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Advancing Electron Transfer Dissociation Technologies For Characterization Of Proteomes And Post Translational Modifications
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Book Synopsis Advancing Electron Transfer Dissociation Technologies for Characterization of Proteomes and Post-translational Modifications by : Nicholas M. Riley
Download or read book Advancing Electron Transfer Dissociation Technologies for Characterization of Proteomes and Post-translational Modifications written by Nicholas M. Riley and published by . This book was released on 2018 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This dissertation presents research focusing on the development of new instrumentation and methodology to leverage ion-ion reactions for proteomic analyses. Electron transfer dissociation (ETD) technologies have proven a valuable alternative to collision-based fragmentation methods for sequencing peptides and proteins to advance global proteome characterization. Chapter 1 outlines the core concepts central to mass spectrometry (MS)-based proteomics, in addition to the basic principles of ETD and various strategies to improve its efficacy - including the technology that is the focus of this work, i.e., activated ion ETD (AI-ETD). Chapter 2 describes the first application of AI-ETD to intact proteins, which are more chemically complex and, thus, more difficult to sequence, than their peptide counterparts. Chapter 3 discusses a new strategy to improve signalto- noise in ETD spectra, which is especially beneficial for intact protein analysis and which has been incorporated into the newest generation of commercially available quadrupole-Orbitrap-linear ion trap hybrid MS systems. AI-ETD capabilities were also recently implemented on this stateof- the-art MS system (Chapter 4), and the ability to perform AI-ETD on this instrument enables comprehensive sequence coverage of moderately-sized intact proteins (Chapter 5), significantly improves proteoform characterization in large-scale analyses of complex mixtures of intact proteins (Chapter 6), and also enhances characterization of larger intact proteins (Chapter 7). Furthermore, AI-ETD improves characterization of post-translational modifications. Chapter 8 demonstrates the utility of AI-ETD for phosphosite localization in phosphopeptides and intact phosphoproteins, and Chapter 9 presents the largest glycoproteomic study to date by using AI-ETD to interrogate intact N-glycopeptides. Beyond positive-mode analyses of peptide and protein cations, ion-ion reactions also bring unique benefits to negative-mode analyses of precursor anions, where collision-based dissociation fails to consistently produce sequence-informative fragments. Chapter 10 describes implementation of negative ETD (NETD) and activated ion NETD (AI-NETD) and their application to whole-proteome sequencing in the negative mode, and Chapter 11 presents a modified search algorithm to improve interpretation of large-scale NETD and AI-NETD data. Conclusions and future directions of these projects are discussed in Chapter 12.
Book Synopsis Advancing Tandem Mass Spectrometry for Characterization of Complex Biopolymers by : Trenton M. Peters-Clarke
Download or read book Advancing Tandem Mass Spectrometry for Characterization of Complex Biopolymers written by Trenton M. Peters-Clarke and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This dissertation details innovations in mass spectrometry-based instrumentation that expand our ability to survey biopolymers, including proteins, peptides, and oligonucleotides, with increased sensitivity, speed, and depth. Chapter 1 provides an overview of mass spectrometry instrumentation at the leading edge of proteomics and for nucleic acid analysis. In Chapter 2, the optical-fiber enabled coupling of a mass spectrometer to an infrared laser improves proteomic characterization. For Chapter 3, electron transfer dissociation-based proteomics is investigated and inefficiencies of related ion-ion reactions are characterized. Chapter 4 introduces a novel nucleic acid sequencing technology with activated ion-negative electron transfer dissociation to profile RNA molecules and their modifications. In Chapter 5, tandem mass spectrometry comprehensively characterizes heavily-modified RNA therapeutics. Chapter 6 focuses on a proteome-wide analysis of the bacterial post-translational modification O-mycoloylation. In Chapter 7, a novel tandem mass spectrometry strategy, termed activated ion-tandem mass tags, is revealed, boosting quantitative reporter ion generation. Chapter 8 expands upon AI-TMT for quantitative single-cell proteomics, realizing sensitivity gains which drive a greater dynamic range of quantification. In Chapter 9, a novel mass spectrometer enables the one hour human proteome and we explore one minute proteome analyses, pushing the limits of high-throughput proteome analysis. Chapter 10 discusses emergent proteomic techniques and suggests future directions of the field.
