| 08:00-09:30 |
Opening Session
Co-Chairs: Rolf Apweiler and Young-Ki Paik
Ballroom, level 2, Convention Center |
| 8:00-8:15 |
Welcome Address; John R. Yates III and Peipei Ping, Congress Co-Chairs |
| 8:15-8:30 |
Welcome Address; John Bergeron; President, HUPO and
Michael Snyder, President, US HUPO |
| 8:30-9:10 |
Opening Address: Future Directions in Advanced Technologies for Molecular-Based Diagnostics and Therapeutics; Anna D. Barker; Deputy Director,
National Cancer Institute |
| 9:10-9:20 |
Questions and Answers |
| 9:20-9:30 |
NIH Roadmap Planning - An Update
Salvatore Sechi; Director, Proteomic Program, National Institute of Health/NIDDK
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| 09:30-10:00 |
Break, Posters and Exhibits; Exhibit Hall B, lower level |
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| 10:00-12:30 |
Plenary Session: Proteomic Investigations and Biomedical Discoveries;
Co-Chairs: Richard Simpson and Peipei Ping
Ballroom, level 2, Convention Center |
Mon Oral B
10:00-10:30 |
Invited Lecture: Analysis of Biochemical Activities and Disease Using Protein Microarrays; Michael P. Snyder; Yale University, New Haven, CT............ 1295 |
| Mon Oral B 10:30-11:00 |
Invited Lecture: Organellar Proteomics as a Paradigm for the Systems Biology Study of Disease; John J.M. Bergeron; Department of Anatomy and Cell Biology;
McGill University, Montreal, QC, Canada................ 1437 |
| Mon Oral B 11:00-11:30 |
Invited Lecture: A Human Protein Atlas for Expression Profiles in Human Tissues and Cells; Mathius Uhlen; Royal Institute of Technology, Stockholm, Sweden............................... 1424 |
| Mon Oral B 11:30-12:00 |
Invited Lecture: Proteomic Technology Development for Biomedical Discoveries; Ruedi Aebersold, Swiss Federal Institute of Technology, Zurich, Switzerland |
| Mon Oral B 12:00-12:30 |
Invited Lecture: Moving towards Rapid Discovery and Validation;
Jan E. Schnitzer; Sidney Kimmel Cancer Center, San Diego, CA............ 1310 |
| 12:30-14:00 |
Posters and Exhibits. Exhibit Hall B, lower level |
| 12:45-13:45 |
Corporate Sponsored Symposia. See schedule on page 7. Please reserve at the company exhibit booth. |
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Monday, October 30, 2006 |
| 14:00-16:30 |
Parallel Sessions |
| 14:00-16:30 |
Featured Symposium: Future Pioneers in Proteomics:
Young Investigator Award Competition
Co-Chairs: John R. Yates III and Catherine Fenselau
Ballroom A, level 2, Convention Center |
| 14:00-14:10 |
Introduction: John R. Yates III |
Mon Oral C
14:10-14:30 |
Quantitative Protein Profiling in Plasma Using both Undirected and Directed Strategies; Michael J. MacCoss1; Greg Finney1; Jesse Canterbury1; Martin LeWinter2; Michael J. Toth2; 1University of Washington, Seattle, WA;
2University of Vermont, Burlington, VT.......................... 1251 |
Mon Oral C
14:30-14:50 |
Proteome-Wide Characterization of in vivo Protein Processing; Kris Gevaert; Petra Van Damme; Francis Impens; Joël Vandekerckhove;
Ghent University, Ghent, Belgium..... 320 |
Mon Oral C
14:50-15:10 |
144-Sample on-Target Parallel Homogenization/Transfer Method for Solvent-Free MALDI-MS Analysis of Peptides and Proteins; Sarah Trimpin1; Charles N. McEwen2; Hong Ji3; Max L. Deinzer3; 1Oregon Health & Science University, Portland, OR; 2DuPont Corporate Center for Analytical Sciences, Wilmington, DE; 3Oregon State University, Corvallis, OR......................... 1097 |
| 15:00-15:10 |
Break |
Mon Oral C
15:10-15:30 |
Toward Automated de novo Peptide Sequencing and Protein Characterization by Combined Electron Capture Dissociation and Activated-Ion Electron Capture Dissociation; Yury O. Tsybin1; Huan He2; Mark R. Emmett1; Christopher L. Hendrickson1; Alan G. Marshall1; 1National High Magnetic Field Laboratory, Tallahassee, FL; 2Florida State University, Tallahassee, FL.. 1012 |
Mon Oral C
15:30-15:50 |
Overlapping MS/MS Spectra and Disease Proteomics; Nuno Bandeira; Pavel Pevzner; University of California, San Diego, La Jolla, CA............................... 1227 |
| 15:50–16:30 |
Questions from the Judges |
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|
Monday, October 30 |
| 14:00-16:30 |
Parallel Session 2: Bioinformatics in Proteomics
Co-Chairs: David Fenyo and Martin McIntosh
Room 201, level 2, Convention Center |
Mon Oral D
14:00-14:30 |
State of the Art Lecture: PSI-MS Data Interchange Standards: Roadmap for the Future; Randall Julian; Purdue University, West Lafayette, IN |
Mon Oral D
14:30-15:00 |
State of the Art Lecture: Integrated Open-Source Platforms for Comprehensive Mining High Resolution LC-MS/MS Data; Martin McIntosh; Molecular Diagnostic Program, FHCRC, Seattle, WA............................... 1423 |
| 15:00-15:10 |
Break |
Mon Oral D
15:10-15:30 |
Automatic Validation of Phosphopeptide Identifications Using Linear Ion Trap Mass Spectrometer; Bingwen Lu; Cristian Ruse; Tao Xu; Sung Kyu Park; John R. Yates III; 1The Scripps Research Institute, La Jolla, CA................ 191 |
| Mon Oral D 15:30-15:50 |
Progress on Data Standards and Reporting Requirements for Gel Electrophoresis; Andrew R Jones1; Frank Gibson2; Christine Hoogland3; 1University of Manchester, Manchester, UK; 2University of Newcastle, Newcastle, UK; 3Swiss Institute of Bioinformatics, Genève, Switzerland................................. 327 |
| Mon Oral D 15:50-16:10 |
Detecting Unpredicted Splice Sites in Tandem Mass Spectra; Franz F. Roos1; Jonas Grossmann2; Sacha Baginsky2; Wilhelm Gruissem2; Riko Jacob1; Peter Widmayer1; 1Institute of Theoretical Computer Science, ETH, Zurich, Switzerland; 2Institute of Plant Science, ETH, Zurich, Switzerland................................. 504 |
| Mon Oral D 16:10-16:30 |
Incorporating Sequence Information into the Scoring Function: A Hidden Markov Model for Improved Peptide Identification; Jainab Khatun; Morgan C Giddings; University of North Carolina, Chapel Hill, NC.... 386 |
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Monday, October 30 |
| 14:00-16:30 |
Parallel Session 3: Human Disease Proteomics I
Co-Chairs: Jan van Oostrum and Thierry Rabilloud
Ballroom B, level 2, Convention Center |
| Mon Oral E 14:00-14:30 |
