Proteomics Today: Protein Assessment and Biomarkers Using Mass Spectrometry, 2D Electrophoresis,and Microarray Technology: 7 (Wiley Series on Mass Spectrometry) - Hardcover

Hamdan, Mahmoud H.; Righetti, Pier G.

Hardcover

ISBN 10: 0471648175 ISBN 13: 9780471648178

Publisher: Wiley-Interscience, 2005

Synopsis

The last few years have seen an unprecedented drive toward the application of proteomics to resolving challenging biomedical and biochemical tasks. Separation techniques combined with modern mass spectrometry are playing a central role in this drive. This book discusses the increasingly important role of mass spectrometry in proteomic research, and emphasizes recent advances in the existing technology and describes the advantages and pitfalls as well.
* Provides a scientifically valid method for analyzing the approximatey 500,000 proteins that are encoded in the human genome
* Explains the hows and whys of using mass spectrometry in proteomic analysis
* Brings together the latest approaches combining separation techniques and mass spectrometry and their application in proteome analysis
* Comments on future challenges and how they may be addressed
* Includes sections on troubleshooting

About this title

About the Author

MAHMOUD HAMDAN, PhD, is the head of Mass Spectrometry & Separation Technologies, GlaxoSmithKline, Verona, Italy.

PIER GIORGIO RIGHETTI, PhD, is Professor of Biochemistry and director of the Laboratory of Proteome Science at the University of Verona, Italy.

From the Back Cover

The latest and most effective uses of mass spectrometry, 2D electrophoresis, and microarray technology for protein analysis

The first step in analyzing complex biochemical systems involves determining the molecular masses of interacting proteins, peptides, and other components. Proteomics, the study of all proteins expressed by a genome, calls for a powerful tool―mass spectrometry―to identify these proteins. A full understanding of the vital role of mass spectrometry in proteomic research necessitates an illuminating text like Proteomics Today.

Over the last several years, new emphasis has been placed on the application of proteomics to perform demanding biomedical and biochemical tasks. Proteomics Today clearly describes the contributions of the latest approaches―separation techniques, modern mass spectrometry, two-dimensional electrophoresis, and microarray technology―in meeting these challenges. The emerging roles of imaging mass spectrometry and protein interaction maps are also addressed. In this single comprehensive source, you will find an invaluable examination of all the newest technologies related to:

• Instrumentation
• Current strategies for protein quantification
• SDS-gel electrophoresis
• Conventional isoelectric focusing in gel matrices, capillaries, and immobilized pH gradients
• Two-dimensional maps
• Proteomics in cancer research

A must-have guide for scientists and laboratory technicians who study proteins in the pharmaceutical and biotechnology industries, Proteomics Today includes helpful introductions to chapters, complete references, plus insights into future challenges. More than any other resource, Proteomics Today explains how mass spectrometry and its associated tools can turn today's proteomic research challenges into tomorrow's biomedical opportunities.

The first step in analyzing complex biochemical systems involves determining the molecular masses of interacting proteins, peptides, and other components. Proteomics, the study of all proteins expressed by a genome, calls for a powerful tool—mass spectrometry—to identify these proteins. A full understanding of the vital role of mass spectrometry in proteomic research necessitates an illuminating text like Proteomics Today.

Over the last several years, new emphasis has been placed on the application of proteomics to perform demanding biomedical and biochemical tasks. Proteomics Today clearly describes the contributions of the latest approaches—separation techniques, modern mass spectrometry, two-dimensional electrophoresis, and microarray technology—in meeting these challenges. The emerging roles of imaging mass spectrometry and protein interaction maps are also addressed. In this single comprehensive source, you will find an invaluable examination of all the newest technologies related to:

• Instrumentation
• Current strategies for protein quantification
• SDS-gel electrophoresis
• Conventional isoelectric focusing in gel matrices, capillaries, and immobilized pH gradients
• Two-dimensional maps
• Proteomics in cancer research

A must-have guide for scientists and laboratory technicians who study proteins in the pharmaceutical and biotechnology industries, Proteomics Today includes helpful introductions to chapters, complete references, plus insights into future challenges. More than any other resource, Proteomics Today explains how mass spectrometry and its associated tools can turn today's proteomic research challenges into tomorrow's biomedical opportunities.

