Proteomics in biomedicine and pharmacology / edited by Rossen Donev.

Format:

Book

Contributor:

Donev, Rossen, editor.

Series:

Advances in protein chemistry and structural biology ; Volume 95.

Advances in Protein Chemistry and Structural Biology, 1876-1623 ; Volume 95

Language:

English

Subjects (All):

Proteomics.

Pharmacology.

Physical Description:

1 online resource (377 pages) : illustrations.

Edition:

First edition.

Place of Publication:

Waltham, Massachusetts : Academic Press, 2014.

Language Note:

English

Summary:

Volume 95 of Advances in Protein Chemistry and Structural Biology focuses on advances in proteomic techniques and their application in biomedicine and pharmacology. This volume describes in detail the applications of these techniques in studying a number of diseases and specific protein modifications and profiles, including phosphoproteomics, glycoproteomics, and more. Published continuously since 1944, the Advances in Protein Chemistry and Structural Biology series is the essential resource for protein chemists. Each volume brings forth new information about protocols and analysis of proteins. Each thematically organized volume is guest edited by leading experts in a broad range of protein-related topics. Describes advances in application of powerful techniques in translational research (biomedicine and pharmacology) Chapters are written by authorities in their field Targeted to a wide audience of researchers, specialists, and students The information provided in the volume is well supported by a number of high quality illustrations, figures, and tables.

Contents:

Front Cover

Proteomics in Biomedicine and Pharmacology

Copyright

Contents

Contributors

Preface

Chapter One: Application of Cutting-Edge Proteomics Technologies for Elucidating Host-Bacteria Interactions