State of the Art Lecture: Throughput and Data Quality Issues and Potential Solutions for Human Disease Proteomics and Biomarker Discovery; Richard D Smith; PNNL, Richland, WA 1421 |
| Mon Oral E 14:30-15:00 |
State of the Art Lecture: Linking Proteomics to Signaling Pathways and Diseases; Jan van Oostrum; Novartis Institute of Biomedical Research, Basel, Switzerland... 1440 |
| 15:00-15:10 |
Break |
| Mon Oral E 15:10-15:30 |
MHC Class I Peptides Motif Discovery; Anik Forest; Sophie Dahan; Lyne Boucher; Francois Denis; Laetitia Cortes; Heather Butler; Dmitri Sitnikov; Paul Kearney; Gregory J Opiteck; Eustache Paramithiothis;
Caprion Pharmaceuticals, Montreal, Canada 461 |
| Mon Oral E 15:30-15:50 |
Molecular Profiling of Murine Prostate Cancer Models for Pathway-Specific Biomarker Discovery; Katharine Ellwood-Yen1; Seema Bhopale1; Justin Wong1; Shunyou Wang1; George Thomas1; Howard Schulman3; Danny Afar2; Hong Wu1; Thomas Graeber1; Charles Sawyers1; 1UCLA, Los Angeles, CA; 2PDL BioPharma, Fremont, CA; 3PPD/SurroMed, Wilmington, NC 1056 |
| Mon Oral E 15:50-16:10 |
Protein Movement during Platelet Activation Revealed using Shotgun Proteomics of Subcellular Compartments; James P McRedmond; Niaobh M O'Donoghue; Matthew J Sullivan; Gerard Cagney; Conway Institute, University College Dublin, Dublin, Ireland.............. 372 |
| Mon Oral E 16:10-16:30 |
Biomarker Discovery from Trace Amounts of Cervical Tissue in Pre-Cancer Stages Using Laser Capture Microdissection of ThinPrep® Slides and LC-MS; Ye Gu1; Shiaw-Lin Wu1; David Hanlom2; Jane Meyer2; James Linder2; William S. Hancock1; Barry L. Karger1; 1Northeastern University, Boston, MA; 2Cytyc Corp., Marlborough, MA 112 |
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Monday, October 30 |
| 14:00-16:30 |
Parallel Session 4:
Mass Spectrometry Technologies and Biomedical Applications I
Co-Chairs: Albert Heck and Joseph Loo
Room 202, level 2, Convention Center |
| Mon Oral F 14:00-14:30 |
State of the Art Lecture: Mechanism-Based Profiling of Enzyme Familes; Ben Cravatt, The Scripps Institute, La Jolla, CA............................... 1444 |
| Mon Oral F 14:30-14:50 |
Top-Down, Bottom-Up and Side-to-Side Proteomics; Rachel R Ogorzalek Loo1; Yanan Yang1; Jason Dunsmore1; Katy Williams3; Pinmanee Boontheung1; Melissa Sondej1; Housna Mouttakki2; David Wong1; Michael McInerney2; Robert Gunsalus1; Joseph A. Loo1; 1University of California-Los Angeles, Los Angeles, CA; 2University of Oklahoma, Norman, OK; 3Applied Biosystems, Foster City, CA................ 1093 |
| Mon Oral F 14:50-15:10 |
Protein and Protein Phophorylation Dynamics Detected by Yin-Yang Multidimensional Liquid Chromatography (Yin-yang-MDLC) Mass Spectrometry Combined with Quantitative Proteomics; Rong Zeng; Jie Dai; Xing-lin Yang; Chia-Hui Shieh; Jia-Rui Wu; Shanghai Institutes for Biological Sciences, Shanghai, China.. 727 |
| Mon Oral F 15:10-15:30 |
Label-Free Quantitative Characterization of Cancer Proteomes by Multidimensional LC-MS/MS Combined with Integrated Ion Intensities and emPAI; Lee Weng1; Eric Y. Chan1; Andrew Keller1; Tsuyoshi Tabata2; Ken Aoshima2; Toshitaka Sato2; Yoshiya Oda2; 1Rosetta Biosoftware, Seattle, WA; 2Eisai Co Ltd, Tsukuba, Japan................................. 404 |
| Mon Oral F 15:30-15:50 |
Comparison of LC-ESI MS/MS and LC-MALDI TOF/TOF Analysis of an iTRAQ Labeled Complex Sample; Leanne Ohlund; Dominic Domanski; Philip Jakubowski; Darryl Hardie; Monica Elliott; Derek Smith; Christoph Borchers; University of Victoria, Victoria, Canada 1231 |
| Mon Oral F 15:50-16:10 |
From Mass Imaging to Class Imaging – New Horizons in MALDI Molecular Imaging; Sören-Oliver Deininger1; Paul J. Kowalski2; Martin Schürenberg1; Arne Fütterer1; Marc Gerhard1; Lübbert Christine1; Christoph Röcken3; Matthias Ebert4; 1Bruker Daltonik GmbH, Bremen, Germany; 2Bruker Daltonics, Billerica, MA; 3Charité University Hospital, Berlin, Germany; 4Klinikum rechts der Isar, Munich, Germany. 900 |
| Mon Oral F 16:10-16:30 |
Producing Qualitative and Quantitative Profiles of Intact Proteins by LC/ESI-TOF MS; Ignatius J. Kass1; Kevin M. Millea2; John C. Gebler1; Ira S. Krull2; Scott J. Berger1; 1Waters Corporation, Milford, MA; 2Northeastern University, Boston, MA........................... 662 |
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Monday, October 30 |
| 14:00-16:30 |
Parallel Session 5: Antibody Arrays: Technologies and Applications
Co-Chairs: Mathias Uhlen and John McCatterty
Room 203, level 2, Convention Center |
| Mon Oral G 14:00-14:30 |
State of the Art Lecture: Antibody Microarrays – Technology and Applications in Oncoproteomics; Carl AK Borrebaeck; Lund University,
Lund, Sweden...... 1260 |
| Mon Oral G 14:30-14:50 |
Proteomic Scale Generation and Utilisation of Recombinant Proteins and Antibodies; John McCafferty; Wellcome Trust Sanger Institute, Cambridgeshire, England................. 536 |
| Mon Oral G 14:50-15:10 |
Analysis of Human Leukaemias and Lymphomas Using Extensive Immunophenotypes from an Antibody Microarray; Richard Christopherson1; Larissa Belov3; Stephen Mulligan2; Nicole Barber1; Adrian Woolfson4; Mike Scott4; Kerryn Stoner4; Jeremy Chrisp3; William Sewell5; Kenneth Bradstock1; Linda Bendall1; Dana Pascovici6; Mervyn Thomas6; Wendy Erber4; Graham Young1; James Wiley7; Surender Juneja8; William Wierda9; Anthony Green4; Michael Keating9; 1University of Sydney, Sydney, NSW; 2Symbion Pathology, North Ryde, Australia; 3Medsaic Pty Ltd, Eveleigh, Australia; 4University of Cambridge, Cambridge, United Kingdom; 5St Vincents Hospital, Darlinghurst, Australia; 6Emphron Informatics Pty Ltd, Chapel Hill, Australia; 7Nepean Hospital, Penrith, Australia; 8Royal Melbourne Hospital, Parkville, Australia; 9MD Anderson Cancer Center, Houston, TX........... 279 |
| Mon Oral G 15:10-15:30 |
A Novel Protein Immobilization on Chip Substrate for High-Throughput Functional Proteomics; Kazuyuki Nakamura; Yamaguchi Univeristy Graduate School of Medicine, Ube, Yamaguchi, Japan...................... 862 |
| Mon Oral G 15:30-15:50 |
Dynamic TNFα/NFκB Signaling Phosphoproteome of Cystic Fibrosis Lung Epithelial Cells; Meera Srivastava; Catherine E. Jozwik; Ofer Eidelman; Wei Huang; Harvey B. Pollard; Uniformed Services University, Bethesda, MD...... 1049 |
