SECTION I Emulsions
Preface ......................................................... v
Contributors ................................................... ix
Part I: Principles of Proteomics Applied to Human
Body Fluids
1. Proteomic Strategies tor Analyzing Body Fluids
Sung-Min Ahn and Richard J. Simpson ....................... 3
2. Sample Preparation of Body Fluids for Proteomics Analysis
Natalia Govorukhina and Rainer Bischoff .................. 31
3. Multiplexed Immunoassays for Protein Profiling
in Human Body Fluids
Silke Wittemann, Dominic P. Eisinger, Laurie L. Stephen,
and Thomas O. Joos ....................................... 71
4. Deciphering the Hieroglyphics of Functional Proteomics
Using Small Molecule Probes
Wayne F. Patton .......................................... 83
5. Modification-Specific Proteomic Analysis of Glycoproteins
in Human Body Fluids by Mass Spectrometry
Jakob Bunkenborg, Per Hagglund, and Ole Norregaard
Jensen .................................................. 107
6. Plasma Proteome Database
Malabika Sarker, G. Hanumanthu, and Akhilesh Pandey ..... 129
7. 2D PAGE Databases for Proteins in Human Body Fluids
Christine Hoogland, Khaled Mostaguir, Jean-Charles
Sanchez, Denis F. Hochstrasser, and Ron D. Appel .........137
8. Bioinformatics and Experimental Design for Biomarker
Discovery
Marc R. Wilkins and Sybille M.N. Hunt ................... 147
9. Integrative Omics, Pharmacoproteomics, and Human Body
Fluids
К.К. Jain ............................................... 175
Part II: Proteomic Analysis of Specific Types of Human Body
Fluids: Methods, Findings, Applications, Perspectives,
and Future Directions
10.The Human Plasma and Serum Proteome
Gilbert S. Omenn, Rajasree Menon, Marcin Adamski,
Thomas Blackwell, Brian B. Haab, Weimin Gao,
and David J. States ..................................... 195
11.Proteomics of Human Urine
Visith Thongboonkerd, Pedro R. Cutillas, Robert J.
Unwin, Stefan Schaub, Peter Nickerson, Marion Haubitz,
Harald Mischak, Dobrin Nedelkov, Urban A. Kiernan,
and Randall W. Nelson ................................... 225
12.Proteomics of Human Cerebrospinal Fluid
Margareta Ramstrom and Jonas Bergquist .................. 269
13.Proteomics of Pleural Effusion
Joost Hegmans, Annabrita Hemmes, and Bart Lambrecht ..... 285
14.Proteomics of Bronchoalveolar Lavage Fluid and Sputum
Ruddy Wattiez, Olivier Michel, and Paul Falmagne ........ 309
15.Proteomics of Sinusitis Nasal Lavage Fluid
Begona Casado, Simona Viglio, and James N. Baraniuk ..... 327
16.Proteomics of Human Saliva
Francisco M.L. Amado, Rui M.P. Vitorino,
Maria J.C. Lobo, and Pedro M.D.N. Domingues ............. 347
17.Proteomics of Human Pancreatic Juice
Mads Grønborg, Anirban Maitra, and Akhilesh Pandey ...... 377
18.Proteomics of Human Bile
Troels Z. Kristiansen, Anirban Maitra, and
Akhilesh Pandey ......................................... 399
19.Proteomics of Amniotic Fluid
David Crettaz, Lynne Thadikkaran, Denis Gallot,
Pierre-Alain Queloz, Vincent Sapin, Joel S. Rossier,
Patrick Hohlfeld, and Jean-Daniel Tissot ................ 415
20.Proteomics of Human Milk
Amedeo Conti, Maria Gabriella Giuffrida, and Maria
Cavaletto ............................................... 437
21.Proteomics of Nipple Aspirate Fluid in Nonlactating
Women
Edward R. Sauter ........................................ 453
22.Proteomics of Seminal Fluid
Benjamin Solomon and Mark W. Duncan ..................... 467
23.Proteomics of Vitreous Fluid
Atsushi Minamoto, Ken Yamane, and Tomoko Yokoyama ....... 495
24.Proteomics of Human Dialysate and Ultrafiltrate Fluids
Yielded by Renal Replacement Therapy
Michael Walden, Stefan Wittke, Harald Mischak,
and Raymond C. Vanholder, for the European
Uremic Toxin Work Group (EUTox) ......................... 509
Index ......................................................... 421
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