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DEFINING THE MANDATE OF PROTEOMICS IN THE POST-GENOMICS ERA WORKSHOP REPORT STEERING COMMITTEE FOR DEFINING THE MANDATE OF PROTEOMICS IN THE PosT-GENoM~cs ERA U.S. National Committee for the International Union of Biochemistry and Molecular Biology Board on International Scientific Organizations Policy and Global Affairs Division and Board on Life Sciences Division of Earth and Life Studies NATIONAL RESEARCH COUNCIL OF THE NATIONAL ACADEMIES THE NATIONAL ACADEMIES PRESS Washington, D.C. www.nap.edu

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THE NATIONAL ACADEMIES PRESS 500 Fifth Street, N.W. Washington, DC 20001 NOTICE: The project that is the subject of this report was approved by the Governing Board of the National Research Council, whose members are drawn from the councils of the National Academy of Sciences, the National Academy of Engineering, and the Institute of Medicine. The members of the committee responsible for the report were chosen for their special competences and with regard for appropriate balance. This study was supported mostly by industry contributions (see Acknowledgments) and by Contract/Grant No. 0222688 between the National Academy of Sciences and the National Science Foundation and Contract/Grant No. N01-OD-4-2139 between the National Academy of Sciences and the National Institutes of Health. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the authoress and do not necessarily reflect the views of the organizations or agencies that provided support for the project. This report is available online at http://www.nap.edu Copyright 2002 by the National Academy of Sciences. All rights reserved. Printed in the United States of America

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THE NATIONAL ACADEMIES Advisers to the Nation on Science, Engineering, an`Medicine The National Academy of Sciences is a private, nonprofit, self-perpetuating society of distinguished scholars engaged in scientific and engineering research, dedicated to the furtherance of science and technology and to their use for the general welfare. Upon the authority of the charter granted to it by the Congress in 1863, the Academy has a mandate that requires it to advise the federal government on scientific and technical matters. Dr. Bruce M. Alberts is president of the National Academy of Sciences. The National Academy of Engineering was established in 1964, under the charter of the National Academy of Sciences, as a parallel organization of outstanding engineers. It is autonomous in its administration and in the selection of its members, sharing with the National Academy of Sciences the responsibility for advising the federal government. The National Academy of Engineering also sponsors engineering programs aimed at meeting national needs, encourages education and research, and recognizes the superior achievements of engineers. Dr. Wm. A. Wulf is president of the National Academy of Engineering. The Institute of Medicine was established in 1970 by the National Academy of Sciences to secure the services of eminent members of appropriate professions in the examination of policy matters pertaining to the health of the public. The Institute acts under the responsibility given to the National Academy of Sciences by its congressional charter to be an adviser to the federal government and, upon its own initiative, to identify issues of medical care, research, and education. Dr. Harvey V. Fineberg is president of the Institute of Medicine. The National Research Council was organized by the National Academy of Sciences in 1916 to associate the broad community of science and technology with the Academy's purposes of furthering knowledge and advising the federal government. Functioning in accordance with general policies determined by the Academy, the Council has become the principal operating agency of both the National Academy of Sciences and the National Academy of Engineering in providing services to the government, the public, and the scientific and engineering communities. The Council is administered jointly by both Academies and the Institute of Medicine. Dr. Bruce M. Alberts and Dr. Wm. A. Wulf are chair and vice chair, respectively, of the National Research Council. www.national-academies.org . . . . 111

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STEERING COMMITTEE FOR DEFINING THE MANDATE OF PROTEOMICS IN THE POST-GENOMICS ERA George Kenyon University ofMichigan, Chair David M. DeMarini U.S. Environmental Protection Agency Elaine Fuchs Rockefeller University David Galas Keck Graduate Institute of Applied Life Sciences Jack Kirsch University of California, Berkeley Contributing author: Thomas Leyh Albert Einstein College of Medicine National Research Council Stag Board on International Scientif c Organizations Laura Sheahan Program Officer Scott Spaulding Program Officer Pamela Gamble Senior Program Assistant Walter Moos MitoKor Gregory Petsko Brandeis University Dagmar Ringe Brandeis University Gerald Rubin Howard Hughes Medical institute Wendy White Director Lois Peterson Assistant Director

