Proteome Analysis

by Speicher

• ISBN13: 9780444510242
• ISBN10: 0444510249
• Edition: 1st
• Format: Hardcover
• Copyright: 2004-03-26
• Publisher: Elsevier Science

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 Görg 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 Nørregaard 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