Computational Methods For Mass Spectrometry Proteomics

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Computational Methods for Mass Spectrometry Proteomics

Author : Ingvar Eidhammer
Publisher : John Wiley & Sons
ISBN 13 : 9780470724293
Total Pages : 296 pages
Book Rating : 4.7/5 (242 download)

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Book Synopsis Computational Methods for Mass Spectrometry Proteomics by : Ingvar Eidhammer

Download or read book Computational Methods for Mass Spectrometry Proteomics written by Ingvar Eidhammer and published by John Wiley & Sons. This book was released on 2008-02-28 with total page 296 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteomics is the study of the subsets of proteins present in different parts of an organism and how they change with time and varying conditions. Mass spectrometry is the leading technology used in proteomics, and the field relies heavily on bioinformatics to process and analyze the acquired data. Since recent years have seen tremendous developments in instrumentation and proteomics-related bioinformatics, there is clearly a need for a solid introduction to the crossroads where proteomics and bioinformatics meet. Computational Methods for Mass Spectrometry Proteomics describes the different instruments and methodologies used in proteomics in a unified manner. The authors put an emphasis on the computational methods for the different phases of a proteomics analysis, but the underlying principles in protein chemistry and instrument technology are also described. The book is illustrated by a number of figures and examples, and contains exercises for the reader. Written in an accessible yet rigorous style, it is a valuable reference for both informaticians and biologists. Computational Methods for Mass Spectrometry Proteomics is suited for advanced undergraduate and graduate students of bioinformatics and molecular biology with an interest in proteomics. It also provides a good introduction and reference source for researchers new to proteomics, and for people who come into more peripheral contact with the field.

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 Data Analysis in Proteomics

Author : Rune Matthiesen
Publisher :
ISBN 13 : 9781627033923
Total Pages : 405 pages
Book Rating : 4.0/5 (339 download)

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Book Synopsis Mass Spectrometry Data Analysis in Proteomics by : Rune Matthiesen

Download or read book Mass Spectrometry Data Analysis in Proteomics written by Rune Matthiesen and published by . This book was released on 2013 with total page 405 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since the publishing of the first edition, the methodologies and instrumentation involved in the field of mass spectrometry-based proteomics has improved considerably. Fully revised and expanded, Mass Spectrometry Data Analysis in Proteomics, Second Edition presents expert chapters on specific MS-based methods or data analysis strategies in proteomics. The volume covers data analysis topics relevant for quantitative proteomics, post translational modification, HX-MS, glycomics, and data exchange standards, among other topics. Written in the highly successful Methods in Molecular Biology series format, chapters include brief introductions to their respective subjects, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Updated and authoritative, Mass Spectrometry Data Analysis in Proteomics, Second Edition serves as a detailed guide for all researchers seeking to further our knowledge in the field of proteomics.

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

Author : Susmita Datta
Publisher : Springer
ISBN 13 : 3319458094
Total Pages : 294 pages
Book Rating : 4.3/5 (194 download)

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Book Synopsis Statistical Analysis of Proteomics, Metabolomics, and Lipidomics Data Using Mass Spectrometry by : Susmita Datta

Download or read book Statistical Analysis of Proteomics, Metabolomics, and Lipidomics Data Using Mass Spectrometry written by Susmita Datta and published by Springer. This book was released on 2016-12-15 with total page 294 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 Data Analysis

Author : Daniela Cecconi
Publisher :
ISBN 13 : 9781071616413
Total Pages : 326 pages
Book Rating : 4.6/5 (164 download)

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Book Synopsis Proteomics Data Analysis by : Daniela Cecconi

Download or read book Proteomics Data Analysis written by Daniela Cecconi and published by . This book was released on 2021 with total page 326 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thorough book collects methods and strategies to analyze proteomics data. It is intended to describe how data obtained by gel-based or gel-free proteomics approaches can be inspected, organized, and interpreted to extrapolate biological information. Organized into four sections, the volume explores strategies to analyze proteomics data obtained by gel-based approaches, different data analysis approaches for gel-free proteomics experiments, bioinformatic tools for the interpretation of proteomics data to obtain biological significant information, as well as methods to integrate proteomics data with other omics datasets including genomics, transcriptomics, metabolomics, and other types of data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detailed implementation advice that will ensure high quality results in the lab. Authoritative and practical, Proteomics Data Analysis serves as an ideal guide to introduce researchers, both experienced and novice, to new tools and approaches for data analysis to encourage the further study of proteomics.

