Preface ......................................................... v
Acknowledgments ............................................... vii
Contributors ................................................. xiii
1. Overview and Introduction to Clinical Proteomics ............ 1
Young-Ki Paik, Hoguen Kim, Eun-Young Lee, Min-Seok
Kwon, and Sang Yun Cho
Part I: Specimen Collection for Clinical Proteomics
2. Specimen Collection and Handling: Standardization
of Blood Sample Collection ................................. 35
Harald Tammen
3. Tissue Sample Collection for Proteomics Analysis ........... 43
Jose I. Diaz, Lisa H. Cazares, and O. John Semmes
Part II: Clinical Proteomics by 2DE and Direct
MALDI/SELDI MS Profiling
4. Protein Profiling of Human Plasma Samples by
Two-Dimensional Electrophoresis ............................ 57
Sang Yun Cho, Eun-Young Lee, Hye-Young Kim, Min-Jung
Kang, Hyoung-Joo Lee, Hoguen Kim, and Young-Ki Paik
5. Analysis of Laser Capture Microdissected Cells by
2-Dimensional Gel Electrophoresis .......................... 77
Daohai Zhang and Evelyn Siew-Chuan Koay
6. Optimizing the Difference Gel Electrophoresis (DIGE)
Technology ................................................. 93
David B. Friedman and Kathryn S. Lilley
7. MALDI/SELDI Protein Profiling of Serum for the
Identification of Cancer Biomarkers ....................... 125
Lisa H. Cazares, Jose I. Diaz, Rick R. Drake, and
O. John Semmes
8. Urine Sample Preparation and Protein Profiling by
Two-Dimensional Electrophoresis and Matrix-Assisted
Laser Desorption Ionization Time of Flight Mass
Spectroscopy .............................................. 141
Panagiotis C. Zerefos and Antonia Vlahou
9. Combining Laser Capture Microdissection and Proteomics
Techniques ................................................ 159
Dana Mustafa, Johan M. Kros, and Theo Luider
Part III: Clinical Proteomics by LC-MS Approaches
10. Comparison of Protein Expression by Isotope-Coded
Affinity Tag Labeling ..................................... 181
Zhen Xiao and Timothy D. Veenstra
11. Analysis of Microdissected Cells by Two-Dimensional
LC-MS Approaches .......................................... 193
Chen Li, Yi-Hong, Ye-Xiong Tan, Jian-Hua Ai, Hu Zhou,
Su-Jun Li, Lei Zhang, Qi-Chang Xia, Jia-Rui Wu,
Hong-Yang Wang, and Rong Zeng
12. Label-Free LC-MS Method for the Identification of
Biomarkers ................................................ 209
Richard E. Higgs, Michael D. Knierman, Valentina
Gelfanova, Jon P. Butler, and John E. Hale
13. Analysis of the Extracellular Matrix and Secreted
Vesicle Proteomes by Mass Spectrometry .................... 231
Zhen Xiao, Thomas P. Conrads, George R. Beck, Jr.,
and Timothy D. Veenstra
Part IV: Clinical Proteomics and Antibody Arrays
14. Miniaturized Parallelized Sandwich Immunoassays ........... 247
Hsin-Yun Hsu, Silke Wittemann, and Thomas O. Joos
15. Dissecting Cancer Serum Protein Profiles Using
Antibody Arrays ........................................... 263
Marta Sanchez-Carbayo
Part V: Statistics and Bioinformatics in Clinical
Proteomics Data Analysis
16. 2D-PAGE Maps Analysis ..................................... 291
Emilio Marengo, Elisa Robotti, and Marco Bobba
17. Finding the Significant Markers: Statistical Analysis
of Proteomic Data ......................................... 327
Sebastien Christian Carpentier, Bart Panis, Rony
Swennen, and Jeroen Lammertyn
18. Web-Based Tools for Protein Classification ................ 349
Costas D. Paliakasis, loannis Michalopoulos, and
Sophia Kossida
19. Open-Source Platform for the Analysis of Liquid
Chromatography-Mass Spectrometry (LC-MS) Data ............. 369
Matthew Fitzgibbon, Wendy Law, Damon May, Andrea
Detter, and Martin McIntosh
20. Pattern Recognition Approaches for Classifying Proteomic
Mass Spectra of Biofluids ................................. 383
Ray L. Somorjai
Index ......................................................... 397
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