HUPO 2005 Scientific Programme

Monday, August 29th
 
7.00 – 8.30 Registration
 
8.30 – 10.15 OPENING AND WELCOME ADDRESS
8.30 – 8.45 Welcome Address
  W.A. Herrmann, President of the Technische Universität München
8.45 – 9.00 Welcome Address
  J.J.M. Bergeron, HUPO President, Montreal, Canada
9.00 – 9.15 Opening Remarks
  A. Görg, Technische Universität München, Germany
M. Mann, Max-Planck Institute of Biochemistry, Martinsried, Germany
9.15 – 9.45 Challenges for Research Funding on the National and International Level
  E.-L. Winnacker, President of the German Research Foundation (DFG)
9.45–10.15 An Organized Effort in Proteomics: The HUPO Initiatives
  S. Hanash, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
 
10.15-10.45 COFFEE and POSTER BREAK
 
10.45-12.45 PROTEOMICS PLENARY LECTURES
  CHAIRS: A. Görg & M. Mann
10.45-11.15 Clinical Chemistry and Proteomics
  D. Hochstrasser, Geneva University Hospital, Geneva, Switzerland
11.15–11.45 Function Prediction at the Protein, Proteome and Community Level
  P. Bork, European Molecular Biology Laboratory EMBL, Heidelberg, Germany
11.45–12.15 Functional Proteomics on Cell-Lines and Tissues
This presentation is supported by a grant from Novartis Institutes for BioMedical Research
  J. van Oostrum, Novartis Institute for Biomedical Research, Basel, Switzerland
12.15-12.45 A Human Proteome Atlas for Normal and Disease Tissue
  M. Uhlen, Royal Institute of Technology (KTH), Stockholm, Sweden
 
12.45-14.15 LUNCHEON INDUSTRY SYMPOSIA
  Sigma-Aldrich / Bruker Daltonics
 
14.15-15.00 POSTER SESSION I
 

PARALLEL SESSIONS
 
15.00-16.55 CANCER PROTEOMICS I
  CHAIRS: R.J. Simpson & M.C.M. Chung
15.00-15.20 Proteomic Analysis of Colorectal Cancer: Strategies for Novel Biomarker Discovery
  R.J. Simpson, Ludwig Institute for Cancer Research and The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
15.20-15.40 Proteome Analyses of Butyrate-Treated HCT 116 Colorectal Cancer Cells
  M.C.M. Chung, National University of Singapore, Singapore
15.40-15.55 Multiplex Detection of Surface Molecules on Colorectal Cancers
  R. Christopherson, University of Sydney, Sydney, Australia
15.55-16.10 Proteomic Analysis of Sulindac and Celecobix Induced Protein Expression
  Profile Changes in Colon Carcinoma Cells
  H. Ji, Ludwig Institute for Cancer Research and The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
16.10-16.25 Proteomics of Human Breast Cancer
  S. Souchelnytskyi, Ludwig Institute for Cancer Research, Uppsala, Sweden
16.25-16.40 Phosphoproteomic Analysis of IGF1R-Driven Proliferation and Signalling in MCF-7 Breast Cancer Cells
  L. Brill, Genomics Institute of The Novartis Research Foundation, San Diego, United States
 
15.00-16.55 CLINICAL PROTEOMICS I
  CHAIRS: Y.K. Paik & D. Speicher
15.00-15.20 In Search for the Biomarker Proteins from the Liver and Lung Cancer Specimens
  Y. Paik, Yonsei University, Seoul, Korea
15.20-15.35 Systematic Analysis for Liver and Liver Cancer Proteome: From Lab to Bedsides
  R. Zeng, Shanghai Institutes for Biological Sciences, Shanghai, P.R. China
15.35-15.50 Strategy Optimization for the Constructing of Chinese Human Liver Proteome Expression Profile
  X. Qian, Beijing Institute of Radiation Medicine, Beijing, P.R. China
15.50-16.05 Impact of the nm23-M1 Metastasis Suppressor Gene Invalidation on Mouse Liver Proteome
  M. Boissan, INSERM 680, UPMC, Paris, France
16.05-16.25 Enhanced Detection of Low Abundance Human Plasma Proteins by Optimizing a Multi-Dimensional Protein/Peptide Separation Strategy
  D. Speicher, The Wistar Institute, Philadelphia, United States
16.25-16.40 A Plasma Protein Reference Set: A Set of Plasma Proteins Identified With Extremely High Confidence Through Two Consecutive Stages of Tandem Mass Spectrometry (MS3) and ppm Precursor Mass Accuracy
  S. Schenk, University of Southern Denmark, Odense, Denmark
16.40-16.55 Characterization of Degradation Markers in Plasma Used For Transfusion
  C. Cren-Olivé, UMR CNRS 8009, Villeneuve D’asq, France
 
