Difference Gel Electrophoresis (DIGE): Methods and Protocols

by Rainer Cramer (Editor), Reiner Westermeier (Editor)

Overview

Protein analysis is increasingly becoming a cornerstone in deciphering the molecular mechanisms of life. Proteomics, the large-scale and high-sensitivity analysis of proteins, is already pivotal to the new life sciences such as Systems Biology and Systems Medicine. Proteomics, however, relies heavily on the past and future advances of protein purification and analysis methods. DIGE, being able to quantify proteins in their intact form, is one of a few methods that can facilitate this type of analysis and still provide the protein isoforms in an MS-compatible state for further identification and characterization with high analytical sensitivity. Differential Gel Electrophoresis: Methods and Prools introduces the concept of DIGE and its advantages in quantitative protein analysis. It provides detailed prools and important notes on the practical aspects of DIGE with both generic and specific applications in the various areas of Quantitative Proteomics. Divided into four concise sections, this detailed volume opens with the basics of DIGE, the technique and its practical details with a focus on the planning of a DIGE experiment and its data analysis. The next section introduces various DIGE methods from those employed by scientists world-wide to more novel methods, providing a glance at what is on the horizon in the DIGE world. The volume closes with an overview of the wide range of DIGE applications from Clinical Proteomics to Animal, Plant, and Microbial Proteomics applications. Written in the highly successful Methods in Molecular Biology™ series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory prools, and notes on troubleshooting and avoiding known pitfalls.

Authoritative and accessible, Differential Gel Electrophoresis: Methods and Prools can be used by novices with some background in biochemistry or molecular biology as well as by experts in Proteomics who would like to deepen their understanding of DIGE and its employment in many hyphenations and application areas. With its many prools, applications, and methodological variants, it is also a unique reference for all who seek fundamental details on the working principle of DIGE and ideas for possible future uses of DIGE in novel analytical approaches.

Product Details

ISBN-13:	9781617795725
Publisher:	Springer-Verlag New York, LLC
Publication date:	02/07/2012
Series:	Methods in Molecular Biology , #854
Edition description:	2012
Pages:	401
Product dimensions:	7.01(w) x 10.00(h) x 0.04(d)

Table of Contents

Part I. Fundamentals

1. DIGE: Past and Future

                Jonathan S. Minden

2. The Basics of 2D DIGE

                Phil Beckett

3. Multifluorescence 2D Gel Imaging and Image Analysis

                Ingo Vormbrock, Sonja Hartwig, and Stefan Lehr

4. Assessing Signal-to-Noise in Quantitative Proteomics: Multivariate Statistical Analysis in DIGE Experiments

                David B. Friedman

5. Analysis of Proteins Using DIGE and MALDI Mass Spectrometry

                Witold M. Winnik, Robert M. DeKroon, Joseph S. Y. Jeong, Mihaela Mocanu, Jennifer B. Robinette, Christina Osorio, Nedyalka N. Dicheva, Eric Hamlett, and Oscar Alzate

6. Synthesis and Validation of Cyanin-Based Dyes for DIGE

                Michael E. Jung, Wan-Joong Kim, Nuraly K. Avliyakulov, Merve Oztug, and Michael J. Haykinson

Part II. Methods

7. 2D DIGE Saturation Labeling for Minute Sample Amounts

                Georg J. Arnold and Thomas Fröhlich

8. Proteomic Analysis of Redox-Dependent Changes Using Cysteine-Labeling 2D DIGE

                Hong-Lin Chan, John Sinclair, and John F. Timms

9. Analysis of Protein Post-Translational Modifications Using DIGE-Based Proteomics

                Robert M. DeKroon, Jennifer B. Robinette, Cristina Osorio, Joseph S. Y. Jeong, Eric Hamlett, Mihaela Mocanu, and Oscar Alzate

10. Comparative Analyses of Protein Complexes by Blue Native DIGE

                Katrin Peters and Hans-Peter Braun

11. 2D DIGE Analysis of Protein Extracts from Muscle Tissue

                Cecilia Gelfi and Sara De Palma

12. Combination of Highly Efficient Hexapeptide Ligand Library-Based Sample Preparation with 2D DIGE for the Analysis of the Hidden Human Serum/Plasma Proteome

                Sonja Hartwig and Stefan Lehr

13. 2D DIGE Analysis of Serum after Fractionation by ProteoMinerTM Beads

                Cynthia Liang, Gek San Tan, and Maxey C. M. Chung

14. Study Design in DIGE-Based Biomarker Discovery

                Alexandra Graf and Rudolf Oehler

15. Comparative 2D DIGE Analysis of the Depleted Serum Proteome for Biomarker Discovery

                Megan Penno, Matthias Ernst, and Peter Hoffman

Part III. Applications in Clinical Proteomics

16. Differential Gel-Based Proteomic Approach for Cancer Biomarker Discovery Using Human Plasma

                Keun Na, Min-Jung Lee, Hye-Jin Jeong, Hoguen Kim, and Young-Ki Paik

17. 2D DIGE for the Analysis of RAMOS Cells Sub-Proteomes

                Marisol Fernández and Juan Pablo Albar

18. Application of Saturation Labeling in Lung Cancer Proteomics

                Gereon Poschmann, Barbara Sitek, Bence Sipos, and Kai Stühler

19. Proteomic Profiling of the Epithelial-Mesenchymal Transition Using 2D DIGE

                Rommel A. Mathias, Hong Ji, and Richard J. Simpson

20. Method for Protein Subfractionation of Cardiovascular Tissues before DIGE Analysis

                Athanasios Didangelos, Xiaoke Yin, and Manuel Mayr

21. Application of DIGE and Mass Spectrometry in the Study of Type 2 Diabetes Mellitus (T2DM) Mouse Models

                Celia Smith, Davinia Mills, and Rainer Cramer

22. Evaluating the Efficacy of Subcellular Fractionation of Blast Cells Using Live Cell Labeling and 2D DIGE

                Yin Ying Ho, Megan Penno, Michelle Perugini, Ian Lewis, and Peter Hoffman

Part IV. Applications in Animal, Plant and Microbial Proteomics

23. DIGE Analysis of Plant Tissue Proteomes Using a Phenolic Protein Extraction Method

                Christina Rode, Traud Winkelmann, Hans-Peter Braun, and Frank Colditz

24. Native DIGE of Fluorescent Plant Protein Complexes

                Veronika Reisinger and Lutz Andreas Eichacker

25. An Overview of 2D DIGE Analysis of Marine (Environmental) Bacteria

                Ralf Rabus

26. Application of 2D DIGE in Animal Proteomics

                Ingrid Miller