
Proteomic Profiling and Analytical Chemistry
The Crossroads
Description
Key Features
- Covers the analytical consequences of protein and peptide modifications that may have a profound effect on how and what researchers actually measure
- Includes practical examples illustrating the importance of problems in quantitation and validation of biomarkers
- Helps in designing and executing proteomic experiments with sound analytics
Readership
Table of Contents
1. Introduction
- 1.1. Why Do Analytics Matter?
- 1.2. Expectations: Who and What?
- 1.3. What Is Next and Where Are We Going?
2. Biomolecules
- 2.1. Major Features and Characteristics of Proteins and Peptides
- 2.2. Hydrophilicity and Hydrophobicity
- 2.3. Effect of Protein Fragmentation
- 2.4. Effect of Posttranslational Modifications
- 2.5. Amino Acid Sequence and Separating Conditions
- 2.6. Cysteine and Methionine: Amino Acids Containing Sulfur
- 2.7. Protein Identification and Characterization
- 2.8. Structure–Function Relationship and Its Significance in Systems Biology Function
- 2.9. Protein Folding and Protein–Protein Interactions
- 2.10. Moonlighting of Proteins
- 2.11. Summary
3. General Strategies for Proteomic Sample Preparation
- 3.1. Introduction
- 3.2. Inhibitors of Proteolytic and Other Enzymes
- 3.3. Homogenization
- 3.4. Homogenization and Isolation of Organelles
- 3.5. Crude Protein Extraction
- 3.6. Serum and Cerebrospinal Fluid Protein Extraction
- 3.7. Fractionation Based on Size-Exclusion Filters
- 3.8. Chromatographic Methods of Protein Fractionation
- 3.9. Peptide Purification
- 3.10. Detergents, Lipids and DNA
- 3.11. Summary
4. Protein Extraction and Precipitation
- 4.1. Introduction
- 4.2. Focus on Hydrophobic Protein Extraction
- 4.3. The Role of Protein Solvation
- 4.4. Protein Precipitation
- 4.5. Salting Out
- 4.6. Isoelectric Point Precipitation
- 4.7. Organic Solvent-Driven Precipitation
- 4.8. Trichloroacetic Acid Precipitation
5. Online and Offline Sample Fractionation
- 5.1. Introduction
- 5.2. Strong Cation Exchange, Weak Cation Exchange, Continuous or Step Gradient?
- 5.3. Protein and Peptide Separation Based on Isoelectric Point
- 5.4. Capillary Columns for Proteomic Analyses
6. Immunoaffinity Depletion of Highly Abundant Proteins for Proteomic Sample Preparation
- 6.1. Introduction
- 6.2. Immunodepletion Techniques
- 6.3. Capacity of Immunodepletion Columns and Other Devices
- 6.4. Reproducibility
- 6.5. Quality Control of Immunodepletion
- 6.6. Albuminome
- 6.7. Summary
7. Gel Electrophoresis
- 7.1. Fundamentals of Gel Electrophoresis
- 7.2. Two-Dimensional Gel Electrophoresis
8. Quantitative Measurements in Proteomics: Mass Spectrometry
- 8.1. Introduction
- 8.2. Absolute Quantitation
- 8.3. Relative Quantitation in Proteomics
- 8.4. Summary
9. SWATH-MS: Data Acquisition and Analysis
- 9.1. Introduction
- 9.2. Tandem Mass Spectrometry for Quantitative Proteomics
- 9.3. SWATH-MS Data Acquisition
- 9.4. Overview of SWATH-MS Data Analysis
- 9.5. Summary
10. Top-Down Proteomics
- 10.1. Introduction
- 10.2. Protein Separation Methods
- 10.3. Mass Spectrometry of Intact Proteins
- 10.4. Software for Data Analysis
11. Proteomic Database Search and Analytical Quantification for Mass Spectrometry
- 11.1. Introduction
- 11.2. Protein Databases
- 11.3. Search Engines
- 11.4. Mass Spectrometry Data Searches: Things to Consider
- 11.5. Post-Database Search Data Processing
- 11.6. Searches for Posttranslational Modifications
- 11.7. Summary
12. Design and Statistical Analysis of Mass-Spectrometry-Based Quantitative Proteomics Data
- 12.1. Introduction
- 12.2. Mass Spectrometry-Based Quantitative Proteomics
- 12.3. Issues and Statistical Consideration on Experimental Design
- 12.4. Data Preprocessing for Statistical Analysis
- 12.5. Statistical Analysis of Protein Expression Data
- 12.6. Summary
13. Principles of Analytical Validation
- 13.1. Introduction
- 13.2. Liquid Chromatographic Methods
- 13.3. Validation of a Liquid Chromatographic Method: Identity, Assay, Impurities
- 13.4. Recovery
- 13.5. Accuracy
- 13.6. Precision
- 13.7. Calibration Curve, Linearity, and Sensitivity
- 13.8. Selectivity and Specificity
- 13.9. Stability
- 13.10. Aberrant Results and Errors in Analyses
- 13.11. Further Development of Methods Validation
14. Validation in Proteomics and Regulatory Affairs
- 14.1. The “Uphill Battle” of Validation
- 14.2. Accuracy and Precision
- 14.3. Experimental Design and Validation
- 14.4. Validation of the Method
- 14.5. Validation of Detection Levels
- 14.6. Validation of Reproducibility and Sample Loss
- 14.7. Validation of Performance of Instruments
- 14.8. Bioinformatics: Validation of Output of Proteomic Data
- 14.9. Cross-Validation of Initial Results
- 14.10. Proteomics and Regulatory Affairs
Product details
- No. of pages: 298
- Language: English
- Copyright: © Elsevier 2016
- Published: March 2, 2016
- Imprint: Elsevier
- Paperback ISBN: 9780444636881
- eBook ISBN: 9780444636904
About the Editors
Pawel Ciborowski

Affiliations and Expertise
Jerzy Silberring

Affiliations and Expertise
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