Excerpt. © Reprinted by permission. All rights reserved.

Proteomics Today

Protein Assessment and Biomarkers Using Mass Spectrometry, 2D Electrophoresis, and Microarray TechnologyBy Mahmoud H. Hamdan Pier G. Righetti

John Wiley & Sons

Copyright © 2005 Mahmoud H. Hamdan
All right reserved.
ISBN: 978-0-471-64817-8

Contents

PREFACE..............................................................................................................XVACKNOWLEDGMENT.......................................................................................................XVIII INTRODUCTION TO PART I.............................................................................................11 INSTRUMENTATION AND DEVELOPMENTS...................................................................................71.1 Introduction....................................................................................................71.2 Ionization Techniques for Macromolecules........................................................................81.3 Examples on Analytical Solutions Based on FAB-MS................................................................121.4 Electrospray Ionization.........................................................................................161.5 Matrix-Assisted Laser Desorption Ionization.....................................................................181.6 Ion Detection...................................................................................................241.7 Types of Analyzers..............................................................................................301.8 Hybrid Analyzers................................................................................................381.9 Tandem Mass Spectrometry........................................................................................421.10 Current MS Instrumentation in Proteome Analyses.................................................................471.11 Current MS-Based Proteomics.....................................................................................521.12 Recent Achievements and Future Challenges.......................................................................591.13 Concluding Remarks..............................................................................................61References...........................................................................................................632 PROTEOMICS IN CANCER RESEARCH......................................................................................692.1 Introduction....................................................................................................692.2 Pancreatic Ductal Adenocarcinoma................................................................................802.3 Proteomic Analysis of Human Breast Carcinoma....................................................................902.4 Proteomic Profiling of Chemoresistant Cancer Cells..............................................................972.5 Signal Pathway Profiling of Prostate Cancer.....................................................................1012.6 Emerging Role of Functional and Activity-Based Proteomics in Disease Understanding..............................1032.7 Activity-Based Protein Profiling................................................................................1052.8 Probing Protein Functions Using Chromophore-Assisted Laser Inactivation.........................................1062.9 Role of Protein-Tyrosine Kinases................................................................................1072.10 Concluding Remarks and Future Prospects.........................................................................109References...........................................................................................................1173 CURRENT STRATEGIES FOR PROTEIN QUANTIFICATION......................................................................1273.1 Introduction.....................................................................................................1273.2 Global Internal Standard Technology.............................................................................1413.3 Differential In-Gel Electrophoresis.............................................................................1443.4 Quantification of Modified Proteins.............................................................................1473.5 Comments and Considerations.....................................................................................1533.6 Other Approaches................................................................................................1593.7 Emerging Role of Microfluidic Devices...........................................................................1683.8 Concluding Remarks..............................................................................................174References...........................................................................................................177II PROTEOMICS TODAY: SEPARATION SCIENCE AT WORK......................................................................1834 CONVENTIONAL ISOELECTRIC FOCUSING IN GEL MATRICES AND CAPILLARIES AND IMMOBILIZED pH GRADIENTS.....................1874.1 Introduction....................................................................................................1874.2 Conventional Isoelectric Focusing in Amphoteric Buffers.........................................................1894.3 Immobilized pH Gradients........................................................................................2254.4 Capillary Isoelectric Focusing..................................................................................2474.5 Separation of Peptides and Proteins by CZE in Isoelectric Buffers...............................................2554.6 Conclusions.....................................................................................................260References...........................................................................................................2615 SODIUM DODECYL SULFATE-POLYACRYLAMIDE GEL ELECTROPHORESIS..........................................................2735.1 Introduction....................................................................................................2735.2 SDS-Protein Complexes: a Refinement of the Model................................................................2755.3 Theoretical Background of Mr Measurement by SDS-PAGE............................................................2775.4 Methodology.....................................................................................................2815.5 Gel Casting and Buffer Systems..................................................................................3035.6 Blotting Procedures.............................................................................................3225.7 Conclusions.....................................................................................................331References...........................................................................................................3326 TWO-DIMENSIONAL MAPS...............................................................................................3416.1 Introduction....................................................................................................3416.2 Some Basic Methodology Pertaining to 2D PAGE....................................................................3466.3 Prefractionation Tools in Proteome Analysis.....................................................................3736.4 Multidimensional Chromatography Coupled to MS...................................................................3906.5 Protein Chips and Microarrays...................................................................................3936.6 Nondenaturing Protein Maps......................................................................................3966.7 Spot Matching in 2D Gels via Commercial Software................................................................3976.8 Conclusions.....................................................................................................403References...........................................................................................................405INDEX................................................................................................................419

