Proteomics Today

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 PREFACE TO PART I.

ACKNOWLEDGMENT.

I: INTRODUCTION TO PART I.

1. INSTRUMENTATION AND DEVELOPMENTS.

1.1 Introduction.

1.2 Ionization Techniques for Macromolecules.

1.3 Examples on Analytical Solutions Based on FAB–MS.

1.4 Electrospray Ionization.

1.5 Matrix-Assisted Laser Desorption Ionization.

1.6 Ion Detection.

1.7 Types of Analyzers.

1.8 Hybrid Analyzers.

1.9 Tandem Mass Spectrometry.

1.10 Current MS Instrumentation in Proteome Analyses.

1.11 Current MS-Based Proteomics.

1.12 Recent Achievements and Future Challenges.

1.13 Concluding Remarks.

References.

2. PROTEOMICS IN CANCER RESEARCH.

2.1 Introduction.

2.2 Pancreatic Ductal Adenocarcinoma.

2.3 Proteomic Analysis of Human Breast Carcinoma.

2.4 Proteomic Profiling of Chemoresistant Cancer Cells.

2.5 Signal Pathway Profiling of Prostate Cancer.

2.6 Emerging Role of Functional and Activity-Based Proteomics in Disease Understanding.

2.7 Activity-Based Protein Profiling.

2.8 Probing Protein Functions Using Chromophore-Assisted Laser Inactivation.

2.9 Role of Protein–Tyrosine Kinases.

2.10 Concluding Remarks and Future Prospects.

References.

3. CURRENT STRATEGIES FOR PROTEIN QUANTIFICATION.

3.1 Introduction.

3.2 Global Internal Standard Technology.

3.3 Differential In-Gel Electrophoresis.

3.4 Quantification of Modified Proteins.

3.5 Comments and Considerations.

3.6 Other Approaches.

3.7 Emerging Role of Microfluidic Devices.

3.8 Concluding Remarks.

References.

II: PROTEOMICS TODAY: SEPARATION SCIENCE AT WORK.

4. CONVENTIONAL ISOELECTRIC FOCUSING IN GEL MATRICES AND CAPILLARIES AND IMMOBILIZED pH GRADIENTS.

4.1 Introduction.

4.2 Conventional Isoelectric Focusing in Amphoteric Buffers.

4.3 Immobilized pH Gradients.

4.4 Capillary Isoelectric Focusing.

4.5 Separation of Peptides and Proteins by CZE in Isoelectric Buffers.

4.6 Conclusions.

References.

5. SODIUM DODECYL SULFATE–POLYACRYLAMIDE GEL ELECTROPHORESIS.

5.1 Introduction.

5.2 SDS–Protein Complexes: a Refinement of the Model.

5.3 Theoretical Background of Mr Measurement by SDS–PAGE.

5.4 Methodology.

5.5 Gel Casting and Buffer Systems.

5.6 Blotting Procedures.

5.7 Conclusions.

References.

6. TWO-DIMENSIONAL MAPS.

6.1 Introduction.

6.2 Some Basic Methodology Pertaining to 2D PAGE.

6.3 Prefractionation Tools in Proteome Analysis.

6.4 Multidimensional Chromatography Coupled to MS.

6.5 Protein Chips and Microarrays.

6.6 Nondenaturing Protein Maps.

6.7 Spot Matching in 2D Gels via Commercial Software.

6.8 Conclusions.

References.

INDEX.

"I highly recommend this book for anyone planning to get involved in proteomics technology or for one who is already involved…it provides an entertaining insight on the field..." (Microbe, March 2006)

"...a must reference for anyone interested in proteomics. For me, if Proteomics Today is not in my backpack it will be within arms reach as a great reference to have on hand as I plan future experiments." (Journal of the American Society for Mass Spectrometry, January 2006)

"…the book is highly recommended to all scientists interested in protein separation science, and well-thumbed copies will certainly be present in every self-respecting proteomic laboratory." (Proteomics, July 2005)

‘This book is well written and thus easy to read. It contains valuable information and extensive references for readers from a variety of backgrounds.’ (Analytical and Bioanalytical Chemistry, 12 January 2007)

"…well-written and thus easy to read. It contains valuable information and extensive references for readers from a variety of backgrounds." (Analytical and Bioanalytical Chemistry, January 2007)

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.

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.