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Proteome analysis : interpreting the genome

Author: David W Speicher
Publisher: Amsterdam ; Boston : Elsevier, 2004.
Edition/Format:   Print book : English : 1st edView all editions and formats
Summary:

Explores the status of proteomics, that has the prospect for advancing our knowledge of basic biological and disease processes. This work discusses the components of proteomics from basic discovery  Read more...

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Document Type: Book
All Authors / Contributors: David W Speicher
ISBN: 9780444510242 0444510249
OCLC Number: 54512571
Description: xvii, 375 pages : illustrations (some color) ; 25 cm
Contents: Machine derived contents note: Chapter 1 --
Overview of Proteome Analysis 1 --
David W. Speicher --
1. Introduction 1 --
2. Scope of the Proteomics Problem 2 --
3. Global versus Targeted Proteomics 4 --
4. Top Down Protein Profiling Methods 5 --
4.1 Two-Dimensional Gels 6 --
4.2 Two-Dimensional Differential Gel Electrophoresis (2D DIGE) 7 --
4.3 Non-2D Gel Separation Methods 8 --
4.4 Protein and Antibody Arrays 9 --
5. Bottom Up Protein Profiling Methods 10 --
5.1 Multi-Dimensional Protein Identification Technology 10 --
5.2 Isotope-Coded Affinity Tags 11 --
5.3 Accurate Mass Tag Based Protein Profiling 12 --
6. Automation, Miniaturization, and Future Prospects 13 --
7. Summary 14 --
Acknowledgements 15 --
References 15 --
Chapter 2 --
Protein Profile Comparisons of Microorganisms, Cells and Tissues --
using 2D Gels 19 --
Angelika G4rg and Walter Weiss --
1. Introduction 20 --
2. Challenges of Protein Separation Methods for Proteome Analysis 21 --
2.1 Highly Alkaline Proteins 22 --
2.2 Zoom Gels, Non-Linear IPGs and Extended Separation Distances --
for Higher Resolution and Improved Detection of Low --
Copy Number Proteins 25 --
2.3 Protein Enrichment and Sample Pre-Fractionation Procedures 28 --
2.4 Low and High Molecular Mass Proteins 30 --
2.5 Very Hydrophobic Proteins 32 --
2.6 Protein Detection and Quantitation 34 --
2.7 Automated Procedures 37 --
3. Current Technology of 2D Electrophoresis with IPGs (IPG-Dalt) 38 --
3.1 Protein Profile Comparisons of Microorganisms, Cells --
and Tissues using 2D Gels 38 --
3.2 Sample Preparation 39 --
3.3 Two-Dimensional Electrophoresis with IPGs (IPG-Dalt) 44 --
3.4 Protein Visualization 58 --
3.5 Computer-Aided Image Analysis 61 --
4. 2D PAGE Databases 64 --
5. Summary 64 --
Acknowledgements 65 --
References 65 --
Chapter 3 --
Protein Profiling using Two-Dimensional Gel Electrophoresis with Multiple --
Fluorescent Tags 75 --
William A. Hanlon and Patrick R. Griffin --
1. Introduction 76 --
2. Mechanics of DIGE Technology 77 --
2.1 Sample Preparation 77 --
2.2 Cyanine Dye Labeling 77 --
2.3 Cyanine Image Visualization 78 --
2.4 Gel Image Analysis 78 --
3. Characterization of DIGE Technology 80 --
3.1 Cyanine Dye Labeling Bias 80 --
3.2 Assessment of Variability 82 --
3.3 Limit of Detection of DIGE 83 --
3.4 Importance of a Pooled Standard 86 --
3.5 Comparison to Other 2D Gel Methods 87 --
4. MS Identification of Cyanine Labeled Proteins 88 --
4.1 Excision of Cyanine Labeled Proteins 88 --
4.2 Protein Identification by LC-MS/MS 89 --
5. Summary 89 --
Acknowledgements 90 --
References 90 --
Chapter 4 --
Electrophoretic Prefractionation for Comprehensive Analysis of Proteomes 93 --
Xun Zuo, KiBeom Lee and David W. Speicher --
1. Introduction 94 --
2. Electrophoretic refractionation Methods 96 --
