1. Affinity Depletion of Plasma and Serum for Mass Spectrometry-Based Proteome Analysis
Julian A. J. Jaros, Paul C. Guest, Sabine Bahn, and Daniel Martins-de-Souza
2. Tissue Sample Preparation for Biomarker Discovery
Yoshiyuki Suehara, Daisuke Kubota, and Tsuyoshi Saito
3. Subcellular Fractionation for Identification of Biomarkers: Serial Detergent Extraction by Subcellular Accessibility and Solubility
Sun-Il Hwang and David K. Han
4. Analysis of Secreted Proteins
Valeria Severino, Annarita Farina, and Angela Chambery
5. Preparation of Human Cerebrospinal Fluid for Proteomics Biomarker Analysis
Timothy J. Waybright
6. Proteomic Analysis of Frozen Tissue Samples Using Laser Capture Microdissection
Sumana Mukherjee, Jaime Rodriguez-Canales, Jeffrey Hanson, Michael R. Emmert-Buck, Michael A. Tangrea, DaRue A. Prieto, Josip Blonder, Donald J. Johann Jr.
7. Use of Formalin Fixed, Paraffin Embedded Tissue for Proteomic Biomarker Discovery
David B. Krizman and Jon Burrows
8. Phosphopeptide Enrichment Using Offline Titanium Dioxide Columns for Phosphoproteomics
Li-Rong Yu and Timothy D. Veenstra
9. iTRAQ-Labeling for Biomarker Discovery
Leroi V. DeSouza, Sébastien N. Voisin, and K. W. Michael Siu
10. Analysis of Glycoproteins for Biomarker Discovery
Jintang He, Yashu Liu, Jing Wu and David M. Lubman
11. SILAC in Biomarker Discovery
Benjamin C. Orsburn
12. Trypsin-mediated 18O/16O Labeling for Biomarker Discovery
Xiaoying Ye, King C. Chan, DaRue A. Prieto, Brian T. Luke, Donald J. Johann Jr,
Luke H. Stockwin, Dianne L. Newton, and Josip Blonder
13. Two-dimensional SDS-PAGE Fractionation of Biological Samples for Biomarker Discovery
Thierry Rabilloud, and Sarah Triboulet
14. Informatics of Protein and Post-Translational Modification Detection via Shotgun Proteomics
Jerry D. Holman, Surendra Dasari, and David L. Tabb
15. Quantitation of C-Met Tyrosine Phosphorylation Using MRM-MS
Zhaojing Meng, Apurva K. Srivastava, Ming Zhou, Timothy D. Veenstra
16. Preparation of Human Serum for Prolactin Measurement by Multiple Reaction Monitoring Mass Spectrometry
Timothy J. Waybright, Xia Xu, Jessica M. Faupel-Badger, Zhen Xiao
17. Label-Free Quantitative Shotgun Proteomics Using Normalized Spectral Abundance Factors
Karlie A. Neilson, Tim Keighley, Dana Pascovici, Brett Cooke, and Paul A. Haynes
18. Employment of Complementary Dissociation Techniques for Body Fluid Characterization and Biomarker Discovery
David M. Good and Dorothea Rutishauser
19. DPhosphopeptide Microarrays for Comparative Proteomic Profiling of Cellular Lysates
Liqian Gao, Hongyan Sun, Mahesh Uttamchandani, and Shao Q. Yao
20. Tissue Preparation for MALDI MS Imaging of Protein and Peptides
Simona Colantonio and Roberta M. Smith
21. Plant Proteogenomics: From Protein Extraction to Improved Gene Predictions
Brett Chapman, Natalie Castellana, Alex Apffel, Ryan Ghan, Grant R. Cramer, Matthew Bellgard, Paul A. Haynes, and Steven C. Van Sluyter
22. Label-free Differential Analysis of Murine Postsynaptic Densities
Scott P. Goulding, Michael J. MacCoss, and Christine C. Wu
23. Fractionation of Peptides by Strong Cation Exchange Liquid Chromatography
King C. Chan and Haleem J. Issaq