| Mon Oral G 15:50-16:10 |
Large Scale Comparative mRNA and Protein Expression Profiling; Peter Nilsson1; Marcus Gry Björklund1; Anna Asplund2; Rebecca Rimini1; Sara Strömberg2; Mathias Uhlen1; Fredrik Ponten2; 1KTH - Royal Institute of Technology, Stockholm, Sweden; 2Uppsala University, Uppsala, Sweden.. 699 |
| Mon Oral G 16:10-16:30 |
Recent Applications of Protein Chips in Biomarker Discovery; Dolores J. Cahill; University College Dublin, Dublin, Ireland..... 363 |
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| 16:30-17:00 |
Posters and Exhibits. Exhibit Hall |
| 17:00-17:30 |
Monday Keynote Lecture:
Annotation and Characterization of Human Proteomes
Co-Chairs: Ruedi Aebersold and John Bergeron
Ballroom A, level 2, Convention Center |
| Mon Oral H 17:00-17:30 |
Keynote Lecture: Annotating the Human Proteome: Beyond Establishing a Parts List; Rolf Apweiler; EMBL-EBI, Hinxton, UK............ 14 |
| 17:30-17:40 |
Introduction to HUPO 6th Annual World Congress, Seoul 2007; Young Mok Park, Richard Simpson and Young-Ki Paik |
| 17:40-18:30 |
HUPO General Assembly – Meeting of Members
Moderator: John Bergeron |
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Monday, October 30 |
| 20:00-22:00 |
Workshops and Panel Discussions |
| 20:00-22:00 |
NHLBI Proteomic Technology Centers Workshop
Co-Chairs: Ruedi Aebersold and Jennifer Van Eyk
Room 201, level 2, Convention Center |
| |
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| 20:00-22:00 |
Career Opportunities in Proteomics Workshop
Co-Chairs: Jasmine Gruia-Gray and Thomas Vondriska
Room 202, level 2, Convention Center |
| 20:00-20:20 |
Jasmine Gruia-Gray, GE Healthcare |
| 20:20-20:40 |
Andrea Mravca, Protein Discovery |
| 20:40-21:00 |
Rong Zeng; Shanghai Institute of Life Sciences |
| 21:00-21:20 |
Robert Barkovich; ThermoElectron |
| 21:20-21:40 |
Lena Jonsson; GE Healthcare |
| 21:40-22:00 |
Wei-Wei Zhang; Genway Biosciences |
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|
| 20:00-22:00 |
Special Symposium: From Swiss-Prot to UniProt and Beyond
The 20th Anniversary
Co-Chairs: Peter Good and Rolf Apweiler
Ballroom A, level 2, Convention Center |
| Mon Oral K 20:00-20:40 |
Featured Speaker: Plus ça change, plus c'est la même chose...The Next 20 Years; Amos Bairoch1,2;; 1Swiss Institute of Bioinformatics, Geneva, Switzerland; 2University of Geneva, DBSB, Geneva, Switzerland......... 1319 |
| Mon Oral K 20:40-21:00 |
Human Protein Atlas – Version 2; Erik Björling1; Per Oksvold1; Mattias Forsberg1; Jan Lund1; Fredrik Pontén2; Mathias Uhlén1; 1KTH Royal Institute of Technology, Stockholm, Sweden; 2Rudbecklaboratory - Uppsala University, Uppsala, Sweden 1195 |
| Mon Oral K 21:00-21:20 |
Increasing the Potential of Proteome Analysis via Comparison of Proteomic Data with Protein Interaction Databases – Discovery of Lymphocyte Pathways; Petra Lutter1; Thomas Wiebringhaus2; Heinrich Brinck2; Helmut Jonuleit3; Edgar Schmitt4; Stefan Muellner1; 1Protagen AG, Dortmund, Germany; 2University of Applied Science of Gelsenkirchen, Recklinghausen, Germany; 3Institute of Dermatology, University of Mainz, Mainz, Germany; 4Institute of Immunology, University of Mainz, Mainz, Germany. 1167 |
| Mon Oral K 21:20-21:40 |
Sociomics: Social Science Perspectives on Proteomics; Ruth M McNally1; Glasner Peter1; 1ESRC CESAGen, Cardiff, UK........................... 224 |
| Mon Oral K 21:40-22:00 |
The Ontology Lookup Service: A Centralized Point of Access for Interactive and Programmatic Controlled Vocabulary Queries; Richard G Côté;
Philip Jones; Rolf Apweiler; Henning Hermjakob; European Bioinformatics Institute, Hinxton, United Kingdom... 719 |
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Monday, October 30 |
| 20:00-22:00 |
HUPO Special Featured Symposium:
Proteomic Initiatives and NCI Perspectives
The National Cancer center supports numerous proteomic-based initiatives that will be presented by its leadership in talks throughout this day. Through panel discussion as well as questions and answers from the audience, this session is meant to summarize the days events and focus on: what are the needs of NCI and the proteomic scientist, what are and need to be new directions for proteomics, and how do we get proteomics from discovery to clinical translation.
Co-Chairs: Gilbert S. Omenn and Thierry Rabilloud
Room 203, level 2, Convention Center |
| Mon Oral L 20:00-20:30 |
State of the Art Lecture: The HUPO Plasma Proteome Project: Next Phase; Gilbert S Omenn1; Young-Ki Paik2; Matthias Mann3; 1University of Michigan, Ann Arbor, MI; 2Yonsei Proteome Research Center, Seoul, Korea; 3Max Planck Institute, Munich, Germany. 667 |
| Mon Oral L 20:30-21:00 |
State of the Art Lecture: Complex Bacteriophages as Protein Standards for Proteomics; Mireille Chevallet1; Hélène Diemer2; Laurent Miguet2; Alain Van Dorsselaer2; Thierry Rabilloud1; 1CEA-grenoble, Grenoble, France; 2LSMBO, Strasbourg, France............................... 1196 |
| Mon Oral L 21:00-21:30 |
State of the Art Lecture:
NCI’s Proteomic Technologies Assessment and Reagents Resource for Cancer Research; Henry Rodriguez ; NCI; Bethesda, MD, USA |
| Mon Oral L 21:30-22:00 |
Panel Discussion: Henry Rodriguez, Jan Schnitzer, Michael Snyder, , John Bergeron, Thirerry Rabilloud, and Gilbert Omenn |
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Tuesday October 31, 2006 |
| 08:00-09:30 |
Plenary Lectures: Pioneers in Proteomics
Co-Chairs: John R. Yates III and Peter Roepstorff
Ballroom, level 2, Convention Center |
Tue Oral A
08:00-08:30 |
Invited Lecture: Laying the Groundwork for Proteomics Mass Spectrometry from 1958 – 1988; Klaus Biemann; Massachusetts Institute of Technology, Cambridge, MA.. 1394 |
| Tue Oral A 08:30-09:00 |
Invited Lecture: Glycoproteomics: Past, Present and Future;
Howard R Morris; Imperial College, London, United Kingdom.............. 1426 |
| Tue Oral A 09:00-09:30 |
Invited Lecture: Identification of Peptides, Intact Proteins and Post-translational Modifications with a Combination of Ion/Ion Chemistry (ETD) and Tandem Mass Spectrometry; Donald F. Hunt; University of Virginia, Charlottesville, VA............................... 1292 |
| 09:30-10:00 |
Break, Posters and Exhibits. Exhibit Hall |
| 10:00-12:30 |
Parallel Sessions |