2.1 Rotofor 96 --
2.2 Free Flow Electrophoresis 97 --
2.3 IsoPrime and Related Multicompartment Electrolyzers 98 --
2.4 Microscale Solution Isoelectrofocusing Combined with Narrow pH --
Range 2D PAGE 99 --
3. Strategies for Analysis of Large Soluble Proteins and Insoluble Proteins 103 --
3.1 Detection of Insoluble Proteins 103 --
3.2 Detection of Large Soluble Proteins 104 --
'. Downstream Proteome Analysis After Sample Fractionation 105 --
4.1 Narrow pH Range 2D PAGE 105 --
4.2 ID PAGE 108 --
4.3 2D DIGE 109 --
4.4 LC-MS/MS and LC/LC-MS/MS Methods 110 --
5. Summary 114 --
Acknowledgments 115 --
References 115 --
Chapter 5 --
Modification Specific Proteomics Applied to Protein Glycosylation --
and Nitration 119 --
Judith Jebanathirajah and Peter Roepstorff --
I Introduction 119 --
2. Glycosylation 121 --
2.1 Why Study Protein Glycosylation? 121 --
2.2 Strategies for Studying Glycosylation 123 --
3. Tyrosine Nitration 133 --
4. Summary 134 --
References 134 --
Chapter 6 --
Phosphoproteomics: Mass Spectrometry Based Techniques for Systematic --
Phosphoprotein Analysis 139 --
Ole Norregaard Jensen --
1. Introduction 140 --
2. Modification-Specific Proteomics and Phosphoproteomics 141 --
2.1 Detection and Visualization of Phosphoproteins 142 --
2.2 Enrichment of Phosphoproteins and Phosphopeptides 145 --
3. Detection and Sequencing of Phosphopeptides by Mass Spectrometry 148 --
3.1 Phosphoprotein Analysis by MALDI Mass Spectrometry 149 --
3.2 Phosphoprotein Analysis by MALDI Tandem Mass Spectrometry 150 --
3.3 Phosphoprotein Analysis by ESI Tandem Mass Spectrometry 150 --
3.4 Integrated Strategies for Phosphoprotein and Phosphoproteome --
Analysis by Mass Spectrometry 152 --
3.5 Phosphoprotein Characterization by Edman Degradation --
and Mass Spectrometry 153 --
4. Cellular Dynamics: Integrated Methods for Quantitative --
Phosphoproteome Analysis 154 --
5. Bioinformatics Tools for Phosphoprotein Sequence Analysis and --
Mass Spectrometry Data Interpretation 155 --
6. Summary 156 --
Acknowledgements 157 --
References 157 --
Chapter 7 --
Protein Identification by In-Gel Digestion and Mass Spectrometry 163 --
Katheryn A. Resing and Natalie G. Ahn --
1. Introduction 164 --
2. In-Gel Digestion 165 --
2.1 Gel Electrophoresis and Staining 165 --
2.2 Gel Excision 166 --
2.3 Digestion 166 --
2.4 Peptide Extraction 168 --
2.5 Assessing Peptide Recovery 169 --
3. Mass Spectrometry 170 --
3.1 Sample Preparation and Data Collection 170 --
3.2 Peptide Mass Fingerprinting 171 --
3.3 Protein Identification using MS/MS Spectra 172 --
3.4 Database Searching Algorithms 176 --
4. Troubleshooting 176 --
4.1 Using Standards 176 --
4.2 What if there are no Peptides in the MS Spectra? 176 --
4.3 Common Contaminants 177 --
4.4 Evaluating Database 'Hits' 178 --
5. Summary 178 --
Acknowledgements 179 --
References 179 --
Chapter 8 --
The Use of Accurate Mass and Time Tags Based Upon High-Throughput --
Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for --
Global Proteomic Characterization 183 --
David G. Camp II and Richard D. Smith --
1. Introduction 184 --
2. Overall Experimental and Data Processing Approach 186 --
3. Sample Processing 188 --
3.1 Fractionation of Complex Peptide Mixtures 188 --
3.2 Preparation of Membrane Proteins 188 --
3.3 Stable-Isotope Labeling Methods 189 --
4. High-Resolution Separations 191 --
5. Chromatographic Separations Coupled to FTICR 194 --
6. Generation of Accurate Mass and Time Tags and Their Utilization 195 --
7. The Dynamic Range of Proteome Coverage 196 --
