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Providing current diverse approaches and techniques used to study the immunoproteome, Immunoproteomics: Methods and Protocols collects chapters from key researchers that deliver information to be used in diagnostics, disease progression, and vaccine correlates of protection analysis, to name but a few. This detailed volume includes techniques used for the study of the antibody targets of bacterial pathogens, viruses, and cancer, mass spectrometry-based approaches to characterize T-cell epitopes, chapters on detection and relative quantification of cytokines in serum, as well as in silico prediction of epitopes using sequence-based or modeling approaches. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Practical and thorough, Immunoproteomics: Methods and Protocols aids researchers in transferring these techniques to their own laboratories in addition to providing a reference to guide researchers toward appropriate techniques.

Immunoproteomics: Methods and Protocols

1. Introduction to the Immune System

Scott McComb, Aude Thiriot, Lakshmi Krishnan, and Felicity Stark

2. Immunoproteomics: Current Technology and Applications

Kelly M. Fulton and Susan M. Twine

3. Antigen Identification Using SEREX

Ugur Sahin and Özlem Türeci

4. Antigen Discovery Using Whole-Genome Phage Display Libraries

Elisa Beghetto and Nicola Gargano

5. Methods and Applications of Serological Proteome Analysis

Kelly M. Fulton, Shannon S. Martin, Lawrence Wolfraim, and Susan M. Twine

6. Pre-Absorbed Immunoproteomics: A Novel Method for the Detection of Bacterial Surface Proteins

Guangjin Liu, Wei Zhang, and Chengping Lu

7. Identification of the Antigen Content of Electroimmunoprecipitates

N. Helena Beyer and Niels H.H. Heegaard

8. An Immunoproteomics Approach to Screen the Antigenicity of the Influenza Virus

Kevin M. Downard

9. In Vivo Microbial Antigen Discovery (InMAD) to Identify Diagnostic Proteins and Polysaccharides that Are Circulating During Microbial Infections

Sindy J. Chaves, Kathleen Schegg, Thomas R. Kozel, and David P. AuCoin

10. Chemo-Enzymatic Production of O-Glycopeptides for the Detection of Serum Glycopeptide Antibodies

Alexander Nostdal and Hans H. Wandall

11. Enrichment and Characterization of Glycopeptide Epitopes from Complex Mixtures

Luc Tessier, Kelly M. Fulton, and Susan M. Twine

12. Whole-Cell MALDI-TOF Mass Spectrometry: A Tool for Immune Cell Analysis and Characterization

Richard Ouedraogo, Julien Textoris, Aurélie Daumas, Christian Capo, and Jean-Louis Mege

13. Cell-Based Arrays for the Identification of Interacting Polypeptide Domains or Epitopes

Richard H. Maier, Christina J. Maier, and Kamil Önder

14. Identification and Quantitation of MHC Class II-Bound Peptides from Mouse Spleen Dendritic Cells by Immunoprecipitation and Mass Spectrometry Analysis

Leonia Bozzacco and Haiqiang Yu

15. Construction and Screening of an Antigen-Derived Peptide Library Displayed on Yeast Cell Surface for CD4+ T Cell Epitope Identification

Fei Wen and Huimin Zhao

16. Profiling of Cytokine and Chemokine Responses Using Multiplex Bead Array Technology

Greg Harris and Wangxue Chen

17. Preparation of the Low Molecular Weight Serum Proteome for Mass Spectrometry Analysis

Timothy J. Waybright, King C. Chan, Timothy D. Veenstra, and Zhen Xiao

18. Identification of Protein Biomarkers in Human Serum Using iTRAQ and Shotgun Mass Spectrometry

Theodoros A. Koutroukides, Julian A.J. Jaros, Bob Amess, Daniel Martins-de-Souza, Paul C. Guest, Hassan Rahmoune, Yishai Levin, Mike Deery, Philip D. Charles, Svenja Hester, Arnoud Groen, Andy Christoforou, Julie Howard, Nick Bond, Sabine Bahn, and Kathryn S. Lilley

19. Genome-Based Bioinformatic Prediction of Major Histocompatibility Complex (MHC) Epitopes

Simon J. Foote

20. Structure-Based Prediction of Major Histocompatibility Complex (MHC) Epitopes

Andrew J. Bordner

21. Prioritization of Therapeutic Targets of Inflammation Using Proteomics, Bioinformatics, and In Silico Cell-Cell Interactomics

Arsalan S. Haqqani and Danica B. Stanimirovic

22. Commercial Considerations for Immunoproteomics

Scott M. Ferguson