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|
| 10:00-12:30 |
Featured Session: Systems Biology and Signaling Networks I
Co-Chairs: Ralph Bradshaw and Young-Ki Paik
Ballroom A, level 2, Convention Center |
| Tue Oral B 10:00-10:30 |
State of the Art Lecture: Systems Biology to Investigate Signaling Networks; Ruedi Aebersold, Swiss Federal Institute of Technology, Zurich, Switzerland |
| Tue Oral B 10:30-10:50 |
Systemic Analysis of Genome-Wide Transcriptional Changes Associated with Olig2-Induced Differentiation of Human Neural Stem Cells; Bonghee Lee1; Kyunghee Byun1; Sungmin Ahn1; Youngmok Park2; Jin Young Kim2; Jong Shin Yoo2; 1Cheju National University, Jeju, Korea; 2Korea Basic Science Institute, Daejeon, Korea........................ 19 |
| Tue Oral B 10:50-11:10 |
Proteomic Deconvolution of Tyrosine Kinase Networks in Heart; Thomas M. Vondriska; Xiaohai Li; David Liem; Jun Zhang; Peipei Ping; UCLA,
Los Angeles, CA.... 989 |
| Tue Oral B 11:10-11:30 |
Unraveling Rho GTPase Interaction Networks Using Formaldehyde Cross-Linking in Live Cells; Peter Schubert; Shujun Lin; Juergen Kast; University of British Columbia, Vancouver, BC...... 986 |
| Tue Oral B 11:30-11:50 |
From Disparate Multi-Disciplinary Data to Coherent Knowledge: Informatics for Systems Biology-Based Disease Profiling; Erich A. Gombocz; Robert A. Stanley; Michael Travers; IO Informatics, Inc., Emeryville, CA........ 93 |
| Tue Oral B 11:50-12:10 |
Proteomics of Metabolic Staging of Hepatocellular Carcinoma; Rong Wang; Heyi Yang; Josep M. Llovet; Mount Sinai School of Medicine, New York, NY................. 823 |
| Tue Oral B 12:10-12:30 |
Molecular Systems Biology of Aging using Calorie-Restricted Yeast as a Model System for Defining a Modular Network Controlling Chronological Aging; Alexander Goldberg; Christopher Gregg; Tatiana Boukh-Viner; Simon Bourque; Pavlo Kyryakov; Tong Guo; Zeinab Aziz; David Cyr; Andrew Naimi; Florentina Negoita; Aloysius Oluoha; Mohammad H. Salah; Eric Scazzosi; Vladimir I. Titorenko; Concordia University, Montreal, Canada 550 |
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Tuesday October 31, 2006 |
| 10:00-12:30 |
Parallel Session 2: Membrane Proteins and Proteomics
Co-Chairs: Julian Whitelegge and Peter James
Room 201, level 2, Convention Center |
| Tue Oral C 10:00-10:30 |
State of the Art Lecture: Pharmacoproteomics: Strategies for Identifying New Diagnostic and Prognostic Markers for Colorectal Cancer;
Richard J. Simpson; Hong Ji; David Greening; Justin Lim; Robert JA Goode; Eugene Kapp; Oliver K Bernhard; Sung-Min Ahn; Robert L Moritz; Ludwig Institute & Walter & Eliza Hall Institute, Parkville, Australia............................... 1305 |
| Tue Oral C 10:30-10:50 |
A Physical Plasma Sub-Proteome Revealed by Methods Developed for Membrane Proteins; Frederic Halgand; Lang Yam; Sara Bassilian; Pedram Ghasri; Puneet Souda; Kym Faull; Verne Shumaker; Don Puppione; Julian Whitelegge; University of California, Los Angeles, CA......... 1105 |
| Tue Oral C 10:50-11:10 |
Exploring the Platelet Proteome by Complementary Strategies; Jan Moebius1; René P. Zahedi1; Urs U. Lewandrowski1; Ulrich Walter2; Albert Sickmann1; 1Rudolf-Virchow-Center, DFG-Research Center, Wuerzburg, Germany; 2Institute of Clinical Biochemistry a Pathobiochemistry, Wuerzburg, Germany................................. 530 |
| Tue Oral C 11:10-11:30 |
Proteomic Characterization of Mouse Kidney Peroxisomes by Tandem MS and Protein Correlation Profiling; Sebastian Wiese1; Thomas Gronemeyer1; Rob Ofman2; Ronald Wanders2; Jorge Azevedo3; Johannes Berger4; Juergen Nolte5; Heiko Hayen5; Christian Stephan1; Martin Eisenacher1; Helmut E. Meyer1; Bettina Warscheid1; 1Ruhr-University Bochum, Bochum, Germany; 2University of Amsterdam, Amsterdam, Netherlands; 3University of Porto, Porto, Portugal; 4University of Vienna, Vienna, Austria; 5Institute of Analytical Sciences, Dortmund, Germany................................. 164 |
| Tue Oral C 11:30-11:50 |
Quantitation of the Cerebellar Synaptic Proteome during Postnatal Development; Daniel B. McClatchy1; Robin Park1; John V. Venable1;
John R. Yates, III1; The Scripps Research Institute, La Jolla, CA................................. 189 |
| Tue Oral C 11:50-12:10 |
Purification of G Protein-Coupled Receptors Interacting Protein under Basal and Activated Conditions; Avais M. Daulat1; Pascal Maurice1; Jean-Luc Guillaume1; Carine Froment2; Bernard Monsarrat2; Philippe Delagrange3; Ralf Jockers1; 1Institut Cochin, Paris, France; 2IPBS, Toulouse, France;
3Institut de Recherche SERVIER, Suresnes, France.................... 183 |
| Tue Oral C 12:10-12:30 |
Proteomic Analysis of Brain Plasma Membranes Purified by Aqueous Polymer Two-Phase Systems; Jens Schindler; Eckhard Friauf; University of Kaiserslautern, Kaiserslautern, Germany................. 864 |
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Tuesday October 31, 2006 |
| 10:00-12:30 |
Parallel Session 3: Proteomic Characterization of the Ubiquitination-Proteasome Systems
Co-Chairs: Robert Cotter and Maria Gaczynska
Room 202, level 2, Convention Center |
| Tue Oral D 10:00-10:30 |
State of the Art Lecture: A Big Picture of the Big Protease; Maria Gaczynska; Pawel A. Osmulski; Brett Mueller; Elzbieta Jankowska; Monika Tokmina-Lukaszewska; Paulina Juszczyk; Karl Rodriguez; Srividya Madabhushi; Lydia Endel; University of Texas Health Science Center, San Antonio, TX.......................... 1140 |
| Tue Oral D 10:30-11:00 |
State of the Art Lecture: Quantitative Analysis of Histone Modifications at Multiple Sites using Tandem Time-of-Flight Mass Spectrometry;
Robert J. Cotter; Wendell P Griffith; Johns Hopkins School of Medicine, Baltimore, MD.... 1193 |
| 11:00-11:10 |
Break |
| Tue Oral D 11:10-11:30 |
Heterogeneity and Organ Specific Assembly of 20S Proteasome Complexes; Aldrin Gomes; Oliver Drews; Xiaohai Li; Glen Young; Chenggong Zong; Peipei Ping; UCLA, Los Angeles, CA........................... 481 |
| Tue Oral D 11:30-11:50 |
Identification of Ubiquitin-Interacting Proteins from Mouse Brain using Multidimensional Protein Identification Technique following Ubiquitin-Affinity Chromatography; Dong Yeon Shin; Jong Hyuk Yoon; Eun Kyung Lee; Hyun Woo Choi; Zee-Yong Park; Yung Joon Yoo; Gwangju Institute of Science & Technolgy (GIST), Gwangju, South Korea.......... 694 |