Preface

Prior to starting Part I of this book, and while searching existing literature on current proteomic activities, I came across a number of statements, that caught my attention and in a way have influenced my choice of the material in Part I. Therefore, it is reasonable to list them in here: First, mass spectrometry is a central component in modern proteomic research, second, the ability to determine statistically significant alterations in protein expression that might be provoked by disease, environmental, pharmacological, or genetic factors is a central component in current proteomic research, third, at the biochemical level, proteins rarely act alone; rather they interact with other proteins to perform a given cellular task. Although data obtained by various expression proteomics strategies have functional relevance by detecting changes in protein abundance, such measurements offer only an indirect readout of dynamics in protein activity. This means that numerous post-translational forms of protein regulation, including those governed by protein-protein interactions, remain undetected; and forth, biomarkers are not necessarily proteins. They can be DNA, RNA, or metabolites that can be associated with a measurable change with a given disease. Having stated that, protein-based analyses have two attractive features: First, proteins can be found regularly in blood, urine, and other biological fluids which make such approaches rather noninvasive, and second, proteins are the real executioners of various biological functions which make them key players in many diseases. To resolve the various issues contained within these statements, the last decade has witnessed an unprecedented use of a wide range of technologies and the fall of conventional barriers among the various disciplines. Within the wide host of technologies employed in the area of proteomic research, mass spectrometry emerges as a central component. The first three chapters of this book is an attempt to capture the recent contribution of this technology and its interaction with other technologies to tackle various proteomic challenges. The organization of Part I begins with a chapter dedicated to the major components of current mass spectrometers with a particular emphasis on the developments which have influenced sensitivity, resolution and the capability to perform various tandem mass spectrometry functions. Chapter 2 deals with the various approaches including mass spctrometry in the field of disease biomarkers. To provide a broader perspective of the role of mass spectrometry in this particular area, some material has been included that is not circumscribed by mass spectrometry, per se. I have dedicated Chapter 3 to the argument of protein quantification including the emerging strategies for the quantification of phosphorylated and glycosylated proteins.

Of course regardless of the size of any given book and the good intentions of the author, it would be a pure scientific arrogance to pretend that such book would provide a comprehensive coverage of the arguments raised within. On the other hand, I would like to think that this text will be looked upon by prospective readers as a contribution to a vast and continuously evolving debate, where single contributions are required to enrich and possibly stimulate such debate.

I can not end this Preface without acknowledging that the years I spent at the University of Wales, Swansea working with Professor J. H. Beynon (founding editor-in-chief of the journal, Rapid Communications of Mass Spectrometry) had an immense impact on my appreciation of mass spectrometry as a tool, that can be applied in a wide range of applications including present day proteomics.

Verona, Italy November 2004 Mahmoud Hamdan

(Continues...)

Excerpted from Proteomics Todayby Mahmoud H. Hamdan Pier G. Righetti Copyright © 2005 by Mahmoud H. Hamdan. Excerpted by permission.
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Edition details

• Publisher: Wiley-Interscience
• Publication date: 2005
• Language: English
• ISBN 10: 0471648175
• ISBN 13: 9780471648178
• Binding: Hardcover
• Edition number: 1
• Number of pages: 448