Takahashi / Isobe / Desiderio Proteomic Biology Using LC/MS

Large Scale Analysis of Cellular Dynamics and Function
1. Auflage 2008
ISBN: 978-0-470-14964-5
Verlag: John Wiley & Sons
Format: PDF
Kopierschutz: Adobe DRM (»Systemvoraussetzungen)

E-Book, Englisch, 264 Seiten, E-Book

Reihe: Wiley-Interscience Series on Mass Spectrometry

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.

Autoren/Hrsg.

Takahashi, Nobuhiro

Isobe, Toshiaki

Desiderio, Dominic M.

Nibbering, Nico M.

Inhaltsverzeichnis

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

Über Autor(innen)

Nobuhiro Takahashi, PhD, is a Professor of Applied BiologicalScience in the Department of Agriculture at Tokyo University ofAgriculture and Technology.
Toshiaki Isobe, PhD, is a Professor of Biochemistry in theDepartment of Chemistry at Tokyo Metropolitan University.