PROTEOMICS – HUMAN DISEASES AND PROTEIN FUNCTIONS Edited by Tsz-Kwong Man and Ricardo J. Flores           Proteomics – Human Diseases and Protein Functions Edited by Tsz-Kwong Man and Ricardo J. Flores Subject Editors: Tsz-Kwong Man and Ricardo J. Flores Published by InTech Janeza Trdine 9, 51000 Rijeka, Croatia Copyright © 2012 InTech All chapters are Open Access distributed under the Creative Commons Attribution 3.0 license, which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. After this work has been published by InTech, authors have the right to republish it, in whole or part, in any publication of which they are the author, and to make other personal use of the work. Any republication, referencing or personal use of the work must explicitly identify the original source. As for readers, this license allows users to download, copy and build upon published chapters even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. Notice Statements and opinions expressed in the chapters are these of the individual contributors and not necessarily those of the editors or publisher. No responsibility is accepted for the accuracy of information contained in the published chapters. The publisher assumes no responsibility for any damage or injury to persons or property arising out of the use of any materials, instructions, methods or ideas contained in the book. Publishing Process Manager Martina Durovic Technical Editor Teodora Smiljanic Cover Designer InTech Design Team First published February, 2012 Printed in Croatia A free online edition of this book is available at www.intechopen.com Additional hard copies can be obtained from orders@intechweb.org Proteomics – Human Diseases and Protein Functions, Edited by Tsz-Kwong Man and Ricardo J. Flores; Subject Editors: Tsz-Kwong Man and Ricardo J. Flores p. cm. ISBN 978-953-307-832-8   Contents  Preface IX Part 1 Proteomic Discovery of Disease Biomarkers 1 Chapter 1 Overview of Current Proteomic Approaches for Discovery of Vascular Biomarkers of Atherosclerosis 3 Lepedda Antonio Junior, Zinellu Elisabetta and Formato Marilena Chapter 2 From Biomarker Discovery to Clinical Evaluation for Early Diagnosis of Lung Surgery-Induced Injury 33 Mei-Ling Tsai, Shu-Hui Chen, Chih-Ching Chang and Ming-Ho Wu Chapter 3 Urinary Exosomes for Protein Biomarker Research 49 Delfin Albert Amal Raj, Immacolata Fiume, Giovambattista Capasso and Gabriella Pocsfalvi Chapter 4 Circadian Proteomics and Its Unique Advantage for Discovery of Biomarkers of Heart Disease 65 Peter S. Podobed, Gordon M. Kirby and Tami A. Martino Chapter 5 Exploring the Role of Biomarkers for the Diagnosis and Management of Traumatic Brain Injury Patients 89 Linda Papa Part 2 Proteomic Analysis of Protein Functions 107 Chapter 6 Comparative Proteomics: An Approach to Elucidating the Function of a Novel Gene Called BRE 109 Kenneth Ka Ho Lee, Mei KuenTang, John Yeuk-Hon Chan, Yiu Loon Chui, Elve Chen, Yao Yao, Olivia Miu Yung Ngan and Henry Siu Sum Lee VI Contents Chapter 7 Proteomic Approaches to Unraveling the RB/E2F Regulatory Pathway 135 Jone Mitxelena, Nerea Osinalde, Jesus M. Arizmendi, Asier Fullaondo and Ana M. Zubiaga Chapter 8 F 0 F 1 ATP Synthase: A Fascinating Challenge for Proteomics 161 Federica Dabbeni-Sala, Amit Kumar Rai and Giovanna Lippe Chapter 9 Proteomic Analysis of Wnt-Dependent Dishevelled-Based Supermolecular Complexes 189 Noriko Yokoyama Chapter 10 Identification of the Novel Plasminogen Receptor, Plg-R KT 219 Lindsey A. Miles, Nicholas M. Andronicos, Emily I. Chen, Nagyung Baik, Hongdong Bai, Caitlin M. Parmer, Shahrzad Lighvani, Samir Nangia, William B. Kiosses, Mark P. Kamps, John R. Yates III and Robert J. Parmer Chapter 11 Posttranslational Modifications of Myosin Light Chains Determine the Protein Fate 239 Virgilio J. J. Cadete and Grzegorz Sawicki Part 3 Proteomic Approaches to Dissecting Disease Processes 255 Chapter 12 Proteomic Study of Esophageal Squamous Cell Carcinoma 257 Yi-Jun Qi and Jen-Fu Chiu Chapter 13 Multidimensional Proteomics for the Identification of Endothelial Post Mortem Signals of Importance in Vascular Remodeling 275 Isabelle Sirois, Alexey V. Pshezhetsky and Marie-Josée Hébert Chapter 14 The Microtubule-Dissociating Tau in Neurological Disorders 291 Francisco José Fernández-Gómez, Susanna Schraen-Maschke and Luc Buée Chapter 15 Identification of Factors Involved in Neurogenesis Recovery After Irradiation of the Adult Mouse Subventricular Zone: A Preliminary Study 327 François Chevalier, Alexandra Chicheportiche, Mathieu Daynac, Jordane Depagne, Pascale Bertrand, François D. Boussin and Marc-André Mouthon Contents VII Part 4 Organelles and Secretome Proteomics 347 Chapter 16 Analysis of Organelle Dynamics by Quantitative Mass Spectrometry Based Proteomics 349 Florian Fröhlich, Tobias C. Walther and Romain Christiano Chapter 17 Mitochondrial Proteomics: From Structure to Function 369 Bernardo A. Petriz, Jeeser A. Almeida, Mirna S. Freire, Luiz A. O. Rocha, Taia M. B. Rezende and Octavio L. Franco Chapter 18 Proteomic Analysis of Plasma Membrane Proteins in an In Vitro Blood-Brain Barrier Model 391 Sophie Duban-Deweer, Johan Hachani, Barbara Deracinois, Roméo Cecchelli, Christophe