1. Introduction

2. Classical Proteomics Strategies for Biomedical Research in General

2.1. Gel-based methods

3. Gel-Free Methods

3.1. Gel-free-labeling methods

3.1.1. Chemical labeling

3.1.2. Metabolic labeling

3.2. Label-free and absolute quantification

4. New Proteomic Methods in Looking for Bacterial Pathogens

5. Proteomic Advances in Looking for Host Organisms

6. Prospects

References

Chapter Two: Phosphoproteomic Techniques and Applications

2. Phosphoproteomic Methodologies

2.1. Phosphopeptide enrichment

2.1.1. Immunoaffinity chromatography

2.1.2. Metal oxide affinity chromatography

2.1.3. Immobilized metal affinity chromatography

2.2. Peptide separation by HPLC

2.2.1. Ion-exchange chromatography

2.2.2. Hydrophilic interaction chromatography and electrostatic repulsion-hydrophilic interaction chromatography

2.3. MS analysis

2.3.1. Collision-induced dissociation

2.3.2. MALDI-TOF MS

2.3.3. Phosphoproteome sequencing by MS/MS

3. Applications of Phosphoproteomics in Biomedicine

3.1. Applications in cancer research

3.2. Applications in stem cell research

3.3. Applications in cardiac research

3.4. Applications in immunity research

4. Discussion

Chapter Three: Recent Advances in Mass Spectrometry-Based Glycoproteomics

2. Glycoproteomic Profiling by MS

2.1. Glycoproteomics methodology

2.2. Affinity enrichment

2.3. Glycoprotein digestion

2.4. Glycan release

2.5. Chromatographic separation and SPE

2.6. Mass spectrometry

2.7. Quantitation

2.8. Bioinformatics.

3. MS-Based Glycoproteomics in Disease Research

3.1. Cancer biomarker research

3.2. Neurodegenerative disease research

4. Concluding Remarks

Acknowledgments

Chapter Four: Proteomics and Proteogenomics Approaches for Oral Diseases

2. An Integrated Proteogenomics Protocol for Personalized Dentistry

2.1. Human samples

2.1.1. Tissues

2.1.2. Blood

2.1.3. Dental plaque and oral biofilms

2.1.4. Gingival crevicular fluid

2.1.5. Saliva

2.1.6. Oral rinse

2.2. Bioinformatics analysis

2.2.1. Bioinformatics resources

2.2.2. Leader-gene algorithm

2.3. Proteomics technologies, with a focus on the label-free tools

2.3.1. Mass spectrometry

2.3.2. Anodic porous alumina

2.3.3. Nucleic acid programmable protein arrays

3. Oral Diseases

3.1. Dental caries

3.2. Periodontitis

3.3. Oral lichen planus

3.4. Oral cancer

Chapter Five: Advances in Nanocrystallography as a Proteomic Tool

2. Langmuir-Blodgett (LB)-Based Crystallization

3. Comparison of LB-Based Crystallization with Other Techniques

4. Fourier Transform Infrared (FTIR) Spectroscopy for Investigating LB-Films

5. Raman Spectroscopy

6. Laser-Induced Microdissection and Microfragmentation

7. Micrograzing-Incidence X-Ray Scattering Angle (μ-GISAXS)

8. In Silico Simulations

9. Bioinformatics

10. Molecular Dynamics

11. Clinically Relevant Proteins

11.1. GroEL

11.2. Casein kinase 2

11.3. Cytochrome P-450 side-chain cleavage

11.4. Rhodopsin

11.5. Globins

11.6. Insulin

12. Conclusions

Chapter Six: Modern Mass Spectrometry-Based Structural Proteomics

2. The Concept of Structural Proteomics

3. Limited Proteolysis

4. Surface Modification.

5. Hydrogen-Deuterium Exchange

6. Cross-linking

7. Additional Mass Spectrometric Techniques for the Protein Structure Analysis

8. Combination of Multiple Structural Proteomics Techniques

9. Use of Experimental Structural Proteomics Constraints in Protein Structure Modeling

10. Future Directions

11. Conclusions

Acknowledgment

Chapter Seven: Organellar Proteomics of Embryonic Stem Cells

2. Organelle Proteome Analysis of ESC

3. Subcellular Fractionation: Current Approaches and Challenges

4. Organelle Proteomics Databases and Tools

5. Concluding Remarks

Chapter Eight: Screening of Protein-Protein and Protein-DNA Interactions Using Microarrays: Applications in Biomedicine

2. Protein Arrays

2.1. Recent achievements of the protein arrays and their application to address the study of the human proteome

2.2. Advantages and limitations of protein arrays

3. Protein-Binding DNA Arrays and Their Application to Address the Study of DNA-Binding Proteins

3.1. Recent achievements of protein-binding DNA arrays and their application to address the study of the human proteome

3.2. Advantages and limitations of protein-binding DNA arrays

4. Databases and Web Resources for PPIs and for PDIs

5. Conclusions and Future Perspectives

Chapter Nine: Application of Proteomics in Diagnosis of ADHD, Schizophrenia, Major Depression, and Suicidal Behavior

2. Analytical Approaches Applied

2.1. Background

2.2. Proteomic analysis

2.3. Genomic and transcriptomic analysis

2.4. Metabolomics

3. Analytical Techniques

3.1. Protein profiling using matrix-assisted laser desorption-ionization time-of-flight mass spectrometry

3.2. Gas chromatography-mass spectrometry.

3.3. Fourier transform infrared spectroscopy

4. Biomarkers

4.1. Background

4.2. Types of biomarker

5. Depression

5.1. Definition of depression

5.2. Symptoms

5.3. Types of depression

5.4. Prevalence of major depression

5.5. Major depression theories

5.6. Comorbidity of other conditions with major depression

5.7. The potential benefit of biomarkers in depression

5.8. Forensic aspects of depressive disorders

6. Suicidal Behavior

6.1. Background

6.2. Definition

6.3. Risk factors

6.4. Prevalence

6.5. Comorbidity

6.6. Biomarkers and suicide

6.7. Forensic aspects of suicide behavior

7. Schizophrenia

7.1. Background

7.2. Symptoms

7.3. Types of schizophrenia

7.4. Biomarkers and schizophrenia

7.5. Forensic aspect of schizophrenic disorders

8. Attention Deficit/Hyperactivity Disorder

8.1. Background

8.2. Symptoms

8.3. ADHD subtypes

8.4. Comorbidity

8.5. Biomarkers and ADHD

8.6. Forensic aspects of ADHD

9. Concluding Remarks

Author Index

Subject Index.

Notes:

Bibliographic Level Mode of Issuance: Monograph

Includes bibliographical references and indexes.

Description based on online resource; title from PDF title page (ebrary, viewed July 23, 2014).

ISBN:

0-12-800595-5