Table Of ContentProteomics 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
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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
