Proteoforms

Proteoforms
Author: Xianquan Zhan
Publisher: BoD – Books on Demand
Total Pages: 92
Release: 2020-07-15
Genre: Science
ISBN: 1838800336
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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.

Proteoform Identification

Proteoform Identification
Author: Liangliang Sun
Publisher: Humana
Total Pages: 0
Release: 2023-06-18
Genre: Science
ISBN: 9781071623275
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This volume discusses the latest mass spectrometry (MS)-based technologies for proteoform identification, characterization, and quantification. Some of the topics covered in this book include sample preparation, proteoform separation, proteoform gas-phase fragmentation, and bioinformatics tools for MS 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. Cutting-edge and comprehensive, Proteoform Identification: Methods and Protocols is a valuable resource for researchers in both academia and the biopharmaceutical industry who are interested in proteoform analysis using MS.

Modern Proteomics – Sample Preparation, Analysis and Practical Applications

Modern Proteomics – Sample Preparation, Analysis and Practical Applications
Author: Hamid Mirzaei
Publisher: Springer
Total Pages: 525
Release: 2016-12-14
Genre: Science
ISBN: 3319414488
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This volume serves as a proteomics reference manual, describing experimental design and execution. The book also shows a large number of examples as to what can be achieved using proteomics techniques. As a relatively young area of scientific research, the breadth and depth of the current state of the art in proteomics might not be obvious to all potential users. There are various books and review articles that cover certain aspects of proteomics but they often lack technical details. Subject specific literature also lacks the broad overviews that are needed to design an experiment in which all steps are compatible and coherent. The objective of this book was to create a proteomics manual to provide scientists who are not experts in the field with an overview of: 1. The types of samples can be analyzed by mass spectrometry for proteomics analysis. 2. Ways to convert biological or ecological samples to analytes ready for mass spectral analysis. 3. Ways to reduce the complexity of the proteome to achieve better coverage of the constituent proteins. 4. How various mass spectrometers work and different ways they can be used for proteomics analysis 5. The various platforms that are available for proteomics data analysis 6. The various applications of proteomics technologies in biological and medical sciences This book should appeal to anyone with an interest in proteomics technologies, proteomics related bioinformatics and proteomics data generation and interpretation. With the broad setup and chapters written by experts in the field, there is information that is valuable for students as well as for researchers who are looking for a hands on introduction into the strengths, weaknesses and opportunities of proteomics.

Proteolytic Signaling in Health and Disease

Proteolytic Signaling in Health and Disease
Author: Andre Zelanis
Publisher: Academic Press
Total Pages: 308
Release: 2021-10-13
Genre: Science
ISBN: 0323856977
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In recent years, powered by evolving technologies and experimental design, studies have better illuminated the regulating role of proteolytic enzymes across human development and pathologies. Proteolytic Signaling in Health and Disease provides an in-depth discussion of fundamental physiological and developmental processes regulated by proteases, from protein turnover and autophagy to antigen processing and presentation and major histocompatibility complex (MHC) molecules. Moving on from basic biology, international chapter authors examine a range of pathological conditions associated with proteolysis, including inflammation, wound healing, and cancer. Later chapters discuss the newly discovered network of connected events among proteases (and their inhibitors), the so-called ‘protease web’, and how best to study it. This book also empowers new research with up-to-date analytical methods and step-by-step protocols for studying proteolytic signaling events. Examines biological events triggered by proteolytic enzyme activity across human development and pathologies Discusses the role of proteolytic signaling in inflammation, wound healing, and cancer, among other disease types Features methods and protocols supporting further study of proteolytic signaling events Includes chapter contributions from international leaders in the field

Proteoforms

Proteoforms
Author: Olga Lima Tavares Machado
Publisher:
Total Pages: 0
Release: 2020
Genre: Science
ISBN:
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The term proteoform is used to denote all the molecular forms in which the protein product of a single gene can be found. The most frequent processes that lead to transcript modification and the biological implications of these changes observed in the final protein product will be discussed. Proteoforms arising from genetic variations, alternatively spliced RNA transcripts and post-translational modifications will be commented. This chapter will present an evolution of the techniques used to identify the proteoforms and the importance of this identification for understanding of biological processes. This chapter highlights the fundamental concepts in the field of top-down mass spectrometry (TDMS), and provides numerous examples for the use of knowledge obtained from the identification of proteoforms. The identification of mutant proteins is one of the emerging areas of proteogenomics and has the potential to recognize novel disease biomarkers and may point to useful targets for identification of therapeutic approaches.

