(Publisher-supplied data) Table of Content 1. Chapter-1 Historical perspectives 1.1 Introduction to Proteomics 1.2 Proteome and Proteomics A. Proteins as cell?s way of accomplishing specific functions B. Pre-genomic proteomics 1.2.1 Genetics of Proteins A. One gene ?one enzyme theory B. One gene ?many proteins I. RNA Splicing II. RNA Editing References 5. Chapter-5 Proteomics of Protein?Protein interactions /Interactomes 5.1 In vivo analysis of Protein ?Protein Interactions A. Yeast two hybrids Assay B. Phage Display 5.2 In vitro Analysis of Protein Interactions A. Mass Spectrometry (MS) B. Functional Protein Micro array 5.3 In Silico analysis of Protein ?Protein Interactions ? Rosetta Stone and other computational analyses 5.4 Synthetic Genetic method to determine Protein-Protein Interactions 5.5 Interactomes 5.5.1 Prokaryotic interactomes 5.5.2 Eukaryotic interactomes A. Yeast B. Fly C. Worm D. Human E. Plasmodium F. Plants 5.5.3 Interactome during Human Development and Disease 5.6 Evolution and Conservation of Interactomes 5.7 Interactome and complexity of organism 5.8 Interaction of proteins with small molecules References III. RNA Silencing 1.2.2 Molecular Biology of genes and proteins 1.2.3 Protein Chemistry before proteomics References 2. Chapter-2 Proteomics - relation to Genomics, Bioinformatics 2.1 Genomics and Functional Genomics and their utilization in Proteomics 2.2 Bioinformatics and Computational aspects of Proteomics References

3 Methodology 3.1 Separation of proteins- via a multidimensional approach A. Electrophoresis I 2D Gel Electrophoresis II Capillary Electrophoresis B. Liquid Chromatography 3.2 Determination of the protein structure 3.2.1Determination of the Amino acid Sequences

primary structure of proteins

I. Proteomics without Mass Spectrometry

A. Amino acid sequence of a protein from DNA sequence

B. Edman Degradation ? N-terminal amino acid sequence analysis3. Chapter- II. Proteomics based on Mass Spectrometry

A. Mass Spectrometry ? Principle, Historical Background and

Instrumentation

B. Bottom-up and Top-down Mass Spectrometry

C. Bioinformatics and Determination of Amino acid sequence of a protein

3.2.2 Analysis of Protein 3 Dimensional Structure

A. X-ray Crystallography,

B. Neutron Scattering

C. NMR

3.3 Determination of the amount of proteins

A. Quantitation of proteins in 2D gel ( Staining , densitometry)

B. Differential gel analysis ( Dige)

C. Quantitative Mass spectrometric protein ( Isotope labeling , ICAT)

D. Protein Micro Array for large-scale analysis

3.4 Structural and Functional Proteomics

References

4. Chapter ? 4 Proteomics of Protein Modifications

4.1. Phosphorylation and phosphoproteiomics

4.2. Glycoproteins and glycoproteiomics

4.3. Ubiquitination and ubiquitinomics

4.4. Miscellaneous modifications of proteins

6. Chapter -6 Applications

I Application of Proteomics in Medicine: Proteomics, Human Disease and Medicine

6.1 Diseasome

6.2 Medical Proteomics: Proteomics of Human Body Parts

A. Body fluid Proteome

a. Blood /Plasma/Serum Proteome

b. Salivary Proteome

c. Others

B. Liver Proteome

C. Brain Proteome

D. Heart/ cardiovascular Proteome

E. Cancer Proteome

F. Organelle Proteome

G. Proteome of Human Parasites

6.3 Clinical Proteomics

A. Genomics and Proteomics of human diseases

B. Proteomics of Diagnostic markers and Drug Development

C. Proteomics & Personalized Medicine

D. Metabolomics

6.4 Meta Proteomics and Human Health

II. Application of Proteomics in Biotechnology, Industry & others

6.5 Biotechnology & Industry of Drug Production

6.6. Metaproteomics of Microbial Fermentation

a. Metabolite- Production

b. Bioremediation

c. Biomass and Energy production

6.7 Beef Industry

6.8. Bioterrorism & Bio-defense

References

7. Chapter -7 Proteomics - Future

7.1 Technical Scope of Proteomics ? Beyond Protein Identification

7.2 Scientific scope of Proteomics- Control of Epigenesis

7.3 Medical Scope of Proteomics

A. Human Diseases

B. Development of Drugs

C. Personalized Medicine

D. Proteomics and Metabolomics

7.4 Proteomics, Energy Production and bioremediation

7.5 Proteomics and Biodefense