Book Synopsis Top Down Characterization of Proteins by Electron Capture Dissociation and Blackbody Infrared Radiative Dissociation Mass Spectrometry by : Ying Ge
Download or read book Top Down Characterization of Proteins by Electron Capture Dissociation and Blackbody Infrared Radiative Dissociation Mass Spectrometry written by Ying Ge and published by . This book was released on 2002 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Analysis of Protein Post-Translational Modifications by Mass Spectrometry by : John R. Griffiths
Download or read book Analysis of Protein Post-Translational Modifications by Mass Spectrometry written by John R. Griffiths and published by John Wiley & Sons. This book was released on 2016-11-07 with total page 414 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Book Synopsis Spectroscopy and Modeling of Biomolecular Building Blocks by : Jean-Pierre Schermann
Download or read book Spectroscopy and Modeling of Biomolecular Building Blocks written by Jean-Pierre Schermann and published by Elsevier. This book was released on 2007-10-16 with total page 499 pages. Available in PDF, EPUB and Kindle. Book excerpt: Spectroscopy and Modeling of Biomolecular Building Blocks presents an overview of recent advances in the intertwining of the following research fields: photon and electron spectroscopy, quantum chemistry, modelling and mass-spectrometry. The coupling of these disciplines offers a new point of view to the understanding of isolated elementary building blocks of biomolecules and their assemblies. It allows the unambiguous separation between intrinsic properties of biomolecular systems and those induced by the presence of their environment. The first chapters provide background in modelling (I), frequency-resolved spectroscopy using microwave, infrared and UV photons, time-resolved spectroscopy in the femtosecond domain and energy-resolved electron spectroscopy (II) and production of gas-phase neutral and ionic biomolecular species, mass-spectrometry, ion mobility and BIRD techniques (III). Chapter IV is devoted to case studies of gas-phase experimental investigations coupled to quantum or classical calculations. The topics are structural studies of nucleobases and oligonucleotides, peptides and proteins, sugars; neuromolecules; non-covalent complexes; chiral systems, interactions of low-energy electrons with biomolecules in the radiation chemistry context and very large gas-phase biomolecular systems. The fifth chapter concerns the link between gas-phase and liquid-phase. Different treatments of solvation are illustrated through examples pointing out the influence of progressive addition of water molecules upon properties of nucleobases, peptides, sugars and neuromolecules. Offer a new perspective to the understanding of isolated elementary building blocks of bio molecules Includes case studies of experimental investigations coupled to quantum or classical calculations
Book Synopsis Proteome Informatics by : Conrad Bessant
Download or read book Proteome Informatics written by Conrad Bessant and published by Royal Society of Chemistry. This book was released on 2016-11-15 with total page 429 pages. Available in PDF, EPUB and Kindle. Book excerpt: The field of proteomics has developed rapidly over the past decade nurturing the need for a detailed introduction to the various informatics topics that underpin the main liquid chromatography tandem mass spectrometry (LC-MS/MS) protocols used for protein identification and quantitation. Proteins are a key component of any biological system, and monitoring proteins using LC-MS/MS proteomics is becoming commonplace in a wide range of biological research areas. However, many researchers treat proteomics software tools as a black box, drawing conclusions from the output of such tools without considering the nuances and limitations of the algorithms on which such software is based. This book seeks to address this situation by bringing together world experts to provide clear explanations of the key algorithms, workflows and analysis frameworks, so that users of proteomics data can be confident that they are using appropriate tools in suitable ways.
