9780444510242

Proteome Analysis

by
  • ISBN13:

    9780444510242

  • ISBN10:

    0444510249

  • Edition: 1st
  • Format: Hardcover
  • Copyright: 2004-03-26
  • Publisher: Elsevier Science
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Summary

This book explores the current status of proteomics, an exciting new discipline, which is less than 10 years old. This new field has rapidly grown into a major commercial and research enterprise with great prospects for dramatically advancing our knowledge of basic biological and disease processes. The contributors to this book are an international panel of proteomics experts, who review and discuss the current status of specific technologies and approaches. Proteomics represents an exciting new way to pursue biological and biomedical science at an unprecedented pace. Proteomics takes a broad, comprehensive, systematic approach to understanding biology that is generally unbiased and not dependent upon existing knowledge. The major components of proteomics from basic discovery using a range of alternative analytical methods to discovery validation and use for clinical applications are discussed. State-of-the-art protein profiling methods include high resolution two-dimensional gels, two-dimensional differential in-gel electrophoresis, LC-MS and LC-MS/MS using accurate mass tags, and protein identifications of proteins from gels using mass spectrometry methods are discussed in depth. Other chapters describe comprehensive characterization of proteomes using electrophoretic prefractionation and analyses of sub-proteomes based on specific posttranslational modifications including the phospho-proteome, the glyco-proteome, and nitrated proteins. These conventional proteome analysis chapters are complemented by discussion of emerging technologies and approaches such as affinity based biosensor proteomics as well as the use of protein microarrays, microfluidics and nanotechnology. Strategies for improving throughput by automation are also discussed. Additional chapters address the application of current proteome techniques to clinical problems and the availability of protein expression library resources for proteome studies.

