Proteomics of Human Body Fluids: Principles, Methods, and Applications PDF
Preview Proteomics of Human Body Fluids: Principles, Methods, and Applications
Proteomics of Human Body Fluids Proteomics of Human Body Fluids Principles, Methods, and Applications Edited by Visith Thongboonkerd, , MD FRCPT Medical Molecular Biology Unit Office for Research and Development Faculty of Medicine Siriraj Hospital, Mahidol University Bangkok, Thailand © 2007 Humana Press Inc. 999 Riverview Drive, Suite 208 Totowa, New Jersey 07512 All rights reserved. No part of this book may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise without written permission from the Publisher. All papers, comments, opinions, conclusions, or recommendations are those of the author(s), and do not necessarily reflect the views of the publisher. This publication is printed on acid-free paper. (cid:104) ANSI Z39.48-1984 (American Standards Institute) Permanence of Paper for Printed Library Materials. 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Printed in the United States of America. 10 9 8 7 6 5 4 3 2 1 eISBN 978-1-59745-432-2 Library of Congress Cataloging in Publication Data Proteomics of human body fluids : principles, methods, and applications / edited by Visith Thongboonkerd. p. ; cm. Includes bibliographical references and index. ISBN: 978-1-58829-657-3 (alk. paper) 1. Body fluids—Analysis. 2. Proteins—Analysis. 3. Proteomics. I. Thongboonkerd, Visith. [DNLM: 1. Body Fluids—chemistry. 2. Body Fluids—secretion. 3. Proteome—analysis. 4. Proteomics—methods. QU 105 P967 2007] RB52.P765 2007 616.07’56—dc22 2006025679 Preface Rapid growth of the “proteomics” field during the past twelve years has con- tributed to significant advances in science. To date, proteomic technologies have been widely applied to examining various kinds of biological materials. Clinical proteomics is the concept of using proteomic techniques to evaluate the proteomes in clinical samples for biomarker discovery and for better understand- ing of normal physiology and pathogenic mechanisms of human diseases. Trans- lating the proteomic information to clinical practice may lead to the ultimate goals of earlier diagnosis, improved therapeutic outcome and successful preven- tion of diseases. Human body fluids are produced, secreted, and/or excreted from various tissues or organs. Major compositions of body fluids are water, organic sub- stances and inorganic compounds. These compositions vary in each body fluid, making one’s function different from the others. Analyses of protein compo- nents in individual fluids would increase current knowledge on the biology and physiology of various organ systems, and on the pathophysiology of diseases, which cause alterations in protein production, secretion, and/or excretion from the affected tissues or organs into the body fluids. Additionally, human body fluids are the main targets and valuable sources for biomarker discovery. As the high-throughput capability and applicability of proteomics for analyzing proteins in the body fluids have been already proven, these desires are most likely achievable by using proteomic technologies. Proteomics of Human Body Fluids: Principles, Methods, and Applications is the first and nearly complete collection of applications of proteomics to analyze various human body fluids, including plasma, serum, urine, cere- brospinal fluid, pleural effusion, bronchoalveolar lavage fluid, sputum, nasal lavage fluid, saliva, pancreatic juice, bile, amniotic fluid, milk, nipple aspi- rate fluid, seminal fluid, vitreous fluid, dialysate, and ultrafiltrate yielded during renal replacement therapy. The book has been divided into two main parts. The first part provides basic principles and strategies for proteomic analysis of human body fluids, written by the leading experts in the proteomics field. The second part offers more details regarding methodolo- gies, recent findings and clinical applications of proteomic analysis of each specific type of human body fluids, written by the authorities in their respec- tive fields. Perspectives and future directions of each subject are also dis- cussed. This book, therefore, covers almost everything one needs to know about proteomics of human body fluids. v vvii PPrreeffaaccee I would like to thank all the authors who have contributed to this book, which would not be possible without their willingness to give the valuable time from their tight schedule and to share their knowledge and experience. I hope that the book will prove to be a useful source of references for all who are interested in this rapidly growing field of science and that the informa- tion inside this book will facilitate the progress of current and future studies on the human body fluid proteomes. Visith Thongboonkerd, MD,FRCPT Contents Preface ..............................................................................................................v Contributors .....................................................................................................ix PART I: PRINCIPLES OF PROTEOMICS APPLIED TO HUMAN BODY FLUIDS 1 Proteomic Strategies for 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 Hägglund, and Ole Nørregaard 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 K. K. 