Part I. Fractionation Strategies for In-depth Blood Proteome Analysis

1. Plasma Biomarker Discovery using 3-D Protein Profiling Coupled with Label-free Quantitation

Lynn A. Beer, Hsin-Yao Tang, Kurt T. Barnhart, and David W. Speicher

2. Intact Protein Separation by 1 and 2-dimension Liquid Chromatography for Comparative Proteomic Separation of Partitioned Serum or Plasma

Simon Sheng, Helena Skalnikova, Andrew Meng, Qin Fu, Allen Everett, and Jennifer E. Van Eyk

3. In-depth Analysis of a Plasma or Serum Proteome using a 4-D Protein Profiling Method

Hsin-Yao Tang, Huan Wang, Lynn A. Beer, and David W. Speicher

4. Intact-protein Analysis System (IPAS) for Discovery of Serum-based Disease Biomarkers

Hong Wang and Samir Hanash

5. Model-based Discovery of Circulating Biomarkers

Maryann S. Vogelsang and Parag Mallick

6. Low-molecular Weight Plasma Proteome Analysis using Centrifugal Ultrafiltration

David W. Greening and Richard J. Simpson

7. High-throughput Analysis of Glycoproteins from Plasma

Yan Li and Hui Zhang

Part II. Blood Collection and Handling Strategies

8. Minimizing Pre-analytical Variation of Plasma Samples by Proper Blood Collection and Handling

Jizu Yi, David Craft, and Craig A. Gelfand

9. Collection and Handling of Blood Specimens for Peptidomics

Harald Tammen and Rüdiger Hess

10. Investigation of Peptide Biomarker Stability in Plasma Samples using Time-course MS Analysis

Jizu Yi, Zhaoxia Liu, Craig A. Gelfand, and David Craft

Part III. Methods for Quantitative Assaying of Blood-Based Biomarkers

11. Biomarker Validation in Blood Specimens by Selected Reaction Monitoring Mass Spectrometry of N-glycosites

Reto Ossola, Ralph Schiess, Paola Picotti, Oliver Rinner, Lukas Reiter, and Ruedi Aebersold

12. A Fluorescent Microsphere-based Method for Assay of Multiple Analytes in Plasma Oliver K. Bernhard, Rommel A. Mathias, Thomas W. Barnes, and Richard J. Simpson

13. Immuno-mass Spectrometry: Quantification of Low Abundance Proteins in Biological Fluids

Vathany Kulasingam, Christopher R. Smith, Ihor Batruch, and Eleftherios P. Diamandis

14. Qualitative and Quantitative Analysis of Glycated Proteins in Human Plasma by Glucose Isotopic Labeling with ¹³C₆-reducing Sugars

Feliciano Priego-Capote, Maria Ramírez-Boo, Denis Hochstrasser, and Jean-Charles Sanchez

Part IV. Proteome Analysis of Blood Cell Components, Vesicles, and Blood-related Fluids

15. Exosome Isolation for Proteomic Analyses and RNA Profiling

Douglas D. Taylor, Wolfgang Zacharias, and Cicek Gercel-Taylor

16. Extraction and Proteome Analysis of Liver Tissue Interstitial Fluid

Wei Sun, Ying Jiang, and Fuchu He

17. A Protocol for the Preparation of Cryoprecipitate and Cryo-depleted Plasma

Rosemary L. Sparrow, David W. Greening, and Richard J. Simpson

18. Preparation of Platelet Concentrates

David W. Greening, Richard J. Simpson, and Rosemary L. Sparrow

19. Phosphoproteome Analysis of the Platelet Plasma Membrane

Thomas Premsler, Urs Lewandrowski, Albert Sickmann, and René Peiman Zahedi

Part V. Bioinformatic Analysis of Blood Proteins and Peptides

20. Statistical Design and Analysis of Label-free LC-MS Proteomic Experiments: A Case Study of Coronary Artery Disease

Timothy Clough, Siegmund Braun, Vladimir Fokin, Ilka Ott, Susanne Ragg, Gunther Schadow, and Olga Vitek