass spectrometry and the new field of proteomics. Two recurring problems that are central to advancing the science of proteomics are the development of reliable mass spectrometry methods to identify proteins and to sequence peptides. The specificity of proteases such as trypsin in combination with the high mass accuracy provided by reflectron time-of-flight mass analyzers, allows the reliable identification of a protein from the mass spectrum of its proteolytic digestion products in an experiment known as peptide mass fingerprinting. Some powerful approaches to improve the confidence of the identification of proteins in the peptide mass fingerprinting experiment have been described in this dissertation. Both approaches described in this dissertation involve the optimization of different aspects of the sample preparation step in the MALDI-TOF mass spectrometry experiment. Precursor-ion scanning in the negative ion mode followed by sequencing in the positive ion mode is a powerful strategy employed to identify and sequence phosphopeptides via nanoelectrospray triple quadrupole mass spectrometry. Less sample and time would be consumed if both of the aforementioned steps could be carried out in the negative ion mode. Nanoelectrospray tandem mass spectrometry in the negative ion mode is usually not successful as traditional gold-coated emitters undergo electrical discharge. Using polyaniline-coated emitters, we have demonstrated that peptides can be sequenced successfully in the negative-ion mode enabling the observation of a wealth of information that is not available in the corresponding positive-ion mode experiment.

Advancing Mass Spectrometry Methods for Quantification and Characterization of Peptides and Proteins in Complex Biological Samples

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Author :
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (939 download)

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Book Synopsis Advancing Mass Spectrometry Methods for Quantification and Characterization of Peptides and Proteins in Complex Biological Samples by :

Download or read book Advancing Mass Spectrometry Methods for Quantification and Characterization of Peptides and Proteins in Complex Biological Samples written by and published by . This book was released on 2015 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein quantification using liquid chromatography mass spectrometry (LC-MS) is a critical component in the discovery and verification of protein candidate biomarkers. Label-free and label-based quantitative methods are both commonly employed, and both have advantages and disadvantages. Label-based methods are capable of analyzing relative protein abundances from multiple samples in one LC-MS experiment, thus enabling high throughput analysis. Unfortunately, the high cost of commercial labels prevents many groups from including them in their proteomics workflows. Our group previously developed a cost-effective isobaric label set, DiLeu, through dimethylation of L-leucine isotopes. The DiLeu reagent performed comparably to commercial options, but multiple improvements and variations to this reagent were needed. For example, the multiplexing capacity of the original DiLeu reagent only permits four quantitative channels, necessitating development of a new label with greater throughput. A portion of this thesis is dedicated to the design, synthesis, and characterization of a new 8-plex DiLeu reagent. This dissertation also recounts the development of isotopic DiLeu (iDiLeu), a 5-plex mass difference variant of DiLeu that allows for researchers to quantify analyte peptide concentrations from a four-point calibration curve in one LC-MS run. One glaring omission in the development of noncommercial isobaric labels is that no protein candidate biomarkers have been discovered by them. Our work rectifies this oversight by identifying several potential biomarkers using custom-synthesized 4-plex DiLeu isobaric tags from the urine of men diagnosed with lower urinary tract symptoms (LUTS). Quantitative strategies presented in this dissertation are complemented by advances in our neuropeptidomics methodologies. In one project, we study the role of protein degradation in crustacean neuropeptidomics and apply a heat stabilization strategy to mitigate the number of protein fragments that interfere with neuropeptide identification. The final project investigates an alternative method to matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) in crab neuropeptide and lipid imaging. This technique, nanostructure initiator mass spectrometry (NIMS), was unable to ionize neuropeptides in C. borealis brain tissue despite its capability to ionize lipids, showing that sometimes traditional methods like MALDI MSI remain advantageous over more recent but less vetted techniques. The future outlook for our LUTS collaboration and quantitative tag projects is positive because of the new directions still being explored. Overall, the new quantitative techniques developed in this dissertation and the advances in neuropeptide identification will benefit research groups interested in cost-effective label-based quantification methods and neuropeptide characterization in LC-MS and MSI studies.