Epigenetics and Proteomics of Leukemia

Author : R ̄uta Navakauskien ̇e
Publisher : Springer Nature
ISBN 13 : 3030687082
Total Pages : 453 pages
Book Rating : 4.0/5 (36 download)

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Book Synopsis Epigenetics and Proteomics of Leukemia by : R ̄uta Navakauskien ̇e

Download or read book Epigenetics and Proteomics of Leukemia written by R ̄uta Navakauskien ̇e and published by Springer Nature. This book was released on 2021-09-14 with total page 453 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book reviews the current state of epigenetics and proteomics of leukemia and introduces the methods that are important to process and evaluate these factors in leukemia. In particular, epigenetic modifiers and their inhibitors in leukemia treatment as well as approaches to the epigenetic treatment of leukemia are covered. Various computational methods for proteome analysis are also described in detail, including 2DE fractionation and visualization, proteomic data processing, image acquisition and data anlaysis, and more. Protein localization in leukemia is also covered, in addition to the future of leukemia therapy. Epigenetics and Proteomics of Leukemia is an ideal book for advanced biomedical scientists and students, medical doctors and students, bioinformatics and health informatics researchers, computational biologists, structural biologists, systems biologists, and bioengineers.

Proteome Informatics

Author : Conrad Bessant
Publisher : Royal Society of Chemistry
ISBN 13 : 1782626735
Total Pages : 429 pages
Book Rating : 4.7/5 (826 download)

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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.

Proteomic and Metabolomic Approaches to Biomarker Discovery

Author : Haleem J. Issaq
Publisher : Academic Press
ISBN 13 : 0123947952
Total Pages : 489 pages
Book Rating : 4.1/5 (239 download)

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Book Synopsis Proteomic and Metabolomic Approaches to Biomarker Discovery by : Haleem J. Issaq

Download or read book Proteomic and Metabolomic Approaches to Biomarker Discovery written by Haleem J. Issaq and published by Academic Press. This book was released on 2013-05-20 with total page 489 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteomic and Metabolomic Approaches to Biomarker Discovery demonstrates how to leverage biomarkers to improve accuracy and reduce errors in research. Disease biomarker discovery is one of the most vibrant and important areas of research today, as the identification of reliable biomarkers has an enormous impact on disease diagnosis, selection of treatment regimens, and therapeutic monitoring. Various techniques are used in the biomarker discovery process, including techniques used in proteomics, the study of the proteins that make up an organism, and metabolomics, the study of chemical fingerprints created from cellular processes. Proteomic and Metabolomic Approaches to Biomarker Discovery is the only publication that covers techniques from both proteomics and metabolomics and includes all steps involved in biomarker discovery, from study design to study execution. The book describes methods, and presents a standard operating procedure for sample selection, preparation, and storage, as well as data analysis and modeling. This new standard effectively eliminates the differing methodologies used in studies and creates a unified approach. Readers will learn the advantages and disadvantages of the various techniques discussed, as well as potential difficulties inherent to all steps in the biomarker discovery process. A vital resource for biochemists, biologists, analytical chemists, bioanalytical chemists, clinical and medical technicians, researchers in pharmaceuticals, and graduate students, Proteomic and Metabolomic Approaches to Biomarker Discovery provides the information needed to reduce clinical error in the execution of research. - Describes the use of biomarkers to reduce clinical errors in research - Includes techniques from a range of biomarker discoveries - Covers all steps involved in biomarker discovery, from study design to study execution

Protein Bioinformatics

Author : Cathy H. Wu
Publisher : Humana
ISBN 13 : 9781493967810
Total Pages : 0 pages
Book Rating : 4.9/5 (678 download)

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Book Synopsis Protein Bioinformatics by : Cathy H. Wu

Download or read book Protein Bioinformatics written by Cathy H. Wu and published by Humana. This book was released on 2017-02-03 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume introduces bioinformatics research methods for proteins, with special focus on protein post-translational modifications (PTMs) and networks. This book is organized into four parts and covers the basic framework and major resources for analysis of protein sequence, structure, and function; approaches and resources for analysis of protein PTMs, protein-protein interactions (PPIs) and protein networks, including tools for PPI prediction and approaches for the construction of PPI and PTM networks; and bioinformatics approaches in proteomics, including computational methods for mass spectrometry-based proteomics and integrative analysis for alternative splice isoforms, for functional discovery. 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 or computational protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Protein Bioinformatics: From Protein Modifications and Networks to Proteomics is a valuable resource for readers who wish to learn about state-of-the-art bioinformatics databases and tools, novel computational methods, and future trends in protein and proteomic data analysis in systems biology. This book is useful to researchers who work in the biotechnology and pharmaceutical industries, and in various academic departments, such as biological and medical sciences and computer sciences and engineering.