| Tue Oral D 11:50-12:10 |
Insoluble Mutant SOD1 is Partly Oligoubiquitinated in Amyotrophic Lateral Sclerosis Mice; Valentina Bonetto1; Manuela Basso1; Tania Massignan1; Giuseppina Samengo1; Cristina Cheroni2; Mario Salmona2; Caterina Bendotti2; 1Dulbecco Telethon Inst. and Mario Negri Inst., Milan, Italy; 2Mario Negri Institute, Milan, Italy................................. 534 |
| Tue Oral D 12:10-12:30 |
The Proteasome and its Interacting Proteins; Fawzia Bardag-Gorce1; Sara Basilian2; Barbara A. French1; Julian Whitelegge2; Samuel W French1; 1LABioMed at Harbor-UCLA Med Center, Torrance, CA; 2The Pasarow Mass Spectrometry Laboratory, UCLA, Los Angeles, CA.... 390 |
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Tuesday October 31, 2006 |
| 10:00-12:30 |
Parallel Session 4: Human Disease Proteomics II
Co-Chairs: Laura Beretta and Pierre Legrain
Ballroom B, level 2, Convention Center |
| Tue Oral E 10:00-10:30 |
State of the Art Lecture: Clinical Biomarker Number and Discovery: Examples in Cerebral, Infectious and Renal Diseases; Denis F. Hochstrasser; Pierre Lescuyer; Solange Moll; Ali Vezzadeh; Jean-Charles Sanchez; Catherine Zimmermann; Geneva University & University Hospital, Geneva, Switzerland............................... 1175 |
| Tue Oral E 10:30-10:50 |
Expanding the Capabilities of Peptide MRM-based Assays in Plasma Using a Hybrid Triple Quadrupole Linear Ion Trap Mass Spectrometer;
Christie L Hunter1; Leigh Anderson2; 1Applied Biosystems, Foster City, CA;
Tthe Plasma Proteome Institute, Washington, DC......................... 1070 |
| Tue Oral E 10:50-11:10 |
Nuclear Proteome Dynamics in Susceptibility to Cancer Development; Monique Slijper1; Eef H.C. Dirksen1; Jacqueline Cloos2; Boudewijn J.M. Braakhuis2; Ruud H. Brakenhoff2; Albert J.R. Heck1; 1Utrecht University, Utrecht, Netherlands; 2VU University Medical Centre, Amsterdam, Netherlands........... 744 |
| Tue Oral E 11:10-11:30 |
Discovery and Qualification of CNS Lymphoma Protein Biomarkers in Cerebrospinal Fluid by DeepLookTM Mass Spectrometry; Sushmita Mimi Roy1; Christopher Becker1; Howard Schulman1; James Rubenstein2; 1Biomarker Discovery Sciences, PPD, Menlo Park, CA; 2University of California, San Francisco, CA....... 465 |
| Tue Oral E 11:30-11:50 |
Analytical Validation of Biomarkers using AQUATM Technology; Jason Christiansen; Robert Pinard; Maciej Zerkowski; Agnes Ang; Marisa Dolled-Filhart; Paul Stroobant; Eric Anderson; Lorah T Perlee; HistoRx, Inc.,
New Haven, CT..... 480 |
| Tue Oral E 11:50-12:10 |
Novel Biomarkers for the Prediction of Prostate Cancer Recurrence; C. Nicole Rosenzweig; Zhen Zhang; Derek Chappell; Jason M. Rosenzweig; Lori J. Sokoll; Alan W. Partin; Daniel W. Chan; Johns Hopkins Medical Institution, Baltimore, MD.... 1015 |
| Tue Oral E 12:10-12:30 |
Quantitative Proteomics of Formalin Fixed Archival Tissue; David B. Krizman1; Brian L. Hood2; Marlene M. Darfler1; Thomas G. Guiel1; Thomas P. Conrads2; Timothy D. Veenstra2; 1Expression Pathology Inc., Gaithersburg, MD; 2SAIC/NCI-Frederick, Frederick, MD...... 766 |
|
|
Tuesday October 31, 2006 |
| 10:00-12:30 |
Parallel Session 5: Databases for Proteomics
Co-Chairs: Cathy Wu and Ron Beavis
Room 203, level 2, Convention Center |
| Tue Oral F 10:00-10:30 |
State of the Art Lecture: Using Annotated Peptide Mass Spectrum Libraries for Protein Indentification; Ronald Beavis; Beavis Informatics Ltd;
Winnipeg, Canada |
| Tue Oral F 10:30-11:00 |
State of the Art Lecture: Scoring Peptide, Protein, and Modification Identifications; Marshall Bern; Palo Alto Research Center, Palo Alto, CA...... 1219 |
| 11:00-11:10 |
Break |
| Tue Oral F 11:10-11:30 |
Data and Bioinformatics Tools at the NIAID Biodefense Proteomics Administrative Resource Center; Peter B. McGarvey1; H. Huang1; J. Zhang1; R. Mazumder1; M. Moore2; P. Yadvish2; B. Sobral3; S. Cammer3; C. Wu1; 1PIR, Georgetown University Medical Center, Washington, DC; 2Social and Scientific Systems, Silver Spring, MD; 3Virginia Bioinformatics Institute, Blacksburg, VA............................ 299 |
| Tue Oral F 11:30-11:50 |
Defining the Human Plasma Proteome with PeptideAtlas; Eric Deutsch1; Nichole King1; Jimmy Eng2; Alexey Nesvizhskii3; Olga Vitek1; Josh Tasman1; Ruedi Aebersold4; 1Institute for Systems Biology, Seattle, WA; 2Fred Hutchinson Cancer Research Center, Seattle, WA; 3University of Michigan Medical School, Ann Arbor, MI; 4Institute for Molecular Systems Biology, Zurich, Switzerland........... 617 |
| Tue Oral F 11:50-12:10 |
A Reference Library of MS/MS Spectra of Peptides Derived from Human Samples; Stephen Stein1; Lisa Kilpatrick2; Yuri Mirokhin1; Long Pu1; Pedatsur Neta1; Jeri Roth1; Sara (Xiaoyu) Yang1; 1NIST, Gaithersburg, MD; 2NIST-HML, Charleston, SC....... 39 |
| Tue Oral F 12:10-12:30 |
HUPO Brain Proteome Project: Summary of the Pilot Phase and Introduction of a Comprehensive Data Reprocessing Strategy; Michael Hamacher1; Christian Stephan1; Katrin Marcus1; Andre Van Hall1; Kai A. Reidegeld1; Lennart Martens2; Rolf Apweiler2; Helmut E. Meyer1; 1Medizinisches Proteom-Center, Ruhr-Universitaet, Bochum, Germany; 2EMBL Outstation, European Bioinformatics Institute, Hinxton, UK................................. 178 |
| 12:30-14:00 |
Posters and Exhibits. Exhibit Hall |
| 12:45-13:45 |
Corporate Sponsored Symposia. |
|
|
Tuesday October 31, 2006 |
| 14:00-16:30 |
Parallel Sessions |
| 14:00-16:30 |
Featured Symposium: HUPO President Symposium:
Cell Organelle Proteomics
Co-Chairs: John Bergeron and Jan Schnitzer
Ballroom A, level 2, Convention Center |
| Tue Oral G 14:00-14:30 |
State of the Art Lecture: Defining the Structure and Function of Macromolecular Complexes; Brian Chait, The Rockefeller University,
New York, NY |
| Tue Oral G 14:30-15:00 |
State of the Art Lecture: The Complexity in Variation of Phosphoralation in the Post Synaptic Signaling Network; Alma Burlingame, University of California, San Francisco, CA..... 1436 |
| Tue Oral G 15:00-15:30 |
State of the Art Lecture: Proteomics of ER Mediates Phagocytosis;
Michael Desjardins, University of Montreal, Canada |
| Tue Oral G 15:30-16:00 |