Advancing Quantitative Proteomics and Protein Post-translational Modification Analyses by Multi-dimensional Mass Spectrometric Approaches

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Author : Zihui Li
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (13 download)

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Book Synopsis Advancing Quantitative Proteomics and Protein Post-translational Modification Analyses by Multi-dimensional Mass Spectrometric Approaches by : Zihui Li

Download or read book Advancing Quantitative Proteomics and Protein Post-translational Modification Analyses by Multi-dimensional Mass Spectrometric Approaches written by Zihui Li and published by . This book was released on 2021 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Quantitative Methods in Proteomics

Author : Katrin Marcus
Publisher :
ISBN 13 : 9781071610244
Total Pages : 483 pages
Book Rating : 4.6/5 (12 download)

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Book Synopsis Quantitative Methods in Proteomics by : Katrin Marcus

Download or read book Quantitative Methods in Proteomics written by Katrin Marcus and published by . This book was released on 2021 with total page 483 pages. Available in PDF, EPUB and Kindle. Book excerpt: This second edition provides new and updated methods on the principles underlying modern protein analysis, from statistical issues to gel-based and mass spectrometry-based applications. Chapters detail protein quantification as basis for realisation of quantitative studies, gel-based and mass spectrometry-based quantification techniques, TMT, IPTL, PRM, MALDI Imaging, SILAC, PTM analysis, DIA, cross-linking, and the up-to-date topics of software and data analysis. 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, Quantitative Methods in Proteomics, Second Edition aims to provide comprehensive and competent overview in the important and still growing field of quantitative proteomics.

Advances in Chemical Proteomics

Author : Xudong Yao
Publisher : Elsevier
ISBN 13 : 012821435X
Total Pages : 270 pages
Book Rating : 4.1/5 (282 download)

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Book Synopsis Advances in Chemical Proteomics by : Xudong Yao

Download or read book Advances in Chemical Proteomics written by Xudong Yao and published by Elsevier. This book was released on 2021-10-22 with total page 270 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advances in Chemical Proteomics provides essential concepts and recent applications on probes, tool compounds and concepts for chemical proteomics and then moves on to applications, including solid-phase reagents, fragment screening, designer compounds and protein lipidation. As the second volume in the Developments in Organic Chemistry series, each chapter is written by experts in the field. Users will find this to be a valuable reference for organic chemists and chemical biologists who are interested in developing tool compounds and reagents to measure and interrogate proteome, develop drug leads, and measure off-target effects and drug toxicity. Analytical chemists who are interested in better understanding organic chemistry behind commonly used reagents for quantitative proteomics and tools compounds in the emerging field of chemical proteomics will also benefit from this comprehensive resource on the topics presented. Provides an ideal, introductory book to chemical proteomics for organic chemists, pharmaceutical chemists and chemical biologists Includes advanced, recent applications and reviews in chemical proteomics Presents valuable work by a global team of experts from the field of proteomics

Introducing Proteomics

Author : Josip Lovric
Publisher : John Wiley & Sons
ISBN 13 : 1119957192
Total Pages : 310 pages
Book Rating : 4.1/5 (199 download)

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Book Synopsis Introducing Proteomics by : Josip Lovric

Download or read book Introducing Proteomics written by Josip Lovric and published by John Wiley & Sons. This book was released on 2011-06-17 with total page 310 pages. Available in PDF, EPUB and Kindle. Book excerpt: Introducing Proteomics gives a concise and coherent overview of every aspect of current proteomics technology, which is a rapidly developing field that is having a major impact within the life and medical sciences. This student-friendly book, based on a successful course developed by the author, provides its readers with sufficient theoretical background to be able to plan, prepare, and analyze a proteomics study. The text covers the following: Separation Technologies Analysis of Peptides/Proteins by Mass Spectrometry Strategies in Proteomics This contemporary text also includes numerous examples and explanations for why particular strategies are better than others for certain applications. In addition, Introducing Proteomics includes extensive references and a list of relevant proteomics information sources; essential for any student. This no-nonsense approach to the subject tells students exactly what they need to know, leaving out unnecessary information. The student companion site enhances learning and provides answers to the end of chapter problems. "I think this book will be a popular and valuable resource for students and newcomers to the field who would like to have an overview and initial understanding of what proteomics is about. The contents are well organized and address the major issues." —Professor Walter Kolch, Director, Systems Biology Ireland & Conway Institute, University College Dublin Companion Website www.wiley.com/go/lovric