Serum/Plasma Proteomics: Methods and Protocols (Hardcover)

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 Rudiger 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 13 C 6 -reducing Sugars Feliciano Priego-Capote, Maria Ramirez-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 Rene 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 21. Data Management in Mass Spectrometry-based Proteomics Lennart Martens 22. Bioinformatics Challenges in the Proteomic Analysis of Human Plasma Joseph M. Foster and Lennart Martens 23. Using the Human Plasma PeptideAtlas to Study Human Plasma Proteins Terry Farrah, Eric W. Deutsch, and Ruedi Aebersold Appendix I Standard operating procedures for plasma collection in clinical research Tuck et al., (2009). J Proteome Res 8, 113-7 Appendix II Standard operating procedures for serum collection in clinical research Tuck et al., (2009). J Proteome Re