State of the Art Lecture: The Pancreatic Zymogen Granule Membrane; Xuequn Chen; Eric S. Simon; John Williams; Philip C. Andrews;
University of Michigan, Ann Arbor, Michigan............... 906 |
| 16:00-16:30 |
Panel Discussion |
|
|
Tuesday October 31, 2006 |
| 14:00-16:30 |
Parallel Session 2:
Mass Spectrometry Technologies and Biomedical Applications II
Co-Chairs: Mark Baker and KW Michael Siu
Ballroom B, level 2, Convention Center |
| Tue Oral H 14:00-14:30 |
State of the Art Lecture: Mass Spectrometry Based Quantitative Analysis of Macromolecular Complexes and Signaling Pathways; Albert J R Heck; 1Utrecht University, Utrecht, Netherlands; 2Netherlands Proteomics Centre, Utrecht, The Netherlands........... 251 |
| Tue Oral H 14:30-14:50 |
PIQS - Parent Ion Quantitation Scanning; Åsa Wåhlander; Peter James;
Lund University, Lund, Sweden........ 181 |
| Tue Oral H 14:50-15:10 |
High Sensitivity, Multiplexed Quantitative Analysis of Biomarkers Using Novel Tandem Mass Tags; Bruno Domon; Hoo-Keun Lee; Vinzenz Lange-Link; Ruedi Aebersold; ETH Zurich, Zurich, Switzerland........... 448 |
| Tue Oral H 15:10-15:30 |
Toward a Comprehensive Quantitative Phosphoproteome Analysis of Hyperphosphorylated PHF tau in Early Alzheimer’s Disease; Yunhu Wan1; Diane Cripps1; Stefani N. Thomas1; Young Jeng2; Peter Davies3; Tim Chen2; Austin J. Yang1; 1University of Maryland Medical School, Baltimore, CA; 2University of Southern California, Los Angeles, CA; 3Albert Einstein College of Medicine, Bronx, NY............... 452 |
| Tue Oral H 15:30-15:50 |
Mass-Tagging Approaches to Discovery and Identification of Endometrial Cancer Biomarkers and their Subsequent Validation Using Immunochemistry; Leroi V. DeSouza1; Valerie Dube2; Shaun Ghanny1; Joerg Grigull1; Alexander D. Romaschin3; Terence J. Colgan2; K.W. Michael Siu1; 1York University, Toronto, ON, Canada; 2Mount Sinai Hospital, Toronto, ON, Canada; 3St. Michael's Hospital, Toronto, ON, Canada................................... 54 |
| Tue Oral H 15:50-16:10 |
Increasing Throughput of Peptide Quantification using Isotope Dilution Mass Spectromety for Monitoring Cardiac Markers in Human Plasma; Tori Richmond1; Xu Shi2; Amol Prakash1; Leo Bonilla1; 1Thermo BRIMS Center, Cambridge, MA; 2Massachusetts General Hospital, Boston, MA.......... 1003 |
| Tue Oral H 16:10-16:30 |
Localization of Phosphorylation Sites in Human Cardiac Troponin I by Top Down Electron Capture Dissociation Mass Spectrometry; Ying Ge1; Jeffery W. Walker1; Dmitry R. Gumerov2; Michael L. Easterling2; J. Paul Speir2; 1University of Wisconsin, Madison, WI; 2Bruker Daltonics, Billerica, MA........................... 263 |
|
|
Tuesday October 31, 2006 |
| 14:00-16:30 |
Parallel Session 3:
Post-translational Modifications and Their Biomedical Implications
Co-Chairs: Ole Noerregaard Jensen and Robert Cotter
Room 201, level 2, Convention Center |
| Tue Oral I 14:00-14:30 |
State of the Art Lecture: Comparative Proteomics: Post-Translational Modifications in Sickle Cell Disease; Mark E McComb; Claire Dauly; Adam Ohiambo; David H Perlman; Hua Huang; Martin H Steinberg; Harrison W Farber; Elizabeth S Klings; Catherine E Costello; Boston University School of Medicine, Boston, MA............ 682 |
| Tue Oral I 14:30-14:50 |
Top Down and Bottom Up Analysis of Modified Ribosomal Proteins; Catherine Fenselau; Faith Hays; University of Maryland, College Park, MD............... 122 |
| Tue Oral I 14:50-15:10 |
Simultaneous Identification and Relative Quantitation of Large Intact Secreted Peptides; Steven W. Taylor; Amylin Pharmaceuticals, San Diego , CA........... 1229 |
| Tue Oral I 15:10-15:30 |
Assessing the Proportion of Post-Translationally Modified Peptides in the Immunopeptidome; Wilfred H. Tang1; Christie L. Hunter1; Frank R. Rooney2; Nicholas A. Williamson3; Anthony W. Purcell3; 1Applied Biosystems, Foster City, CA; 2Applied Biosystems, Melbourne, Australia;
3University of Melbourne, Melbourne, Australia................................. 343 |
| Tue Oral I 15:30-15:50 |
Arginylation of Beta Actin Regulates Actin Cytoskeleton and Cell Motility; Marina Karakozova1; Marina Kozak1; Catherine CL Wong2; Aaron Bailey2; John R. Yates III2; Alexander Mogilner3; Henry Zebroski4; Anna Kashina1; 1University of Pennsylvania, Philadelphia, PA; 2The Scripps Research Institute, La Jolla, CA; 3University of California, Davis, CA; 4The Rokefeller University, New York, NY............................ 260 |
| Tue Oral I 15:50-16:10 |
Simultaneous Analysis of Phosphorylation and Glycosylation Structures of Membrane Proteins by Extended Range Proteomic Analysis with Electron-Transfer and Collisional-Induced Dissociation; Shiaw-Lin Wu1; Andreas FR. Hühmer2; Zhiqi Hao2; Barry L. Karger1; 1Northeastern University, Boston, MA; 2Thermo Electron, San Jose, CA............................. 99 |
| Tue Oral I 16:10-16:30 |
Automatic Off-Line Enrichment of Phosphopeptides using Titanium Dioxide; Manfred Raida; Marcus Bantscheff; Birgit Duempelfeld; Markus Schirle; Bernhard Kuster; Cellzome AG, Heidelberg, Germany................................. 619 |
|
|
Tuesday October 31, 2006 |
| 14:00-16:30 |
Parallel Session 4: Proteomics and Therapeutics
Co-Chairs: Jan van Oostrum and Pengyuan Yang
Room 202, level 2, Convention Center |
| Tue Oral J 14:00-14:30 |
State of the Art Lecture: Proteomics of the Transplanted Heart;
Michael J Dunn; UCD Conway Institute, Dublin, Ireland... 1316 |
| Tue Oral J 14:30-15:00 |
State of the Art Lecture: Proteomics Applications for Biomarkers in Early Drug Development; Scott D. Patterson; Amgen, Inc., Thousand Oaks, CA................................. 277 |
| 15:00-15:10 |
Break |
| Tue Oral J 15:10-15:30 |
Kinase Inhibitors: Chemical Genomics Based Screening, Selectivity Profiling, and Mode-of-Action Studies; Bernhard Kuster; Cellzome AG, Heidelberg, Germany............................... 1171 |
| Tue Oral J 15:30-15:50 |
Temporal Profile of Human Brain Endothelial Cells in Oxidative Stress: a Bench-side Model for Endothelial Response to Ischemic Injury; MingMing Ning1; Alvin T Kho2; David A Sarracino1; Shu Zhen Guo1; Xiaoying Wang1; Sun-Ryung Lee1; Bryan Krastins3; Eng H Lo1; 1Massachusetts General Hospital/Harvard Med School, Boston, MA; 2Children's Hospital Boston, Boston, MA; 3Harvard Partners Center for Genetics and Genomics, Boston, MA......................... 1146 |