Proteomic Profiling and Analytical Chemistry

Proteomic Profiling and Analytical Chemistry
Author: Pawel Ciborowski
Publisher: Elsevier
Total Pages: 300
Release: 2016-03-02
Genre: Science
ISBN: 0444636900
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Proteomic Profiling and Analytical Chemistry: The Crossroads, Second Edition helps scientists without a strong background in analytical chemistry to understand principles of the multistep proteomic experiment necessary for its successful completion. It also helps researchers who do have an analytical chemistry background to break into the proteomics field. Highlighting points of junction between proteomics and analytical chemistry, this resource links experimental design with analytical measurements, data analysis, and quality control. This targeted point of view will help both biologists and chemists to better understand all components of a complex proteomic study. The book provides detailed coverage of experimental aspects such as sample preparation, protein extraction and precipitation, gel electrophoresis, microarrays, dynamics of fluorescent dyes, and more. The key feature of this book is a direct link between multistep proteomic strategy and quality control routinely applied in analytical chemistry. This second edition features a new chapter on SWATH-MS, substantial updates to all chapters, including proteomic database search and analytical quantification, expanded discussion of post-hoc statistical tests, and additional content on validation in proteomics. Covers the analytical consequences of protein and peptide modifications that may have a profound effect on how and what researchers actually measure Includes practical examples illustrating the importance of problems in quantitation and validation of biomarkers Helps in designing and executing proteomic experiments with sound analytics

Statistical Analysis of Proteomics, Metabolomics, and Lipidomics Data Using Mass Spectrometry

Statistical Analysis of Proteomics, Metabolomics, and Lipidomics Data Using Mass Spectrometry
Author: Susmita Datta
Publisher: Springer
Total Pages: 294
Release: 2016-12-15
Genre: Medical
ISBN: 3319458094
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This book presents an overview of computational and statistical design and analysis of mass spectrometry-based proteomics, metabolomics, and lipidomics data. This contributed volume provides an introduction to the special aspects of statistical design and analysis with mass spectrometry data for the new omic sciences. The text discusses common aspects of design and analysis between and across all (or most) forms of mass spectrometry, while also providing special examples of application with the most common forms of mass spectrometry. Also covered are applications of computational mass spectrometry not only in clinical study but also in the interpretation of omics data in plant biology studies. Omics research fields are expected to revolutionize biomolecular research by the ability to simultaneously profile many compounds within either patient blood, urine, tissue, or other biological samples. Mass spectrometry is one of the key analytical techniques used in these new omic sciences. Liquid chromatography mass spectrometry, time-of-flight data, and Fourier transform mass spectrometry are but a selection of the measurement platforms available to the modern analyst. Thus in practical proteomics or metabolomics, researchers will not only be confronted with new high dimensional data types—as opposed to the familiar data structures in more classical genomics—but also with great variation between distinct types of mass spectral measurements derived from different platforms, which may complicate analyses, comparison, and interpretation of results.

Proteomics for Biomarker Discovery

Proteomics for Biomarker Discovery
Author: Virginie Brun
Publisher: Humana Press
Total Pages: 293
Release: 2019-05-04
Genre: Science
ISBN: 9781493991631
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This volume presents modern and enhanced methods that detail techniques to perform proteomics analyses dedicated to biomarker discovery for human health. Chapters guide readers through pre/post analytical factors, protocols for the preparation of extracellular vesicles and exosomes, and various analytical pipelines including Data Independent Acquisition (DIA), discovery, as well as targeted and top-down proteomics analysis workflows. Bioinformatics tools and workflows to select and evaluate candidate biomarkers or combinations of biomarkers are also presented. 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, Proteomics for Biomarker Discovery: Methods and Protocols aims to ensure successful results in the further study of this vital field.

Fundamentals and Applications of Fourier Transform Mass Spectrometry

Fundamentals and Applications of Fourier Transform Mass Spectrometry
Author: Philippe Schmitt-Kopplin
Publisher: Elsevier
Total Pages: 778
Release: 2019-08-11
Genre: Science
ISBN: 0128140143
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Fundamentals and Applications of Fourier Transform Mass Spectrometry is the first book to delve into the underlying principles on the topic and their linkage to industrial applications. Drs. Schmitt-Kopplin and Kanawati have brought together a team of leading experts in their respective fields to present this technique from many different perspectives, describing, at length, the pros and cons of FT-ICR and Orbitrap. Numerous examples help researchers decide which instruments to use for their particular scientific problem and which data analysis methods should be applied to get the most out of their data. Covers FT-ICR-MS and Orbitrap’s fundamentals, enhancing researcher knowledge Includes details on ion sources, data processing, chemical analysis and imaging Provides examples across the wide spectrum of applications, including omics, environmental, chemical, pharmaceutical and food analysis

Computational Methods for Predicting Post-Translational Modification Sites

Computational Methods for Predicting Post-Translational Modification Sites
Author: Dukka B. KC
Publisher: Springer Nature
Total Pages: 337
Release: 2022-06-13
Genre: Science
ISBN: 1071623176
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This volume describes computational approaches to predict multitudes of PTM sites. Chapters describe in depth approaches on algorithms, state-of-the-art Deep Learning based approaches, hand-crafted features, physico-chemical based features, issues related to obtaining negative training, sequence-based features, and structure-based features. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Authoritative and cutting-edge, Computational Methods for Predicting Post-Translational Modification Sites aims to be a useful guide for researchers who are interested in the field of PTM site prediction.