Proteomic Applications in Cancer Detection and Discovery

TIMOTHY D. VEENSTRA, PhD, Director of the Laboratory of Proteomics and Analytical Technologies at the Frederick National Laboratory for Cancer Research. Dr. Veenstra and his lab group develop and apply chromatography and mass spectrometry approaches to characterize protein complexes and the role of post-translational modifications in these complexes. Additionally, they use high-throughput proteomic approaches for the discovery of biomarkers for disease as well as proteomic and metabolomic technology for the interrogation of clinical samples. Dr. Veenstra has coauthored more than 300 peer-reviewed publications and is the coeditor of Proteomics for Biological Discovery.

Preface x

Acknowledgements xii

1 Systems Biology 1

2 Mass Spectrometry in Cancer Research 44

3 Quantitative Proteomics 93

4 Proteome Analysis of Post-translational Modifications 145

5 Characterization of Protein Complexes 196

6 Global Phosphorylation Analysis 242

7 The Search for Biomarkers in Biofluids 281

8 Proteomic Patterns: A New Paradigm in Diagnostics and Therapeutics? 309

9 The Emergence of Protein Arrays 370

10 The Role of Proteomics in Personalized Medicine 413

11 The Critical Role of Bioinformatics 449

12 Future Prospects of Proteomics in Cancer Research 480

Index 516

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