Table of Contents

Preface v
List of Contributors xv
Chapter 1 Overview of Proteome Analysis 1(18)
David W. Speicher
1. Introduction
1(1)
2. Scope of the Proteomics Problem
2(2)
3. Global versus Targeted Proteomics
4(1)
4. Top Down Protein Profiling Methods
5(5)
4.1 Two-Dimensional Gels
6(1)
4.2 Two-Dimensional Differential Gel Electrophoresis (2D DIGE)
7(1)
4.3 Non-2D Gel Separation Methods
8(1)
4.4 Protein and Antibody Arrays
9(1)
5. Bottom Up Protein Profiling Methods
10(3)
5.1 Multi-Dimensional Protein Identification Technology
10(1)
5.2 Isotope-Coded Affinity Tags
11(1)
5.3 Accurate Mass Tag Based Protein Profiling
12(1)
6. Automation, Miniaturization, and Future Prospects
13(1)
7. Summary
14(1)
Acknowledgements
15(1)
References
15(4)
Chapter 2 Protein Profile Comparisons of Microorganisms, Cells and Tissues using 2D Gels 19(56)
Angelika G÷rg and Walter Weiss
1. Introduction
20(1)
2. Challenges of Protein Separation Methods for Proteome Analysis
21(17)
2.1 Highly Alkaline Proteins
22(3)
2.2 Zoom Gels, Non-Linear IPGs and Extended Separation Distances for Higher Resolution and Improved Detection of Low Copy Number Proteins
25(3)
2.3 Protein Enrichment and Sample Pre-Fractionation Procedures
28(2)
2.4 Low and High Molecular Mass Proteins
30(2)
2.5 Very Hydrophobic Proteins
32(2)
2.6 Protein Detection and Quantitation
34(3)
2.7 Automated Procedures
37(1)
3. Current Technology of 2D Electrophoresis with IPGs (IPG-Dalt)
38(26)
3.1 Protein Profile Comparisons of Microorganisms, Cells and Tissues using 2D Gels
38(1)
3.2 Sample Preparation
39(5)
3.3 Two-Dimensional Electrophoresis with IPGs (IPG-Dalt)
44(14)
3.4 Protein Visualization
58(3)
3.5 Computer-Aided Image Analysis
61(3)
4. 2D PAGE Databases
64(1)
5. Summary
64(1)
Acknowledgements
65(1)
References
65(10)
Chapter 3 Protein Profiling using Two-Dimensional Gel Electrophoresis with Multiple Fluorescent Tags 75(18)
William A. Hanlon and Patrick R. Griffin
1. Introduction
76(1)
2. Mechanics of DIGE Technology
77(3)
2.1 Sample Preparation
77(1)
2.2 Cyanine Dye Labeling
77(1)
2.3 Cyanine Image Visualization
78(1)
2.4 Gel Image Analysis
78(2)
3. Characterization of DIGE Technology
80(8)
3.1 Cyanine Dye Labeling Bias
80(2)
3.2 Assessment of Variability
82(1)
3.3 Limit of Detection of DIGE
83(3)
3.4 Importance of a Pooled Standard
86(1)
3.5 Comparison to Other 2D Gel Methods
87(1)
4. MS Identification of Cyanine Labeled Proteins
88(1)
4.1 Excision of Cyanine Labeled Proteins
88(1)
4.2 Protein Identification by LC-MS/MS
89(1)
5. Summary
89(1)
Acknowledgements
90(1)
References
90(3)
Chapter 4 Electrophoretic Prefractionation for Comprehensive Analysis of Proteomes 93(26)
Xun Zuo, KiBeom Lee and David W. Speicher
1. Introduction
94(2)
2. Electrophoretic Prefractionation Methods
96(7)
2.1 Rotofor
96(1)
2.2 Free Flow Electrophoresis
97(1)
2.3 IsoPrime and Related Multicompartment Electrolyzers
98(1)
2.4 Microscale Solution Isoelectrofocusing Combined with Narrow pH Range 2D PAGE
99(4)
3. Strategies for Analysis of Large Soluble Proteins and Insoluble Proteins
103(2)
3.1 Detection of Insoluble Proteins
103(1)
3.2 Detection of Large Soluble Proteins
104(1)
4. Downstream Proteome Analysis After Sample Fractionation
105(9)
4.1 Narrow pH Range 2D PAGE
105(3)
4.2 1D PAGE
108(1)
4.3 2D DIGE
109(1)
4.4 LC-MS/MS and LC/LC-MS/MS Methods
110(4)
5. Summary
114(1)
Acknowledgments
115(1)
References
115(4)
Chapter 5 Modification Specific Proteomics Applied to Protein Glycosylation and Nitration 119(20)
Judith Jebanathirajah and Peter Roepstorff
1. Introduction
119(2)
2. Glycosylation
121(12)
2.1 Why Study Protein Glycosylation?
121(2)
2.2 Strategies for Studying Glycosylation
123(10)
3. Tyrosine Nitration
133(1)
4. Summary
134(1)
References
134(5)
Chapter 6 Phosphoproteomics: Mass Spectrometry Based Techniques for Systematic Phosphoprotein Analysis 139(24)
Ole N°rregaard Jensen
1. Introduction
140(1)
2. Modification-Specific Proteomics and Phosphoproteomics
141(7)
2.1 Detection and Visualization of Phosphoproteins
142(3)
2.2 Enrichment of Phosphoproteins and Phosphopeptides
145(3)
3. Detection and Sequencing of Phosphopeptides by Mass Spectrometry
148(6)
3.1 Phosphoprotein Analysis by MALDI Mass Spectrometry
149(1)
3.2 Phosphoprotein Analysis by MALDI Tandem Mass Spectrometry
150(1)
3.3 Phosphoprotein Analysis by ESI Tandem Mass Spectrometry
150(2)
3.4 Integrated Strategies for Phosphoprotein and Phosphoproteome Analysis by Mass Spectrometry
152(1)
3.5 Phosphoprotein Characterization by Edman Degradation and Mass Spectrometry
153(1)
4. Cellular Dynamics: Integrated Methods for Quantitative Phosphoproteome Analysis
154(1)
5. Bioinformatics Tools for Phosphoprotein Sequence Analysis and Mass Spectrometry Data Interpretation
155(1)
6. Summary
156(1)
Acknowledgements
157(1)
References
157(6)
