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Introduction. <p><b>Chapter 1. Overview of Proteomics.</b></p> <p>What is the proteomics?</p> <p>1-2 Proteomic analysis using two-dimensional gel electrophoresis (2DE) and mass spectrometry .</p> <p>1-2-1 Protein separations by 2DE.</p> <p>1-2-2 Development of the technologies for protein identification .</p> <p>1-2-3 The protein identification based on gel separation and mass spectrometry.</p> <p>1-3 Strategies for characterizing an entire proteome and understanding the proteome function.</p> <p>1-3-1 Modification-specific proteomics.</p> <p>1-3-2 Activity-based profiling.</p> <p>1-3-3 Sub-cellular (Organelle) proteomics.</p> <p>1-3-4 Machinery [complex (interaction)] proteomics.</p> <p>1-3-5 Dynamic proteomics.</p> <p><b>Chapter 2. Proteomic Tools for Analysis of Cellular Dynamics.</b></p> <p>2-1 LC-BASED PROTEOMICS TECHNOLOGIES.</p> <p>  2-1-1 LC system for peptide separation .</p> <p>  LC-MS interface.</p> <p>  ESI apparatus .</p> <p>  Micro- and nano-capillary columns.</p> <p>  Packing materials.</p> <p>1D-LC system.</p> <p>  Application of 1D-LC-MS/MS to shotgun analysis of moderately complex protein mixtures.</p> <p>Experimental example 2-1.</p> <p>2D LC-MS system.</p> <p>Experimental example 2-2.</p> <p>  2-1-2 Application of LC-MS methods to functional proteomics.</p> <p>Sub-cellular (organelle) using a cell-surface modification reagent and cell fractionation.</p> <p>Experimental example 2-3 .</p> <p>Modification proteomics.</p> <p>  Phosphorylation site mapping.</p> <p>Experimental example 2-4.</p> <p>  Glycosylation site mapping.</p> <p>Experimental example 2-5.</p> <p>  Ubiquitinated protein identification by using ubiquitin-specific antibody .</p> <p>Experimental example 2-6.</p> <p>2-2 Development of quantitative proteomics.</p> <p>2-2-1 Isotope labeling for quantitative analysis using MS.</p> <p>in vivo labeling.</p> <p>in vitro labeling.</p> <p>2-2-2 Quantitation strategies for LC-MS analysis of isotope labeled peptide mixture and software for computer analysis.</p> <p>2-2-3 Label free quantitation software.</p> <p>2-2-4 Absolute quantitation.</p> <p>Method using stable isotope labeled reference peptides.</p> <p>Method without using internal standards.</p> <p><b>Chapter 3. Dynamics of Functional Cellular Machinery: From Statics to Dynamics in Proteomic Biology.</b></p> <p>From statics to dynamics in proteomic biology.</p> <p>3-1 DYNAMIC ANALYSIS OF CELLULAR FUNCTION.</p> <p>3-1-1 Strategy for dynamic analysis of cellular machineries (multi-protein complexes).</p> <p>Approach collecting time dependent data.</p> <p>Approach utilizing stage specific protein association.</p> <p>3-1-2 Methods for the isolation of a cellular machinery/multi-protein complex.</p> <p>Affinity-tag purification.</p> <p>Affinity chromatography with an antibody- or a protein-immobilized column.</p> <p>  Immuno-affinity purification using antibody-fixed beads.</p> <p>  Experimental example 3-1.</p> <p>  Pull-down purification using immobilized protein beads.</p> <p>  Experimental example 3-2.</p> <p>3-1-3 Cellular machinery (multi-protein complex).</p> <p>3-2 Dynamics of Ribosome Biogenesis .</p> <p>3-2-1 Snapshot Analyses of Preribosomal Particles in Yeast .</p> <p>3-2-2 Snapshot Analyses of Preribosomal Particles in Mammals.</p> <p>Experimental example 3-3.</p> <p>3-2-3 Quantitative (dynamic) analysis using isotope labeled reagents.</p> <p>  Experimental example 3-4.</p> <p>3-2-4 Orthogonal Comparison of the Process of Ribosome Biogenesis.</p> <p>3-3 Dynamic analyses of Sub-cellular structures.</p> <p>3-3-1 Proteome dynamics of the nucleolus.</p>

"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." (<i>Quarterly Review of Biology</i>, December 2008)

<p>Nobuhiro Takahashi, PhD, is a Professor of Applied Biological Science in the Department of Agriculture at Tokyo University of Agriculture and Technology.</p> <p>Toshiaki Isobe, PhD, is a Professor of Biochemistry in the Department of Chemistry at Tokyo Metropolitan University.</p>

<p>A comprehensive guide to LC-MS applications that probe the dynamic aspectS of proteomes</p> <p>The systematic identification and characterization of proteins and proteomes is one of the major interdisciplinary research areas of the life sciences in the post-genomic era. One of the primary goals of current proteomic research is the description of the composition, dynamics, and connections of the multi-protein "modules" and "machineries" that perform a wide range of biological functions in the cell. Proteomic Biology Using LC-MS: Large Scale Analysis of Cellular Dynamics and Function examines the latest LC-MS technologies in depth and explores their application to the analysis of the dynamic aspects of cellular function. After an overview of proteomics and proteomic technologies, it covers:</p> <ul> <li> <p>The basic aspects of LC-MS technology, including the principle of the method and assembly of the LC-MS system</p> </li> <li> <p>Integrated LC-based MS methodologies coupled with quantitative methodologies and/or bioinformatics</p> </li> <li> <p>The most recent applications, such as the analyses of signal transduction complexes following stimulation of cells and the analysis of the dynamic processes of ribosome biogenesis</p> </li> <li> <p>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</p> </li> </ul> <p>Detailed experimental examples help readers explore various applications in action. With comprehensive coverage of LC-MS technologies applicable to the analysis of dynamic cellular functions in proteomic scale, this is a unique reference for investigators and laboratory staffs in academic institutions and industries. It is also a valuable resource for students as well as for scientists in other fields who want to bridge the gap between their specialties and proteomic biology.</p>

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