LC-MS/MS in Proteomics

Author : Pedro R. Cutillas
Publisher : Humana Press
ISBN 13 : 9781607617815
Total Pages : 330 pages
Book Rating : 4.6/5 (178 download)

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Book Synopsis LC-MS/MS in Proteomics by : Pedro R. Cutillas

Download or read book LC-MS/MS in Proteomics written by Pedro R. Cutillas and published by Humana Press. This book was released on 2011-04-06 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: With the development of new quantitative strategies and powerful bioinformatics tools to cope with the analysis of the large amounts of data generated in proteomics experiments, liquid chromatography with tandem mass spectrometry (LC-MS/MS) is making possible the analysis of proteins on a global scale, meaning that proteomics can now start competing with cDNA microarrays for the analysis of whole genomes. In LC-MS/MS in Proteomics: Methods and Applications, experts in the field provide protocols and up-to-date reviews of the applications of LC-MS/MS, with a particular focus on MS-based methods of protein and peptide quantification and the analysis of post-translational modifications. Beginning with overviews of the use of LC-M/MS in protein analysis, the book continues with topics such as protocols for the analysis of post-translational modifications, with particular focus on phosphorylation and glycosylation, popular techniques for quantitative proteomics, such as multiple reaction monitoring, metabolic labelling, and chemical tagging, biomarker discovery in biological fluids, as well as novel applications of LC-MS/MS. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective subjects, lists of necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Comprehensive and cutting-edge, LC-MS/MS in Proteomics: Methods and Applications presents the techniques and concepts necessary in order to aid proteomic practitioners in the application of LC-MS/MS to essentially any biological problem.

Computational Methods in Biomedical Research

Author : Ravindra Khattree
Publisher : CRC Press
ISBN 13 : 9781420010923
Total Pages : 432 pages
Book Rating : 4.0/5 (19 download)

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Book Synopsis Computational Methods in Biomedical Research by : Ravindra Khattree

Download or read book Computational Methods in Biomedical Research written by Ravindra Khattree and published by CRC Press. This book was released on 2007-12-12 with total page 432 pages. Available in PDF, EPUB and Kindle. Book excerpt: Continuing advances in biomedical research and statistical methods call for a constant stream of updated, cohesive accounts of new developments so that the methodologies can be properly implemented in the biomedical field. Responding to this need, Computational Methods in Biomedical Research explores important current and emerging computational statistical methods that are used in biomedical research. Written by active researchers in the field, this authoritative collection covers a wide range of topics. It introduces each topic at a basic level, before moving on to more advanced discussions of applications. The book begins with microarray data analysis, machine learning techniques, and mass spectrometry-based protein profiling. It then uses state space models to predict US cancer mortality rates and provides an overview of the application of multistate models in analyzing multiple failure times. The book also describes various Bayesian techniques, the sequential monitoring of randomization tests, mixed-effects models, and the classification rules for repeated measures data. The volume concludes with estimation methods for analyzing longitudinal data. Supplying the knowledge necessary to perform sophisticated statistical analyses, this reference is a must-have for anyone involved in advanced biomedical and pharmaceutical research. It will help in the quest to identify potential new drugs for the treatment of a variety of diseases.

Quantitative Methods in Proteomics

Author : Katrin Marcus
Publisher : Humana Press
ISBN 13 : 9781617798849
Total Pages : 539 pages
Book Rating : 4.7/5 (988 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 Humana Press. This book was released on 2012-06-08 with total page 539 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein modifications and changes made to them, as well as the quantities of expressed proteins, can define the various functional stages of the cell. Accordingly, perturbations can lead to various diseases and disorders. As a result, it has become paramount to be able to detect and monitor post-translational modifications and to measure the abundance of proteins within the cell with extreme sensitivity. While protein identification is an almost routine requirement nowadays, reliable techniques for quantifying unmodified proteins (including those that escape detection under standard conditions, such as protein isoforms and membrane proteins) is not routine. Quantitative Methods in Proteomics gives a detailed survey of topics and methods on the principles underlying modern protein analysis, from statistical issues when planning proteomics experiments, to gel-based and mass spectrometry-based applications. The quantification of post-translational modifications is also addressed, followed by the “hot” topics of software and data analysis, as well as various overview chapters which provide a comprehensive overview of existing methods in quantitative proteomics. Written in the successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easily accessible, Quantitative Methods in Proteomics serves as a comprehensive and competent overview of the important and still growing field of quantitative proteomics.