Flahaut and Yannis Karamanos Chapter 19 Quantitative Proteomics for Investigation of Secreted Factors: Focus on Muscle Secretome 417 Jeanette Henningsen, Blagoy Blagoev and Irina Kratchmarova  Preface  Advances in the biological and computational fields during the past two decades have unsealed new realms of possibilities embodied in the Omics fields. Genomics, the study of the genome, has made great strides toward unraveling and characterizing important gene functions and regulations of numerous organisms. However, because of the lack of correlation between mRNA and proteins, and the importance of post- transcriptional regulations and protein modifications in protein functions and human diseases, proteomics has become increasingly important in the research field. Proteomics is the study of the proteome in the cell, which represents the complete set of proteins encoded by the genome. Since the introduction of gel electrophoresis for protein separation in the 1960’s, the methods for protein collection, identification, and quantification have continued to rapidly evolve and be refined. Protein research has expanded from the biochemical characterization of individual proteins to the high- throughput proteomics analysis of a cell, complex cell populations, and even an entire organism. This remarkable development highlights the potential of using proteomics methods to study protein functions and human diseases. New generations of mass spectrometry with higher resolutions and better quantification capabilities have also fueled the use of proteomics in biomarker and functional research. Proteomics approaches have been commonly used in the recent literature to identify biomarkers for disease screening, diagnosis, classification and monitoring. A potential application of proteomics in the field of oncology is in the discovery and validation of prognostic and predictive biomarkers, which play a fundamental role in personalized therapy for cancer patients. The goal of this book is to provide a succinct overview of proteomics advances, including descriptions of the challenges that have been conquered and those yet to be resolved. The intended readers of this book include scientists and students involved in protein research from a basic, translational, or clinical perspective. The book consists of 19 chapters written by leaders in their fields and is organized into four major sections. The first section is comprised of five chapters on proteomics research for disease biomarkers, which include discovery of atherosclerosis biomarkers, proteomics analysis of bronchial fluids after lung injury, proteomics approaches for urinary exosome characterization, traumatic brain injury diagnosis and management, and circadian proteomics. The second section focuses on the use of proteomics to unravel and characterize important human protein functions. The section consists of X Preface six chapters, which include elucidation of the function of a novel gene (BRE), characterization of the RB/E2F transcriptional regulatory pathway, analyses of essential proteins such as ATP synthetase and Wnt-dependent Disheveled-based supermolecular complexes, identification of a novel plasminogen receptor (Plg-R KT), and the study of posttranslational modifications of myosin light chains. The third section contains four chapters that recapitulate proteomics efforts in dissecting human disease processes. The first two chapters describe proteomics studies on esophageal squamous cell carcinoma and identification of endothelial signals for vascular remodeling. The last two chapters in this section focus on the role of microtubule- dissociating Tau in neurological disorders, and identification of factors involved in neurogenesis recovery following adult mouse brain irradiation. The final section reports recent proteomics research on specific subproteomes and cellular organelles. The section consists of four chapters, which detail the analyses on organelle dynamics, mitochondrial proteome, plasma membrane of the blood brain barrier, and muscle secretome. Finally, we would like to thank everyone who has made this book a reality and helped us to serve as subject editors of the InTech Proteomics Book series, and as editors of this volume. The whole experience has been very rewarding and exciting for us. This book would not have been created without the constant assistance and support of InTech staff members, especially our Publishing Process Manager, Ms. Martina Durovic. We truly appreciate the kind assistance from all of you!  Tsz-Kwong Man, PhD and Ricardo J. Flores, MD Baylor College of Medicine, Texas Children’s Hospital, USA . PROTEOMICS – HUMAN DISEASES AND PROTEIN FUNCTIONS Edited by Tsz-Kwong Man and Ricardo J. Flores           Proteomics – Human Diseases and Protein Functions Edited. 6 proteins ↓ 11 proteins 2 proteins with isoform dependent distributions signal transduction transport cell growth metabolism Olson et al., 2 010 Proteomics – Human Diseases and Protein. arteries (2 /14 ), carotid arteries (11 /14 ), and aortas (1/ 14). Most of them were conducted by using two-dimensional electrophoresis coupled to mass spectrometry as analytical method (10 /14 ). The