7.1 Dynamic Range Expansion by DREAMS FTICR MS 199 --
8. Demonstration of Global Proteomic Characterization 205 --
9. Overcoming Challenges to Proteome-wide Measurements 211 --
9.1 The Membrane Subproteome 211 --
9.2 The Phosphoproteome 212 --
10. Summary 215 --
Acknowledgements 218 --
References 219 --
Chapter 9 --
Clinical Applications of Proteomics 225 --
Sam M. Hanash --
1. Introduction 225 --
2. Correlative Studies Using Proteomics and Transcriptomics 226 --
3. Disease Marker Identification Using Proteomics 228 --
4. Disease Tissue Analysis Using Proteomics 231 --
5. Protein Microarrays as a Novel Technology for Disease Investigations 234 --
6. Summary 237 --
References 237 --
Chapter 10 --
Affinity-based Biosensors, Microarrays and Proteomics 243 --
Edouard Nice and Bruno Catimel --
1. Introduction 244 --
2. Biosensor Technology 246 --
2.1 Instrumentation 246 --
2.2 Sensitivity 250 --
2.3 Sensor Surfaces 250 --
2.4 Surface Immobilisation 253 --
3. Biosensor Applications 253 --
3.1 Biosensor-based Ligand Searching 253 --
3.2 Preparative Biosensor Ligand Fishing and Proteomics 254 --
3.3 Cuvette-based Biosensors as Microaffinity Purification Platforms 258 --
4. Protein Chip Mass Spectrometry Using SELDI 260 --
4.1 SELDI Technology 260 --
4.2 SELDI Applications 263 --
5. Protein Chips and Microarrays 266 --
5.1 Protein Profiling Arrays 267 --
5.2 Protein Function Arrays 271 --
6. Summary 275 --
References 275 --
Chapter 11 --
Protein Expression Library Resources for Proteome Studies 287 --
Joshua LaBaer and Gerald Marsischky --
1. Introduction 287 --
1.1 Public Full-Length cDNA Clone Projects 288 --
1.2 Cloning Formats 288 --
1.3 Site-specific Recombination-based Cloning Systems 290 --
2. Clone Collections 290 --
2.1 Human 290 --
2.2 Mouse 294 --
2.3 Caenorhabditis Elegans 295 --
2.4 Drosophila Melanogaster 296 --
2.5 Saccharomyces Cerevisiae 297 --
2.6 Pseudomonas Aeruginosa 299 --
2.7 Arabidopsis Thaliana 300 --
3. Summary 300 --
Acknowledgements 300 --
References 301 --
Chapter 12 --
Automation of Proteome Analysis 305 --
Peter James --
1. Introduction 306 --
2. Experimental Design 307 --
2.1 Experimental Approaches 307 --
2.2 Experimental Design Factors 308 --
3. Sample Preparation 308 --
3.1 Pre-Fractionation 310 --
3.2 Protein Extraction 310 --
4. 2DPAGE 311 --
4.1 Resolution 311 --
4.2 Gel Stability 312 --
5. Image AnalyMs 312 --
6. Robotics for Cutting, Digestion and Spotting 313 --
7. Protein Fingerprinting by MALDI MS 314 --
7.1 Automated In-Gel Digestion and Data Acquisition 318 --
7.2 Data Extraction and Database Searching 318 --
7.3 Confidence and Coverage Levels 319 --
S. Peptide Fingerprinting by MS/MS 319 --
8.1 Algorithms 320 --
8.2 New MALDI MS-based Workflows 320 --
8.3 New ESI-based Workflows 321 --
9. The Crucial Elements: LIMS and Data Mining 321 --
9.1 Pre-Packed Solutions 321 --
9.2 Data Mining 323 --
S0. Summary 323 --
Acknowledgements 324 --
References 324 --
Chapter 13 --
Micro- and Nanotechnology for Proteomics 327 --
G. Marko-Varga, J. Nilsson and T. Laurell --
1. Introduction 327 --
2. Benefits of Miniaturisation 329 --
3. Miniaturisation in Proteomics 330 --
4. Fabrication of Microstructures 332 --
5. Microstructures for Proteomics 335 --
5.1 Protein Digestion On-Chip 335 --
5.2 Microchip Solid Phase Enrichment 338 --
5.3 Microdispensing to Interface MALDI 341 --
5.4 Nanovial MALDI Target Arrays 347.
Responsibility: edited by David W. Speicher.
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