Chapter 7 Protein Identification by In-Gel Digestion and Mass Spectrometry 163(20)
Katheryn A. Resing and Natalie G. Ahn
1. Introduction
164(1)
2. In-Gel Digestion
165(5)
2.1 Gel Electrophoresis and Staining
165(1)
2.2 Gel Excision
166(1)
2.3 Digestion
166(2)
2.4 Peptide Extraction
168(1)
2.5 Assessing Peptide Recovery
169(1)
3. Mass Spectrometry
170(6)
3.1 Sample Preparation and Data Collection
170(1)
3.2 Peptide Mass Fingerprinting
171(1)
3.3 Protein Identification using MS/MS Spectra
172(4)
3.4 Database Searching Algorithms
176(1)
4. Troubleshooting
176(2)
4.1 Using Standards
176(1)
4.2 What if there are no Peptides in the MS Spectra?
176(1)
4.3 Common Contaminants
177(1)
4.4 Evaluating Database 'Hits'
178(1)
5. Summary
178(1)
Acknowledgements
179(1)
References
179(4)
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(42)
David G. Camp II and Richard D. Smith
1. Introduction
184(2)
2. Overall Experimental and Data Processing Approach
186(2)
3. Sample Processing
188(3)
3.1 Fractionation of Complex Peptide Mixtures
188(1)
3.2 Preparation of Membrane Proteins
188(1)
3.3 Stable-Isotope Labeling Methods
189(2)
4. High-Resolution Separations
191(3)
5. Chromatographic Separations Coupled to FTICR
194(1)
6. Generation of Accurate Mass and Time Tags and Their Utilization
195(1)
7. The Dynamic Range of Proteome Coverage
196(9)
7.1 Dynamic Range Expansion by DREAMS FTICR MS
199(6)
8. Demonstration of Global Proteomic Characterization
205(6)
9. Overcoming Challenges to Proteome-wide Measurements
211(90)
9.1 The Membrane Subproteome
211(1)
9.2 The Phosphoproteome
212(3)
10. Summary
215(3)
Acknowledgements
218(1)
References
219(6)
Chapter 9 Clinical Applications of Proteomics 225(18)
Sam M. Hanash
1. Introduction
225(1)
2. Correlative Studies Using Proteomics and Transcriptomics
226(2)
3. Disease Marker Identification Using Proteomics
228(3)
4. Disease Tissue Analysis Using Proteomics
231(3)
5. Protein Microarrays as a Novel Technology for Disease Investigations
234(3)
6. Summary
237(1)
References
237(6)
Chapter 10 Affinity-based Biosensors, Microarrays and Proteomics 243(44)
Edouard Nice and Bruno Catimel
1. Introduction
244(2)
2. Biosensor Technology
246(7)
2.1 Instrumentation
246(4)
2.2 Sensitivity
250(1)
2.3 Sensor Surfaces
250(3)
2.4 Surface Immobilisation
253(1)
3. Biosensor Applications
253(7)
3.1 Biosensor-based Ligand Searching
253(1)
3.2 Preparative Biosensor Ligand Fishing and Proteomics
254(4)
3.3 Cuvette-based Biosensors as Microaffinity Purification Platforms
258(2)
4. Protein Chip Mass Spectrometry Using SELDI
260(6)
4.1 SELDI Technology
260(3)
4.2 SELDI Applications
263(3)
5. Protein Chips and Microarrays
266(9)
5.1 Protein Profiling Arrays
267(4)
5.2 Protein Function Arrays
271(4)
6. Summary
275(1)
References
275(12)
Chapter 11 Protein Expression Library Resources for Proteome Studies 287(18)
Joshua LaBaer and Gerald Marsischky
1. Introduction
287(3)
1.1 Public Full-Length cDNA Clone Projects
288(1)
1.2 Cloning Formats
288(2)
1.3 Site-specific Recombination-based Cloning Systems
290(1)
2. Clone Collections
290(10)
2.1 Human
290(4)
2.2 Mouse
294(1)
2.3 Caenorhabditis Elegans
295(1)
2.4 Drosophila Melanogaster
296(1)
2.5 Saccharomyces Cerevisiae
297(2)
2.6 Pseudomonas Aeruginosa
299(1)
2.7 Arabidopsis Thaliana
300(1)
3. Summary
300(1)
Acknowledgements
300(1)
References
301(4)
Chapter 12 Automation of Proteome Analysis 305(22)
Peter James
1. Introduction
306(1)
2. Experimental Design
307(1)
2.1 Experimental Approaches
307(1)
2.2 Experimental Design Factors
308(1)
3. Sample Preparation
308(3)
3.1 Pre-Fractionation
310(1)
3.2 Protein Extraction
310(1)
4. 2D PAGE
311(1)
4.1 Resolution
311(1)
4.2 Gel Stability
312(1)
5. Image Analysis
312(1)
6. Robotics for Cutting, Digestion and Spotting
313(1)
7. Protein Fingerprinting by MALDI MS
314(5)
7.1 Automated In-Gel Digestion and Data Acquisition
318(1)
7.2 Data Extraction and Database Searching
318(1)
7.3 Confidence and Coverage Levels
319(1)
8. Peptide Fingerprinting by MS/MS
319(2)
8.1 Algorithms
320(1)
8.2 New MALDI MS-based Workflows
320(1)
8.3 New ESI-based Workflows
321(1)
9. The Crucial Elements: LIMS and Data Mining
321(2)
9.1 Pre-Packed Solutions
321(2)
9.2 Data Mining
323(1)
10. Summary
323(1)
Acknowledgements
324(1)
References
324(3)
Chapter 13 Micro- and Nanotechnology for Proteomics 327(44)
G. Marko-Varga, J. Nilsson and T. Laurell
1. Introduction
327(2)
2. Benefits of Miniaturisation
329(1)
3. Miniaturisation in Proteomics
330(2)
4. Fabrication of Microstructures
332(3)
5. Microstructures for Proteomics
335(29)
5.1 Protein Digestion On-Chip
335(3)
5.2 Microchip Solid Phase Enrichment
338(3)
5.3 Microdispensing to Interface MALDI
341(6)
5.4 Nanovial MALDI Target Arrays
347(17)
6. Summary
364(1)
Acknowledgements
365(1)
References
365(6)
Index 371

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