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E-grāmata: Proteomic Biology Using LC/MS: Large Scale Analysis of Cellular Dynamics and Function

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Takahashi (applied biological science, Tokyo University of Agriculture and Technology) and Isobe (biochemistry, Tokyo Metropolitan University) examine the latest liquid chromatography-mass spectrometry (LC-MS) technologies in depth, and explore their application to the analysis of the dynamic aspects of cellular function at the proteomic scale. After an overview of proteomics and proteomic technologies, they look at basic aspects of LC-MS technology, and describe integrated LC-based MS methodologies coupled with quantitative methodologies and/or bioinformatics. Recent applications are examined, such as the analysis of signal transduction complexes following stimulation of cells, and the analysis of the dynamic processes of ribosome biogenesis. They present a new concept, the "dynamome," or the expression of a comprehensive molecular set that participates in the whole dynamic process of a series of cellular events. The readership for the book includes investigators, staff, and students at academic and industrial laboratories, and scientists in other fields who want to bridge the gap between their specialties and proteomic biology. Annotation ©2008 Book News, Inc., Portland, OR (booknews.com)

This is one of the first books to focus on the dynamic aspect of proteomes. The book introduces proteomics to the newcomer, reviews the theoretical aspects of proteomics and its state-of-the art technologies, along with a number of biological applications using "classical" proteomic technology. The book also presents a new concept, the Dynamome, or the expression of a comprehensive molecular set that participates in the whole dynamic process of a series of cellular events.

Recenzijas

"The book covers the topic of proteomics and mass spectrometry analysis well and does so at a reasonably advanced level. This volume would be suitable for advanced graduate students and for nonexpert scientists to learn about the application of mass spectrometry techniques for proteomic studies." (Quarterly Review of Biology, December 2008)

Introduction vii
1 Overview of Proteomics 1
1-1 What Is Proteomics?,
1
1-2 Establishment of Proteomics Using Mass Spectrometry,
3
1-2-1 Protein Separations by Two-Dimensional Electrophoresis,
3
1-2-2 Development of the Technologies for Protein Identification,
5
1-2-3 Protein Identification Based on Gel Separation and Mass Spectrometry,
6
1-3 Strategies for Characterizing Proteomes and Understanding Proteome Function,
15
1-3-1 Modification-Specific Proteomics,
17
1-3-2 Activity-Based Protein Profiling/Enzyme Substrate Proteomics,
31
1-3-3 Subcellular (Organellar) Proteomics,
41
1-3-4 Machinery or Complex Interaction Proteomics,
45
1-3-5 Dynamic Proteomics,
46
References,
49
2 Proteomic Tools for Analysis of Cellular Dynamics 63
2-1 LC-Based Proteomics Technologies,
63
2-1-1 LC-MS system for Peptide Separation and Identification,
71
2-1-2 Application of LC-MS Methods to Functional Proteomics,
101
2-2 Development of Quantitative Proteomics,
131
2-2-1 Isotope Labeling for Quantitative Analysis Using MS,
132
2-2-2 Quantification Strategy for LC-MS Analysis of Isotope-Labeled Peptide Mixture and Software for Computer Analysis,
140
2-2-3 Label-Free Quantification Software,
145
2-2-4 Absolute Quantification,
147
References,
153
3 Dynamics of Functional Cellular Machinery: From Statics to Dynamics in Proteomic Biology 167
3-1 Dynamic Analysis of Cellular Function,
167
3-1-1 Strategy for Dynamic Analysis of Cellular Machinery (Multiprotein Complexes),
168
3-1-2 Methods for the Isolation of a Cellular Machine/Multiprotein Complex,
174
3-1-3 Cellular Machinery (Multiprotein Complex),
196
3-2 Dynamics of Ribosome Biogenesis,
198
3-2-1 Snapshot Analysis of Preribosomal Particles in Yeast,
201
3-2-2 Snapshot Analysis of Preribosomal Particles in Mammals,
207
3-2-3 Quantitative (Dynamic) Analysis Using Isotope-Labeled Reagents,
224
3-2-4 Outline of Human/Mammalian Ribosome Biogenesis,
231
3-3 Dynamic Analysis of Subcellular Structures,
232
3-3-1 Proteome Dynamics of the Nucleolus,
233
References,
236
Index 249


Nobuhiro Takahashi, PhD, is a Professor of Applied Biological Science in the Department of Agriculture at Tokyo University of Agriculture and Technology.

Toshiaki Isobe, PhD, is a Professor of Biochemistry in the Department of Chemistry at Tokyo Metropolitan University.