Proteomic Biology Using LC/MS (eBook)

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.

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 and
mass spectrometry.

1-3 Strategies for characterizing an entire proteome and
understanding 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 Cellular
Dynamics.

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 of
moderately complex protein mixtures.

Experimental example 2-1.

2D LC-MS system.

Experimental example 2-2.

2-1-2 Application of LC-MS methods to functional
proteomics.

Sub-cellular (organelle) using a cell-surface modification
reagent 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 using
ubiquitin-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 isotope
labeled 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: From
Statics 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 cellular
machinery/multi-protein complex.

Affinity-tag purification.

Affinity chromatography with an antibody- or a
protein-immobilized column.

Immuno-affinity purification using antibody-fixed
beads.

Experimental example 3-1.

Pull-down purification using immobilized protein
beads.

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 in
Mammals.

Experimental example 3-3.

3-2-3 Quantitative (dynamic) analysis using isotope labeled
reagents.

Experimental example 3-4.

3-2-4 Orthogonal Comparison of the Process of Ribosome
Biogenesis.

3-3 Dynamic analyses of Sub-cellular structures.

3-3-1 Proteome dynamics of the nucleolus.

"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)