The Urinary Proteome

1. Front Matter

   Pages i-xi

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2. Introduction to Urinalysis: Historical Perspectives and Clinical Application

   • Germán Echeverry, Glen L. Hortin, Alex J. Rai

   Pages 1-12

3. A Primer on Clinical Applications and Assays Using Urine: Focus on Analysis of Plasma Cell Dyscrasias Using Automated Electrophoresis and Immunofixation

   • Brianne Olivieri, Alex J. Rai

   Pages 13-26

4. Application of Free Flow Electrophoresis to the Analysis of the Urine Proteome

   • Aude L. Foucher, David R. Craft, Craig A. Gelfand

   Pages 27-45

5. Standardized Preprocessing of Urine for Proteome Analysis

   • Georg Martin Fiedler, Uta Ceglarek, Alexander Leichtle, Joachim Thiery

   Pages 47-63

6. Different Sample Preparation and Detection Methods for Normal and Lung Cancer Urinary Proteome Analysis

   • Supachok Sinchaikul, Payungsak Tantipaiboonwong, Supawadee Sriyam, Ching Tzao, Suree Phutrakul, Shui-Tein Chen

   Pages 65-88

7. Isolation and Purification of Exosomes in Urine

   • Patricia A. Gonzales, Hua Zhou, Trairak Pisitkun, Nam Sun Wang, Robert A. Star, Mark A. Knepper et al.

   Pages 89-99

8. Bioinformatics of the Urinary Proteome

   • Laurence D. Parnell, Christine M. E. Schueller

   Pages 101-122

9. PROTIS: Use of Combined Biomarkers for Providing Diagnostic Information on Disease States

   • Walter Hofmann, Cornelia Sedlmeir-Hofmann, Miroslav Ivandic´, Dagmar Ruth, Peter Luppa

   Pages 123-142

10. Statistical Contributions to Proteomic Research

    • Jeffrey S. Morris, Keith A. Baggerly, Howard B. Gutstein, Kevin R. Coombes

    Pages 143-166

11. A Review of Experimental Design Best Practices for Proteomics Based Biomarker Discovery: Focus on SELDI-TOF

    • Rebecca E. Caffrey

    Pages 167-183

12. Urine Proteomic Profiling for Biomarkers of Acute Renal Transplant Rejection

    • Shu-Ling Liang, William Clarke

    Pages 185-191

13. Surface Plasmon Resonance Biosensorics in Urine Proteomics

    • Peter B. Luppa, Jochen Metzger, Heike Schneider

    Pages 193-221

14. Urinary Proteins for the Diagnosis of Obstructive Sleep Apnea Syndrome

    • Ayelet Snow, David Gozal, Roland Valdes Jr., Saeed A. Jortani

    Pages 223-241

15. Immune Response Biomarker Profiling Application on ProtoArray® Protein Microarrays

    • Barry Schweitzer, Lihao Meng, Dawn Mattoon, Alex J. Rai

    Pages 243-252

16. Design and Validation of an Immunoaffinity LC–MS/MS Assay for the Quantification of a Collagen Type II Neoepitope Peptide in Human Urine: Application as a Biomarker of Osteoarthritis

    • Olga Nemirovskiy, Wenlin Wendy Li, Gabriella Szekely-Klepser

    Pages 253-270

17. Cell-Specific Biomarkers in Renal Medicine and Research

    • Martin Shaw

    Pages 271-302

18. Proteomic Assays for the Detection of Urothelial Cancer

    • Kris E. Gaston, H. Barton Grossman

    Pages 303-323

19. Urine Proteomic Analysis: Use of Two-Dimensional Gel Electrophoresis, Isotope Coded Affinity Tags, and Capillary Electrophoresis

    • Kimia Sobhani

    Pages 325-346

20. Proteomic Analysis of Pancreatic Secretory Trypsin Inhibitor/Tumor-Associated Trypsin Inhibitor from Urine of Patients with Pancreatitis or Prostate Cancer

    • Leena Valmu, Suvi Ravela, Ulf-Håkan Stenman

    Pages 347-357

This book is intended for scientifc researchers, clinical laboratorians, clinical and translational scientists, and others interested in proteomics and biomarker discovery. Urine is one of the most easily accessible biological samples, and it provides a treasure trove of molecules important in clinical diagnostics. In this book, we review briefly the classical urine tests that are performed in the clinical laboratory and then delve into the state-of-the-art methods for proteomic analysis using urine specimens. The most recent advances are discussed with regard to sample preparation, data analysis, and fnally methods and applications. A multitude of examples are provided including procedural details for the identifcation and characterization of urine biomarkers that hold potential for the diagnosis and treatment of many different disease conditions. The text is arranged so as to read systematically: introduction, sample preparation methods, applications, and data analysis. However, it does not necessarily require the reader to read it from start to fnish. Each chapter is organized such that it can be read individually without requiring knowledge from other chapters. I would like to thank the many individuals who made this book possible. These include the many authors who contributed to each of the individual chapters, the corresponding authors who took responsibility in providing the complete and fnished versions solicited for the peer review process, and the many scientifc reviewers who provided their valuable input and guidance.

• Clinical diagnostics
• Data analysis
• Microarray
• Proteomics
• Sample preparation
• Translation
• Urine biomarkers
• bioinformatics
• molecular biology

• Medical Center, Dept. Pathology & Cell Biology, Columbia University, New York, USA

  Alex J. Rai

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