Main description:

Protein microarrays have been used for a wide variety of important tasks, such as identifying protein-protein interactions, discovering disease biomarkers, identifying DNA-binding specificity by protein variants, and for characterization of the humoral immune response. In Protein Microarray for Disease Analysis: Methods and Protocols, expert researchers provide concise descriptions of the methodologies currently used to fabricate microarrays for the comprehensive analysis of proteins or responses to proteins that can be used to dissect human disease. These methodologies are the toolbox for revolutionizing drug development and cell-level biochemical understanding of human disease processes. Beginning with a section on protein-detecting analytical microarrays, the volume continues with sections covering antigen microarrays for immunoprofiling, protein function microarrays, the validation of candidate targets, proteomic libraries, as well as signal detection strategies and data analysis techniques. Written in the highly successful Methods in Molecular Biology (TM) series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls.

Practical and cutting-edge, Protein Microarray for Disease Analysis: Methods and Protocols serves as a solid framework to aid scientists in understanding how protein microarray technology is presently developing and how it can be applied to transform our analysis of human disease.

Contents:

Part I: Protein-Detecting Analytical Microarrays

1. Detecting and Quantifying Multiple Proteins in Clinical Samples in High-Throughput Using Antibody Microarrays

Tanya Knickerbocker and Gavin MacBeath

2. Analysis of Serum Protein Glycosylation with Antibody-Lectin Microarray for High-Throughput Biomarker Screening

Chen Li and David M. Lubman

3. Antibody Suspension Bead Arrays

Jochen M. Schwenk and Peter Nilsson

4. Reverse Protein Arrays Applied to Host-Pathogen Interaction Studies

Victor J. Cid, Ekkehard Kauffmann, and Maria Molina

5. Identification and Optimization of DNA Aptamer Binding Regions Using DNA Microarrays

Nicholas O. Fischer and Theodore M. Tarasow

6. Recombinant Lectin Microarrays for Glycomic Analysis

Daniel C. Propheter, Ku-Lung Hsu, and Lara K. Mahal

Part II: Antigen Microarrays for Immunoprofiling

7. Recombinant Antigen Microarrays for Serum/Plasma Antibody Detection

Persis P. Wadia, Bita Sahaf, and David B. Miklos

8. SPOT Synthesis as a Tool to Study Protein-Protein Interactions

Dirk F.H. Winkler, Heiko Andresen, and Kai Hilpert

9. Native Antigen Fractionation Protein Microarrays for Biomarker Discovery

Robert J. Caiazzo, Jr., Dennis J. O'Rourke, Timothy J. Barder, Bryce P. Nelson, and Brian C.-S. Liu

10. Immunoprofiling Using NAPPA Protein Microarrays

Sahar Sibani and Joshua LaBaer

Part III: Protein Function Microarrays

11. High-Throughput Mammalian Two-Hybrid Screening for Protein-Protein Interactions Using Transfected Cell Arrays (CAPPIA)

Andrea Fiebitz and Dominique Vanhecke

12. Protein-Protein Interactions: An Application of Tus-Ter Mediated Protein Microarray System

Kalavathy Sitaraman and Deb K. Chatterjee

13. Kinase Substrate Interactions

Michael G. Smith, Jason Ptacek, and Michael Snyder

14. A Functional Protein Microarray Approach to Characterizing Posttranslational Modifications on Lysine Residues

Jun Seop Jeong, Hee-Sool Rho, and Heng Zhu

Part IV: Strategies for Validation of Candidate Targets

15. Multiplexed Detection of Antibodies Using Programmable Bead Arrays

Karen S. Anderson

16. A Co-Precipitation-Based Validation Methodology for Interactions Identified Using Protein Microarrays

Ovidiu Marina, Jonathan S. Duke-Cohan, and Catherine J. Wu

Part V: Generation of Proteomic Libraries

17. Development of Expression-Ready Constructs for Generation of Proteomic Libraries

Charles Yu, Kenneth H. Wan, Ann S. Hammonds, Mark Stapleton, Joseph W. Carlson, and Susan E. Celniker

Part VI: Detection Methods

18. Reverse Phase Protein Microarrays: Fluorometric and Colorimetric Detection

Rosa I. Gallagher, Alessandra Silvestri, Emanuel F. Petricoin III, Lance A. Liotta, and Virginia Espina

19. Foerster Resonance Energy Transfer Methods for Quantification of Protein-Protein Interactions on Microarrays

Michael Schaferling and Stefan Nagl

20. Label-Free Detection with Surface Plasmon Resonance Imaging

Christopher Lausted, Zhiyuan Hu, and Leroy Hood

Part VII: Data Analysis Techniques for Protein Function Microarrays

21. Data Processing and Analysis for Protein Microarrays

David S. DeLuca, Ovidiu Marina, Surajit Ray, Guang L. Zhang, Catherine J. Wu, and Vladimir Brusic

22. Database Resources for Proteomics-Based Analysis of Cancer

Guang Lan Zhang, David S. DeLuca, and Vladimir Brusic