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 vii viii Contents 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 Ramström 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, Joël 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............................................................................................................521 Contributors MARCIN ADAMSKI • Michigan Proteomics Alliance for Cancer Research, Center for Computational Medicine and Biology, University of Michigan Medical School, Ann Arbor, MI. Present address: Faculty of Biological and Chemical Sciences, Integrative Biology School, The University of Queensland, Brisbane, Australia SUNG-MIN AHN • Joint ProteomicS Laboratory, Ludwig Institute for Cancer Research & the Walter and Eliza Hall Institute of Medical Research, P.O. Box 2008, Royal Melbourne Hospital Parkville, Victoria 3050, Australia FRANCISCO M. L. AMADO • Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal RON D. APPEL • Proteome Informatics Group, Swiss Institute of Bioinformatics and Computer Science Department, University of Geneva, Geneva, Switzerland JAMES N. BARANIUK • Proteomics Laboratory, Georgetown University, Washington, DC JONAS BERGQUIST • Department of Chemistry, Analytical Chemistry, Uppsala University, Uppsala, Sweden RAINER BISCHOFF • University of Groningen, Center of Pharmacy, Department of Analytical Biochemistry, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands THOMAS BLACKWELL • Michigan Proteomics Alliance for Cancer Research, Center for Computational Medicine and Biology, University of Michigan Medical School, Ann Arbor, MI JAKOB BUNKENBORG • Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark BEGONA CASADO • Proteomics Laboratory, Georgetown University, Washington, DC; and Department of Biochemistry “A Castellani”, University of Pavia, Italy MARIA CAVALETTO • Department of Enviroment and Life Sciences, University of Piemonte Orientale, Alessandria, Italy AMEDEO CONTI • National Council of Research—Institute of Science of Food Production, Section of Torino, Italy DAVID CRETTAZ • Service Régional Vaudois de Transfusion Sanguine, Lausanne, Switzerland ix x Contributors PEDRO R. CUTILLAS • Ludwig Institute for Cancer Research, University College London Branch; and Department of Biochemistry and Molecular Biology, University College London, London, UK PEDRO M. D. N. DOMINGUES • Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal MARK W. DUNCAN • Division of Endocrinology, Metabolism & Diabetes, Department of Pediatrics, University of Colorado Cancer Center Proteomics Core, University of Colorado Health Sciences Center, Denver, CO DOMINIC P. EISINGER • Upstate USA, Lake Placid, NY PAUL FALMAGNE • Department of Proteomics and Protein Biochemistry, 6 Avenue du Champs de Mars, University of Mons-Hainaut, B-7000, Belgium DENIS GALLOT • Unité de Médecine Materno-Fœtale, Hôtel-Dieu, CHU, Clermont-Ferrand, France WEIMIN GAO • Michigan Proteomics Alliance for Cancer Research. Present address: The Institute of Environmental and Human Health, Department of Environmental Toxicology, Texas Tech University, Lubbock, TX MARIA GABRIELLA GIUFFRIDA • National Council of Research—Institute of Science of Food Production, Section of Torino, Italy NATALIA GOVORUKHINA • University of Groningen, Center of Pharmacy, Department of Analytical Biochemistry, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands MADS GRØNBORG • McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, MD; and Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M, Denmark BRIAN B. HAAB • Michigan Proteomics Alliance for Cancer Research, Van Andel Research Institute, Grand Rapids, MI PER HÄGGLUND • Biochemistry and Nutrition Group, Biocentrum DTU 224-124, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark G. HANUMANTHU • Institute of Bioinformatics, Bangalore, India MARION HAUBITZ • Department of Nephrology, Medizinische Hochschule Hannover, D-30623 Hannover, Germany JOOST HEGMANS • Department of Pulmonary Medicine, Erasmus MC, Rotterdam, The Netherlands ANNABRITA HEMMES • Department of Pulmonary Medicine, Erasmus MC, Rotterdam, The Netherlands DENIS F. HOCHSTRASSER • Clinical Chemistry Laboratory, Geneva University Hospital, Geneva, Switzerland PATRICK HOHLFELD • Département de Gynécologie et Obstrétrique, CHUV, Lausanne, Switzerland Contributors xi CHRISTINE HOOGLAND • Proteome Informatics Group, Swiss Institute of Bioinformatics, Geneva, Switzerland SYBILLE M. N. HUNT • Proteome Systems, Locked Bag 2073, North Ryde 1670, Sydney, Australia K. K. JAIN • Jain PharmaBiotech, Blaesiring 7, CH-4057 Basel, Switzerland OLE NØRREGAARD JENSEN • Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark THOMAS O. JOOS • NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany URBAN A. KIERNAN • Intrinsic Bioprobes, Inc., 625 S. Smith Road, Suite #22, Tempe, AZ TROELS Z. KRISTIANSEN •(cid:31)McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, MD; and Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M, Denmark BART LAMBRECHT • Department of Pulmonary Medicine, Erasmus MC, Rotterdam, The Netherlands MARIA J. C. LOBO • High Institute of Health Sciences-North, Department of Dental Sciences, 4585-116 Gandra PRD, Portugal ANIRBAN MAITRA • McKusick-Nathans Institute of Genetic Medicine, The Sol Goldman Pancreatic Cancer Research Center, and Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University, Baltimore, MD RAJASREE MENON • Michigan Proteomics Alliance for Cancer Research, Center for Computational Medicine and Biology, University of Michigan Medical School, Ann Arbor, MI OLIVIER MICHEL • Clinical of Allergology and Respiratory Diseases, CHU Saint-Pierre- ULB. Brussels, B-1000, Belgium ATSUSHI MINAMOTO • Department of Ophthalmology and Visual Science, Division of Frontier Medical Science, Graduate School of Biomedical Sciences, Hiroshima University, Japan HARALD MISCHAK • Mosaiques Diagnostics and Therapeutics AG, Mellendorfer Str. 7, D-30625 Hannover; and Department of Nephrology, Medizinische Hochschule Hannover, D-30623 Hannover, Germany KHALED MOSTAGUIR • Proteome Informatics Group, Swiss Institute of Bioinformatics, Geneva, Switzerland DOBRIN NEDELKOV • Intrinsic Bioprobes, Inc., 625 S. Smith Road, Suite #22, Tempe, AZ RANDALL W. NELSON • Intrinsic Bioprobes, Inc., 625 S. Smith Road, Suite #22, Tempe, AZ
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