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ACKNOWLEDGMENTS The U.S. National Committee for the International Union of Biochemistry and Molecular Biology (USNC/TUBMB) and the Board on Life Sciences of the National Research Council (NRC) are grateful to the many individuals whose efforts made possible the symposium and the report. The symposium was supported by grants from the National Institute of General Medical Sciences/National Institutes of Health and the National Science Foundation, as well as by generous support from industry: ActiviX Biosciences, Applied Biosystems, Aventis Pharmaceuticals, DuPont Pharmaceuticals, Genentech, GeneProt, Large Scale Biology, Lynx Therapeutics, Micromass UK, MitoKor, Oxford GlycoSciences, Pfizer, Phylos, Prolinx, Proteome Systems., Structural Bioinformatics, and Structural GenomiX. The American Chemical Society also helped to support the symposium. People who were especially helpful in preparing for this meeting included Pamela Gamble, Laura Sheahan, Scott Spaulding, Lois Peterson, and Wendy White, all of the Board of International Scientific Organizations (BISO) of the NRC. George Kenyon, chair of both the U.S. National Committee for the International Union of Biochemistry and Molecular Biology (USN/lUBMB) and the ad hoc symposium steering committee, conceived of the workshop in an effort to encourage discussion about the future of proteomics, similar to the preliminary meetings held for the Human Genome Project. The workshop was organized by an ad hoc steering committee derived from two committees of the National Research Council (NRC): the USNC/lUBMB and the Board on Life Sciences. The steering committee selected the speakers and some of its members wrote the workshop report. The committee members are George Kenyon (Chair), David DeMarini, Elaine Fuchs, David Galas, Jack Kirsch, Walter Moos, Gregory Petsko, Dagmar Ringe, and Gerald Rubin. Breakout session chair, Tom Leyh, Albert Einstein College of Medicine was the only renort nllthor not part of the original steering committee. ~ ~ _# 1 meetings held for the Human Genome Project. , ,, . . ~ . . . . ~ _ , ~~~ ~ Or -- - I---__ ___ This report has been reviewed in draft form by individuals chosen for their diverse perspectives and technical expertise, in accordance with procedures approved by the NRC's Report Review Committee. The purpose of this independent review is to provide candid and critical comments that will assist the institution in making its published report as sound as possible and to ensure that the report meets institutional standards for objectivity and evidence. The review comments and draft manuscript remain confidential to protect the integrity of the deliberative process. We wish to thank the following individuals for their review of this report: Cheryl Arrowsmith, University of Toronto; Patricia Babbitt, University of California, San Francisco; David Baker, University of Washington; Samir Hanash, University of Michigan; John Quakenbush, Institute for Genomic Research, and Russell Thomas, Kalypsys, Inc. Although the reviewers listed above have provided many constructive comments and suggestions, they were not asked to endorse the content of the report, nor did they see the final draft before its release. The review of this report was overseen by Cynthia Beall, Case Western Reserve University, who was responsible for making certain that an independent examination of this report was carried out in accordance with institutional procedures and that all review comments were carefully considered. Responsibility for the final content of this report rests entirely with the authoring committee and the institution. . . V11

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CONTENTS Summary eve Introduction en 1 Proteomics ~ 2 Discussion of General Topics Covered at the Symposium 4 Lessons Learned from the Human Genome Project Sources of Proteins....... Protein Separation e 9 Protein Identification 12 Data Collection 14 Proteomics and the Problem of Function 17 . 1 9 ...20 Bioinformatics......... Structural Proteomics. Cellular Function..... Applications....... Samples.. Ethical Considerations....... Development of Diagnostics Computational Methods and Bioinformatics................ Database infrastructure and interface design...... Development of new methods.... Protein Structural Initiative. Research Coll:ahorntinn Conclusion References....... ..... 23 ... 23 ................. 25 ................ 27 .......................................... 27 Proteomics: A Coordinated International Effort 27 28 28 . 30 .................................................................... 31 1X

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BOXES BOX 1 Symposium Speakers and Affiliations. BOX 2 Comments from Francis Collins....... FIGURES Figure 1: Potential plasma proteins observable at various concentration ranges... 10 Figure 2: The Molecular Scanner 13 Figure 3: Technologies for (quantitative) global analysis 14 Figure 4: Isotope coded affinity tags (ICAT) 15 Figure 5: The Basic TCAT Approach 16 Figure 6: Selective identification of differentially expressed proteins 17 APPENDIXES A Speaker Biographies............................ B Symposium Agenda and Breakout Sessions. C Workshop Participants.......................... x .31 36 ................................................... 40

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