| Tue Oral J 15:50-16:10 |
Cryptomics: Identification of Novel Bioactive Peptides from Human Tissue Extracts; A. Ian Smith1; Dominic J Autelitano2; Antonio Rajic2; Michael C Berndt1; Leodevico L Ilag2; Mathew Vadas3; 1Monash University, Melbourne, Australia; 2Cryptome Pharmaceuticals, Melbourne, Australia; 3Institute of Medical and Veterinary Science, Adelaide, Australia................ 438 |
| Tue Oral J 16:10-16:30 |
Development of Peptidomic and Proteomic Biomarkers for Colorectal Cancer; Lina P. Aristoteli1; Stephen J. Clarke2; Mark S. Baker1; Mark P. Molloy1; 1Australian Proteome Analysis Facility, Sydney, Australia; 2Concord Repatration Hospital, Sydney, Australia.................. 45 |
|
|
Tuesday October 31, 2006 |
| 14:00-16:30 |
Parallel Session 5: Stem Cells and Proteomics
Co-Chairs: Denis Hochstrasser and Rong Zeng
Room 203, level 2, Convention Center |
| Tue Oral K 14:00-14:30 |
State of the Art Lecture: Proteomics of Differentiating Embryonic Stem Cells; Jeroen Krijgsveld; Utrecht University, Utrecht, The Netherlands... 579 |
| Tue Oral K 14:30-15:00 |
State of the Art Lecture: Proteomic Characterization to Determine the Fate of Embryonic and Cardiac Stem Cells; S. Sheng1, S. Elliott1, C. Murray1, D. Chen3, M. Gucek3, R. Cole3, D. Crider2, Y. Tarasova4, K. Boheler2 and Jennifer Van Eyk1; 1Dept. of Medicine, 3Proteomics Mass Spectrometry Facility, Johns Hopkins University Baltimore, MD, 2Laboratory of Cardiovascular Science, National Institute on Aging, Baltimore, MD.... 1447 |
| 15:00-15:10 |
Break |
| Tue Oral K 15:10-15:30 |
Neuronal Differentiation of Human Embryonic Stem Cells by Noggin Exposure Induces a Novel Protein Signature Identified by iTRAQ Analysis; John R. Strahler; Theresa E. Gratsch; Nancy S. Leff; George Michailidis; Gilbert S. Omenn; K. Sue O'Shea; Philip C. Andrews; University of Michigan,
Ann Arbor, MI..... 1018 |
| Tue Oral K 15:30-15:50 |
Proteomic Studies of Fluoxetine Induced Adult Neurogenesis in Hippocampus Compared with Cerebellum; Linda Paulson1; Thorsten Klint2; Carina Sihlbom3; Peter Eriksson1; 1Institution of Neuroscience and Physiology, Göteborg, Sweden; 2Clinical Development, NeuroSearch A/S, Ballerup, Denmark; 3Institution of Biomedicine, Göteborg, Sweden 156 |
| Tue Oral K 15:50-16:10 |
Combined Proteomic and Metabolomic Analysis of ApoE-/- Smooth Muscle Cells and their Vascular Progenitors; Manuel Mayr1; Ursula Mayr1; Anna Zampetaki1; Xiaoke Yin1; Anissa Sidibe1; Yuen-Li Chung2; John R. Griffiths2; Qingbo Xu1; 1King's College, London, UK; 2St. George's, London, UK............................... 1185 |
| Tue Oral K 16:10-16:30 |
The Testicular Stem Cell Proteome Pilot Project: Focus on the Automated MS Data Processing Pipeline; Charles G. Pineau1; Nathalie Guitton1; Morgane Couvet1; Regis Lavigne1; Djibril Ousmanou1; Jorg Glandorf2; Herbert Thiele2; 1Inserm U625, Campus de Beaulieu, 35042 Rennes, France; 2Bruker Daltonik GmbH, 28359 Bremen, Germany................. 742 |
| 16:30-17:00 |
Posters and Exhibits, Exhibit Hall |
|
|
Tuesday October 31, 2006 |
| 17:00-18:20 |
Keynote Lectures III:
Mass Spectrometry Technologies and Biomedical Applications
Co-Chairs: Donald F. Hunt and Klaus Biemann
Ballroom A, level 2, Convention Center |
| Tue Oral L 17:00-17:40 |
Keynote Lecture: Top Down for Human Proteotyping - Has its Time Come? Neil L. Kelleher; University of Illinois, Urbana, IL................................. 551 |
| Tue Oral L 17:40-18:20 |
Keynote Lecture: Driving Biological Discovery using Mass Spectrometry;
John R. Yates III, The Scripps Research Institute, La Jolla, CA............................... 1446 |
| 20:00-22:00 |
Workshops and Panel Discussions |
|
|
| 20:00-22:00 |
NCRR Panel Discussion: NCRR Biomedical Technology Research Centers in Proteomics and Glycomics
Co-Chairs: Catherine Costello and John R. Yates, III
Room 201, level 2, Convention Center |
| The National Center for Research Resources supports Biomedical Technology Research Centers (BTRCs) to create and provide access to new technologies in a variety of areas, including proteomics and glycomics. Principal investigators of four proteomics-oriented BTRCs will describe the program, the technology development and proteomics problems being pursued in their labs, and the resources that they make available to the biomedical research community. |
| 20:00-20:20 |
What is the Biomedical Technology Research Center? Catherine Costello;
Boston University School of Medicine |
| 20:20-20:40 |
Richard D. Smith; Pacific Northwest National Laboratory |
| 20:40-21:00 |
Philip C. Andrews; University of Michigan |
| 21:00-21:20 |
Alma L. Burlingame; University of California, San Francisco |
| 21:20-22:00 |
Panel Discussion: Moderator: John R. Yates III |
|
|
Tuesday October 31, 2006 |
| 20:00-22:00 |
PSI and Publications Committee Panel Discussion
Co-Chairs: Rolf Apweiler and Mathias Uhlen
Room 202, level 2, Convention Center |
| HUPO Proteomic Standards Initiative (PSI) and Publications Committee wish to facilitate discussions on the following topics: 1) regarding publishing HUPO-related Editorials and the page space that will be provided for them; 2) regarding pre-review and approve of a HUPO-related manuscript by the publications committee; 3) regarding issues on proteomic data standardization efforts (e.g., use of standardized data formats; support for a network of proteomics repositories collaborating on a coordinated data curation; how best structure interactions between journals, databases and researchers to improve accessibility and to facilitate direct comparisons of data). |
| 20:00-20:20 |
Michael Dunn; PROTEOMICS |
| 20:20-20:40 |
TBA, Nature Publishing Group |
| 20:40-21:00 |
Sandra Orchard/Randy Julian, PSI |
| 21:00-21:20 |
TBA, Vendor Perspective |
| 21:20-22:00 |
Panel Discussion: Bill Hancock, Ralph Bradshaw, Naoyuki Taniguchi, Laura Beretta, Helmut Meyer, Martin McIntosh, Harald Schmidt, Albert Heck, Angelika, Gorg, Thierry Rabilloud, and Gilbert Omenn |
| All Congress registrants who care about issues related to publications and/or official HUPO journals are encouraged to attend and to actively participate in the discussions. |
|
|