Book Synopsis Biomarker Discovery in the Developing World: Dissecting the Pipeline for Meeting the Challenges by : Sanjeeva Srivastava
Download or read book Biomarker Discovery in the Developing World: Dissecting the Pipeline for Meeting the Challenges written by Sanjeeva Srivastava and published by Springer. This book was released on 2016-09-30 with total page 120 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is oriented towards post-graduates and researchers with interest in proteomics and its applications in clinical biomarker discovery pipeline. Biomarker discovery has long been the research focus of many life scientists globally. However, the pipeline starting from discovery to validation to regulation as a diagnostic or therapeutic molecule follows a complex trajectory. This book aims to provide an in-depth synopsis on each of these developmental phases attendant to biomarker “life cycle” with emphasis on the emerging and significant role of proteomics. The book begins with a perspective on the role of biorepositories and need for biobanking practices in the developing world. The next chapter focuses on disease heterogeneity in context to geographical bias towards susceptibility to the disease and the role of multi-omics techniques to devise disruptive innovations towards biomarker discovery. Chapter 3 focuses on various omics-based platforms that are currently being used for biomarker discovery, their principles and workflow. Mass spectrometry is emerging as a powerful technology for discovery based studies and targeted validation. Chapter 4 aims at providing a glimpse of the basic workflow and considerations in mass spectrometry based studies. Rapid and aptly targeted research funding has often been deemed as one of the decisive factors enabling excellent science and path breaking innovations. With the need for sophistication required in multi-omics research, Chapter 5 focuses on innovative funding strategies such as crowdfunding and Angel philanthropy. Chapter 6 provides the latest advances in education innovation, the premise and reality of bioeconomy especially in a specific context of the developing world, not to mention the new concept of “social innovation” to link biomarkers with socially responsible and sustainable applications. Chapter 7, in ways similar to biomarkers, discusses the biosimilars as a field that has received much focus and prominence recently due to their immense potential in clinical and pharmaceutical innovation literatures. The broader goal post-biomarker discovery is to translate their use in clinics. However, the road from bench-to-bed side is arduous and complex that is subject to oversight from various national and international regulatory bodies. Chapter 8 underscores these regulatory science considerations and provides a concise overview on intellectual property rights in biomarker discovery. Thus, this book contributed by eminent biomarker scientists, clinicians, translational researchers and social scientists holistically covers the various facets of the biomarker discovery journey from “cell to society” in developing world. The lessons learned and highlighted here are of interest to the life sciences community in a global and interdependent world.
Book Synopsis Development and Application of Novel Electron Transfer Dissociation-based Technologies for Proteomics by : C. K. Frese
Download or read book Development and Application of Novel Electron Transfer Dissociation-based Technologies for Proteomics written by C. K. Frese and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Deamidation and Related Problems in Structural Analysis of Peptides and Proteins by : Nadezda Sargaeva
Download or read book Deamidation and Related Problems in Structural Analysis of Peptides and Proteins written by Nadezda Sargaeva and published by . This book was released on 2012 with total page 354 pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract: Electron capture dissociation (ECD) and electron transfer dissociation (ETD) can generate unique fragments and preserve post-translational modifications (PTMs), enabling their detection in biological samples. They have been used to differentiate isomeric aspartic (Asp) and isoaspartic acids (isoAsp) produced upon non-enzymatic deamidation of asparagine (Asn) -- a frequently occurring PTM. IsoAsp formation was detected in amyloid-B (AB) peptides in the specimens of Alzheimer's disease (AD) patients, and is a potential biomarker for AD if it can be detected early in biofluids of live individuals. Synthetic isoAsp-containing AB fragments were studied using ECD to test the method's applicability. IsoAsp-7 and -23 were detected in top-down analysis of the 4.5kDa AB42 protein and in AB17-28 peptide. Further, a related method, electron ionization/impact dissociation (EID), was successfully applied to Asp/isoAsp differentiation for the first time. High-performance liquid chromatography (HPLC) is a powerful technique for the separation of complex mixtures. HPLC separation of Asp- and isoAsp-containing peptides revealed inconsistent elution orders, especially when isoAsp was located at the N-terminus, requiring ECD for identification. New diagnostic fragments were proposed for N-terminal isoAsp based on the ECD and ETD results. Challenges in detection of such fragments were improved by supplemental activation and chemical modifications. Furthermore, a model for retention time prediction was applied to isoAsp-containing peptides and suggested for their improved identification in HPLC-MS/MS approach. IsoAsp is a B-amino acid, which distinctively contains an additional methylene group in the backbone, forming a C a -CB bond. Cleavage of this bond provides diagnostic fragments for isoAsp by ECD. The same was proposed for other B-amino acids. However, the Ca -CB ; bond cleavages were rare due to the instability of the CB radical. Alternatively, in-source decay (ISD) fragmentation during matrix-assisted laser desorption/ionization (MALDI) process can produce abundant ECD-like fragmentation. It was proposed that use of hydrogen-accepting matrices may lead to Ca -CB bond cleavage in B-amino acids, because the resulting radical would be stabilized by the carbonyl group. To test this, B-amino acid-containing peptides were analyzed by MALDI-ISD using 5-nitrosalicylic acid matrix. The Ca -CB bond cleavages were observed. Overall, new and improved methods were implemented allowing better characterization and differentiation of B-amino acids.