Computational Biology

Author : Ralf Blossey
Publisher : CRC Press
ISBN 13 : 1420010786
Total Pages : 276 pages
Book Rating : 4.4/5 (2 download)

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Book Synopsis Computational Biology by : Ralf Blossey

Download or read book Computational Biology written by Ralf Blossey and published by CRC Press. This book was released on 2006-05-25 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt: Quantitative methods have a particular knack for improving any field they touch. For biology, computational techniques have led to enormous strides in our understanding of biological systems, but there is still vast territory to cover. Statistical physics especially holds great potential for elucidating the structural-functional relationships in bi

Proteomics for Biological Discovery

Author : Timothy D. Veenstra
Publisher : John Wiley & Sons
ISBN 13 : 0470007737
Total Pages : 361 pages
Book Rating : 4.4/5 (7 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 2006-06-12 with total page 361 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by recognized experts in the study of proteins, Proteomics for Biological Discovery begins by discussing the emergence of proteomics from genome sequencing projects and a summary of potential answers to be gained from proteome-level research. The tools of proteomics, from conventional to novel techniques, are then dealt with in terms of underlying concepts, limitations and future directions. An invaluable source of information, this title also provides a thorough overview of the current developments in post-translational modification studies, structural proteomics, biochemical proteomics, microfabrication, applied proteomics, and bioinformatics relevant to proteomics. Presents a comprehensive and coherent review of the major issues faced in terms of 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 Discusses higher level integrative aspects, including technical challenges and applications for drug discovery Accessible to the novice while providing experienced investigators essential information Proteomics for Biological Discovery is an essential resource for students, postdoctoral fellows, and researchers across all fields of biomedical research, including biochemistry, protein chemistry, molecular genetics, cell/developmental biology, and bioinformatics.

Peptidomics

Author : Michael Schrader
Publisher : Humana
ISBN 13 : 9781493985142
Total Pages : 423 pages
Book Rating : 4.9/5 (851 download)

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Book Synopsis Peptidomics by : Michael Schrader

Download or read book Peptidomics written by Michael Schrader and published by Humana. This book was released on 2019-06-04 with total page 423 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Protein Structure Analysis

Author : Roza Maria Kamp
Publisher : Springer Science & Business Media
ISBN 13 : 3642592198
Total Pages : 311 pages
Book Rating : 4.6/5 (425 download)

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Book Synopsis Protein Structure Analysis by : Roza Maria Kamp

Download or read book Protein Structure Analysis written by Roza Maria Kamp and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 311 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Protein Structure Analysis - Preparation and Characterization" is a compilation of practical approaches to the structural analysis of proteins and peptides. Here, about 20 authors describe and comment on techniques for sensitive protein purification and analysis. These methods are used worldwide in biochemical and biotechnical research currently being carried out in pharmaceu tical and biomedical laboratories or protein sequencing facilities. The chapters have been written by scientists with extensive ex perience in these fields, and the practical parts are well documen ted so that the reader should be able to easily reproduce the described techniques. The methods compiled in this book were demonstrated in student courses and in the EMBO Practical Course on "Microsequence Analysis of Proteins" held in Berlin September 10-15, 1995. The topics also derived from a FEBS Workshop, held in Halkidiki, Thessaloniki, Greece, in April, 1995. Most of the authors participated in these courses as lecturers and tutors and made these courses extremely lively and successful. Since polypeptides greatly vary depending on their specific structure and function, strategies for their structural analysis must for the most part be adapted to each individual protein. Therefore, advantages and limitations of the experimen tal approaches are discussed here critically, so that the reader becomes familiar with problems that might be encountered.

Proteoform Identification

Author : Liangliang Sun
Publisher : Humana
ISBN 13 : 9781071623244
Total Pages : 240 pages
Book Rating : 4.6/5 (232 download)

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Book Synopsis Proteoform Identification by : Liangliang Sun

Download or read book Proteoform Identification written by Liangliang Sun and published by Humana. This book was released on 2022-07-04 with total page 240 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.