Proteome analysis: interpreting the genome
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Amsterdam
Elsevier
2004
|
| Ausgabe: | 1. ed. |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | xvii, 375 S. Ill. : graph. Darst. |
| ISBN: | 0444510249 |
Internformat
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| 245 | 1 | 0 | |a Proteome analysis |b interpreting the genome |c ed. by David W. Speicher |
| 250 | |a 1. ed. | ||
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| 300 | |a xvii, 375 S. |b Ill. : graph. Darst. | ||
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| 650 | 4 | |a Génomique | |
| 650 | 4 | |a Protéomique | |
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Datensatz im Suchindex
| _version_ | 1804132837963595776 |
|---|---|
| adam_text | PROTEOME ANALYSIS
INTERPRETING THE GENOME
Edited by
David W Speicher
The Wistar Institute
3601 Spruce Street
Philadelphia, PA 19104
USA
ELSEVIER
Amsterdam - Boston - Heidelberg - London - New York - Oxford
Paris - San Francisco - Singapore - Sydney - Tokyo
Contents
Preface v
List of Contributors xv
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 Gorg 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
viii Contents
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 Prefractionation Methods 96
2 1 Rotofor 96
Contents ix
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
4 Downstream Proteome Analysis After Sample Fractionation 105
4 1 Narrow pH Range 2D PAGE 105
4 2 ID PAGE 108
4 3 2DDIGE 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
1 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 N0rregaard 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
x Contents
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
Contents xi
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 1 9 9
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
xii Contents
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 Analysis 312
6 Robotics for Cutting, Digestion and Spotting 313
Contents xiii
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
8 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
10 Summary 323
Acknowledgements 324
References 324
Chapter 13
Micro- and Nanotechnology for Proteomics 327
G Marko-Varga, J Nilsson and T Laurel!
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
6 Summary 364
Acknowledgements 365
References 365
Index 371
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| spelling | Proteome analysis interpreting the genome ed. by David W. Speicher 1. ed. Amsterdam Elsevier 2004 xvii, 375 S. Ill. : graph. Darst. txt rdacontent n rdamedia nc rdacarrier Génomique Protéomique Genomics Proteomics Proteomanalyse (DE-588)4596545-6 gnd rswk-swf Proteomanalyse (DE-588)4596545-6 s DE-604 Speicher, David W. Sonstige oth HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=012852499&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Proteome analysis interpreting the genome Génomique Protéomique Genomics Proteomics Proteomanalyse (DE-588)4596545-6 gnd |
| subject_GND | (DE-588)4596545-6 |
| title | Proteome analysis interpreting the genome |
| title_auth | Proteome analysis interpreting the genome |
| title_exact_search | Proteome analysis interpreting the genome |
| title_full | Proteome analysis interpreting the genome ed. by David W. Speicher |
| title_fullStr | Proteome analysis interpreting the genome ed. by David W. Speicher |
| title_full_unstemmed | Proteome analysis interpreting the genome ed. by David W. Speicher |
| title_short | Proteome analysis |
| title_sort | proteome analysis interpreting the genome |
| title_sub | interpreting the genome |
| topic | Génomique Protéomique Genomics Proteomics Proteomanalyse (DE-588)4596545-6 gnd |
| topic_facet | Génomique Protéomique Genomics Proteomics Proteomanalyse |
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