Download or read book Proteoforms written by Xianquan Zhan and published by BoD – Books on Demand. This book was released on 2020-07-15 with total page 92 pages. Available in PDF, EPUB and Kindle. Book excerpt: A proteoform is the basic unit in a proteome, defined as its amino acid sequence + post-translational modifications + spatial conformation + localization + cofactors + binding partners + a function, which is the final functional performer of a gene. Studies on proteoforms offer in-depth insights and can lead to the discovery of reliable biomarkers and therapeutic targets for effective prediction, diagnosis, prognostic assessment, and therapy of disease. This book focuses on the concept, study, and applications of proteoforms. Chapters cover such topics as methodologies for identifying and preparing proteoforms, proteoform pattern alteration in pituitary adenomas, and proteoforms in leukemia.
Book Synopsis Post-translational Modifications That Modulate Enzyme Activity by :
Download or read book Post-translational Modifications That Modulate Enzyme Activity written by and published by Academic Press. This book was released on 2019-10-12 with total page 648 pages. Available in PDF, EPUB and Kindle. Book excerpt: Post-translational Modifications That Modulate Enzyme Activity, Volume 626 in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. Updated chapters include Crosstalk between cellular metabolism and histone acetylation, Isolation of protein complexes and modifications that regulate transcriptional machinery, High-throughput phosphoproteome mapping through multiplexed mass spectrometry, Differentiation of D and L epimerization in proteins, Biochemical analysis of protein arginylation, Site-specific Determination of lysine acetylation stoichiometries on the proteome-scale, Genomic and biochemical analysis of RNA post-transcriptional modifications, Isolation and characterization of glycosylated (neuro)peptides, and more. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Methods in Enzymology series Includes the latest information on Post-translational Modifications that Modulate Enzyme Activity
Book Synopsis Applications of Nanomaterials in Proteomics by : Nianrong Sun
Download or read book Applications of Nanomaterials in Proteomics written by Nianrong Sun and published by Springer Nature. This book was released on 2021-09-28 with total page 431 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a comprehensive and systematic overview of the latest advances in nanomaterials for proteomics, both theoretical and practical. Consisting of seven chapters, it first covers the synthesis methods, characterization, principles, and performance of functional nanomaterials in various branches of proteomics in detail. This is followed by the applications of nanomaterials for the separation and analysis of various proteins and peptides. Given its scope, the book appeals to a broad readership, including those active in proteomics and materials science; it can also serve as a reference book for students majoring in proteomics analysis.