| 20:00-22:00 |
Pharmaceutical/Biotech Liaison Panel Discussion
Co-Chairs: Jan van Oostrum and Scott D. Patterson
Room 203, level 2, Convention Center |
| A joint discussion on scientific goals shared by proteomic leaders in the industry and academic worlds. Topics of discussion include: 1) What are the current technology limitations? 2) What would be the areas of investigations need emphasis? 3) Any common goals that may benefit from a joint effort? |
| 20:00-20:20 |
Hanno Langen; Roche |
| 20:20-20:40 |
Guenter Thesseling; GE Healthcare |
| 20:40-21:00 |
Workflows for Biomarker Discovery and Functional Proteomics; Nelson Cooke;
Bio-Rad |
| 21:00-22:00 |
Panel Discussion: Ian Humphery-Smith, Cathy Mainini, Kumar Bala, Stanley Hefta, and Wei-Wei Zhang |
| All Congress registrants who are interested in issues related to HUPO Industrial partnerships are encouraged to attend and to actively participate in the discussions. |
|
|
Wednesday, November 1, 2006 |
| 08:00-09:00 |
Keynote Lectures IV:
Proteomic Facilitated Advancement in Biology and Medicine
Co-Chairs: John Bergeron and Peipei Ping
Ballroom A, level 2, Convention Center |
| Wed Oral A 08:00-08:30 |
Keynote Lecture: Exploring the Ubiquitin Proteome; Raymond Deshaies; Thibault Mayor; Johannes Graumann; Caltech/HHMI, Pasadena, CA..... 1252 |
| Wed Oral A 08:30-09:00 |
Keynote Lecture: Global and Local Features of Biological Networks;
Michael D Tyers; Samuel Lunenfeld Research Institute, Toronto, Canada 1322 |
| 09:00-10:00 |
Break, Posters and Exhibits. Exhibit Hall |
| 10:00-12:30 |
Parallel Sessions |
|
|
| 10:00-12:30 |
Featured Symposium:
Protein Microarrays for Probing Health and Disease
Co-Chairs: Mathias Uhlen and Michael Snyder
Ballroom A, level 2, Convention Center |
| Wed Oral B 10:00-10:30 |
State of the Art Lecture: Functional Proteomics for Biomarker and Target Discovery; Joshua LaBaer; Harvard Institute of Proteomics, Cambridge, MA.... 557 |
| Wed Oral B 10:30-11:00 |
State of the Art Lecture: Reverse Phase Protein Microarrays for Theranostic Applications and Targeted Therapy; Emanuel F Petricoin;
George Mason University, Manassas, VA.......................... 1257 |
| Wed Oral B 11:00-11:30 |
State of the Art Lecture: Novel Array-Based Analyses of Cancer-Associated Serum Protein Alterations; Brian Haab; Van Andel Research Institute,
Grand Rapids, MI 1445 |
| Wed Oral B 11:30-12:00 |
State of the Art Lecture: Interactions of the Human bZIP Transcription Factors: Protein Microarray Measurements and Computational Predictions; Amy E. Keating1; John R. S. Newman1; Gevorg Grigoryan1; Jessica Fong2; Mona Singh2; 1Massachusetts Institute of Technology, Cambridge, MA; 2Princeton University, Princeton, NJ...... 1308 |
|
|
| 10:00-12:30 |
Parallel Session 2: The Next Generation in Proteomics
Co-Chairs: Ian Humphrey-Smith and Rolf Apweiler
Room 201, level 2, Convention Center |
| Wed Oral C 10:00-10:30 |
Invited Lecture: Comparative Proteomic Profiling of Mouse Models of Heart Failure; Andrew Emili; University of Toronto, Toronto, ON, Canada................................. 977 |
| Wed Oral C 10:30-11:00 |
Invited Lecture: Panning the Data: Looking for Gold within and across Proteomics Experiments; Lennart Martens; EMBL-EBI, Hinxton,
United Kingdom... 597 |
| Wed Oral C 11:00-11:30 |
Invited Lecture: The Protein Signaling Network Integration through the Establishment of Clonal Cell Lines and the Proteome Analyses; Young Yil Bahk; Protein Network Research Center, Yonsei University, Seoul, Korea.................... 1293 |
| Wed Oral C 11:30-12:00 |
Invited Lecture: Applications of Quantitative Proteomics; Kathryn Lilley;
University of Cambridge, Cambridge, United Kingdom.............. 1400 |
| Wed Oral C 12:00-12:30 |
Invited Lecture: Annotated Spectrum Libraries (ASL) for Sensitive High Speed Protein Identification; David Fenyo1; Rob Craig2; John Cortens2; Ronald Beavis3; 1Rockefeller University, New York, NY, USA; 2Beavis Informatics Ltd., Winnipeg, MB, Canada; 3University of British Columbia, Vancouver, BC, Canada.................. 655 |
|
|
Wednesday, November 1, 2006 |
| 10:00-12:30 |
Parallel Session 3: Systems Biology and Signaling Networks II
Co-Chairs: Ruedi Aebersold and Jack Greenblatt
Ballroom B, level 2, Convention Center |
| Wed Oral D 10:00-10:30 |
State of the Art Lecture: A Comprehensive Proteomic Analysis of Dauer and Cholesterol Signaling Pathway in Caenorhabditis elegans; Young-Ki Paik; Keun Na; Mi Jeong Jeong; Pan-Young Jeong; Yhong-Hee Shim; Yonsei Proteome Research Center, Yonsei University, Seoul, South Korea.......... 715 |
| Wed Oral D 10:30-10:50 |
Predicting Proteotypic Peptides as Probes for Quantitative Proteomics; Parag Mallick1; Markus Schirle2; Bernhard Kuster2; Ruedi Aebersold3; 1Cedars-Sinai Medical Center, Los Angeles, CA; 2Cellzome AG, Heidelberg, Germany; 3Institute for Molecular Systems Biology, Zurich, Switzerland......... 1150 |
| Wed Oral D 10:50-11:10 |
Proteomics Test of the Role of Peri-Golgi COPI Vesicles in Cisternal Maturation; Catherine E. Au1; Annalyn Gilchrist1; Sophie Dahan1; Alexander W. Bell1; Robert E. Kearney1; Tommy Nilsson2; Jacques Paiement3; John J.M. Bergeron1; 1McGill University, Montreal, Canada; 2Göteborg University, Göteborg, Sweden; 3Université de Montréal, Montreal, Canada.................. 811 |
| Wed Oral D 11:10-11:30 |
Characterization of Regulatory DNA Elements; Harald Seitz1; Anna Politis1; Björn S. Persson2; Sabine Horn3; Annie Näslund2; Meike Werther4; 1MPI for Molecular Gentics, Berlin, Germany; 2Biacore AB, Uppsala, Sweden; 3Scienion AG, Berlin, Germany; 4Inst. of Pathology, Uni-Klinikum Kassel, Kassel, Germany... 419 |
| Wed Oral D 11:30-11:50 |
Proteome Analysis of Transcription Factor Complexes during the Mammalian Cell Cycle; Annemieke Kolkman1; W.W.M. Pim Pijnappel2; H. Th. Marc Timmers2; Albert J.R. Heck1; 1Utrecht University, Utrecht, The Netherlands; 2UMC Utrecht, Utrecht, The Netherlands........... 625 |
| Wed Oral D 11:50-12:10 |
Computationally Optimized DNA Assembly; Rick H. Lathrop1; Liza Z. Larsen1; Chris D. Wassman1; Richard Colman2; She-Pin Hung2; Hans Wunsch1; Joseph D. Kittle2; G. Wesley Hatfield1; 1University of California Irvine, Irvine, CA; 2CODA Genomics, Laguna Hills, CA................. 776 |