Book Synopsis Multi-Omics Technologies for Optimizing Synthetic Biomanufacturing by : Young-Mo Kim
Download or read book Multi-Omics Technologies for Optimizing Synthetic Biomanufacturing written by Young-Mo Kim and published by Frontiers Media SA. This book was released on 2022-01-31 with total page 165 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis International Plant Proteomics Organization (INPPO) World Congress 2014 by : Joshua L. Heazlewood
Download or read book International Plant Proteomics Organization (INPPO) World Congress 2014 written by Joshua L. Heazlewood and published by Frontiers Media SA. This book was released on 2017-02-08 with total page 409 pages. Available in PDF, EPUB and Kindle. Book excerpt: The field of proteomics has advanced considerably over the past two decades. The ability to delve deeper into an organism’s proteome, identify an array of post-translational modifications and profile differentially abundant proteins has greatly expanded the utilization of proteomics. Improvements to instrumentation in conjunction with the development of these reproducible workflows have driven the adoption and application of this technology by a wider research community. However, the full potential of proteomics is far from being fully exploited in plant biology and its translational application needs to be further developed. In 2011, a group of plant proteomic researchers established the International Plant Proteomics Organization (INPPO) to advance the utilization of this technology in plants as well as to create a way for plant proteomics researchers to interact, collaborate and exchange ideas. The INPPO conducted its inaugural world congress in mid 2014 at the University of Hamburg (Germany). Plant proteomic researchers from around the world were in attendance and the event marked the maturation of this research community. The Research Topic captures the opinions, ideas and research discussed at the congress and encapsulates the approaches that were being applied in plant proteomics.
Book Synopsis Biomedical Translational Research by : R.C. Sobti
Download or read book Biomedical Translational Research written by R.C. Sobti and published by Springer Nature. This book was released on 2022-05-26 with total page 500 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book, which is the first volume of Biomedical Translational Research, summarizes emerging technologies in healthcare. The book reviews the advancements in biomedical sciences in genomics, immunology, stem cell, tissue engineering, nanotechnology, computational and structural biology, biomedical engineering, and telemedicine biology. The book highlights the applications of artificial intelligence in the diagnosis of infectious diseases and examines the role of system biology approaches for understanding human complexity, variability, and its influence on health and diseases. It presents the applications of flow cytometry in monitoring the progression and treatment of disease. It covers emerging technologies in cancer research, including CRISPR-Cas9, NGS, and nanotechnology. This book is a useful source of information for clinical researchers, basic scientists, biomedical engineers, and computational biologists.
Book Synopsis Protein Mass Spectrometry by : Julian Whitelegge
Download or read book Protein Mass Spectrometry written by Julian Whitelegge and published by Elsevier. This book was released on 2008-10-09 with total page 563 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is designed to be a central text for young graduate students interested in mass spectrometry as it relates to the study of protein structure and function as well as proteomics. It is a definite must-have work for:- libraries at academic institutions with Master and Graduate programs in biochemistry, molecular biology, structural biology and proteomics- individual laboratories with interests covering these areas - libraries and individual laboratories in the pharmaceutical and biotechnology industries. *Serves as an essential reference to those working in the field*Incorporates the contributions of prominent experts *Features comprehensive coverage and a logical structure
Book Synopsis Mass Spectrometry of Proteins and Peptides by : Mary S. Lipton
Download or read book Mass Spectrometry of Proteins and Peptides written by Mary S. Lipton and published by Humana Press. This book was released on 2014-11-27 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: When the last edition of this book was published in 2000, the field of proteomics was in its infancy. At that time, multidimensional liquid chromatographic separations were being introduced as an alternative to traditional gel-based techniques for separating complex protein and peptide mixtures prior to mass spectrometric detection. Today, this approach – referred to as shotgun proteomics – is considered routine for lar- scale global analyses of protein mixtures. Now in its adolescence, proteomics is fundamentally transforming biological and medical research. Much of this transformation can be attributed to technological advancements, particularly in mass spectrometry. Much wider accessibility of hi- resolution and mass measurement accuracy instrumentation in recent years has ini- ated a new revolution in the field by providing more reliable data and shifting the focus from cataloging proteins to precisely quantifying changes in protein abundance over time and in response to stimuli. Advanced mass spectrometers and novel ion d- sociation schemes such as electron transfer/capture dissociation make it possible to venture boldly into the maze of protein posttranslational modifications, which are an integral component of understanding functional proteomics in the spatial and t- poral domains. Another area that has benefited from these advancements is top-down proteomics, an emerging method essential for characterizing various protein variants that has potentially high impact in biomedical research.