15.00-16.55 ANTIBODIES / ARRAYS
  CHAIRS: M. Uhlen & A. Archakov
15.00-15.20 Antibody-Based Proteomics For Human Tissue Profiling – The Swedish Human Proteome Resource Project (HPR)
  F. Ponten, IPG, Rudbeck Laboratory, Uppsala, Sweden
15.20-15.35 Antibody Microarrays: Technology and Analysis of Serum Proteomes from Cancer Patients
  C. Wingren, Lund University, Lund, Sweden
15.35-15.50 Serum Microarrays for Screening of Protein Levels
  P. Nilsson, KTH – Royal Institute of Technology, Stockholm, Sweden
15.50-16.05 Protein Microarray Technology: Technologies & Applications & Market
  T. Joos, NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
16.05-16.20 High-throughput Identification of Arabidopsis MAP Kinase Substrates Using Protein Microarrays
  B. Kersten, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
16.20-16.40 AFM Nanotechnology with Biospecific Irreversible Fishing is the Way to Reverse Avogadro Number
  A. Archakov, Research Institute of Biomedical Chemistry RAMS, Moscow, Russia
16.40-16.55 Towards Single Cell Fingerprinting in Microfluidic Device Format: Cell Manipulation, Protein Separation and Label-Free Detection
  A. Ros, Bielefeld University, Bielefeld, Germany
 
15.00-16.55 STRUCTURAL PROTEOMICS / NANOTECHNOLOGY
  CHAIRS: A. Skerra & Y. Baba
15.00-15.20 Strep-tag and Anticalins: Molecular Tools for Structural Proteome Research
  A. Skerra, Technische Universität München, Freising, Germany
15.20-15.40 Protocol for NMR-Based Structural Proteomics
  T. Szyperski, State University of New York at Buffalo, Buffalo, NY, United States
15.40-16.00 3D Structures of Human Proteins: From Narrow Focus to Large-Scale Data Gathering and Back
  U. Heinemann, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
16.00-16.15 Structural Proteomics of Mycobacterium tuberculosis: Structure-Based Research on Potential Targets for New Anti-TB Drugs
  H. Bartunik, Max-Planck Unit for Structural Molecular Biology, Hamburg, Germany
16.15-16.35 Nanobiotechnology in Proteomics
  Y. Baba, Nagoya University, Nagoya, and National Institute of Advanced Industrial Science and Technology, Takamatsu, Japan
16.35-16.55 Miniaturization Technology and Mass Spectrometry Coupling
  F. Foret, Institute of Analytical Chemistry, Brno, Czech Republic
 
17.00-17.30 COFFEE and POSTER BREAK
 
17.30-19.25 CANCER PROTEOMICS II
  CHAIRS: N. Nakamura & C. Borrebaeck
17.30-17.50 Progress in Proteome Profiling of Hepatocellular Carcinoma Tissues From Patients Infected with Hepatitis C Virus and its Possible Clinical Application
  K. Nakamura, Yamaguchi University School of Medicine, Yamaguchi, Japan
17.50-18.10 From Gene Expression Profiling to Tissue Microarrays – A Way to Find Clinical Targets in Mantle Cell Lymphoma
  C. Borrebaeck, Lund University, Lund, Sweden
18.10-18.25 Proteomic Identification of Oncogenic Chromosomal Translocation Partners Encoding Chimeric ALK Fusion Proteins
  K. Elenitoba-Johnson, University of Utah, Salt Lake City, United States
18.25-18.40 Identification of Major Histocompatibility Complex (MHC) Class I Associated Tumor Peptides via NanoLC MALDI MS/MS
  S. Hofmann, J.W. Goethe University Frankfurt, Frankfurt am Main, Germany
18.40-18.55 Proteomic Mapping of Distinct Molecular Signatures at Luminal Endothelial Cell Surfaces in Organs and Solid Tumors for Imaging and Therapy
  J. Schnitzer, Sidney Kimmel Cancer Center, San Diego, United States
18.55-19.10 Identification of Serological Biomarkers of Cancer Using a Novel Multi-Dimensional Method to Analyze Serum From Mouse Models
  N. Ali-Khan, The Wistar Institute, Philadelphia, United States
19.10-19.25 Identifying Cancer Biomarkers Using 2D-DIGE
  M.J. O’Connor, KuDOS Pharmaceuticals, Cambridge, UK
 
17.30-19.20 ORGANELLAR PROTEOMICS
  CHAIRS: L. Foster & H.-P. Braun
17.30-17.50 A Mammalian Organellae Map by Protein Correlation Profiling
  L. Foster, University of British Columbia, Vancouver, Canada
17.50-18.05 Proteomic Approach to Investigate the Supramolecular Structure of the Oxydative Phosphorylation System in Mitochondria
  H.-P. Braun, Universität Hannover, Hannover, Germany
18.05-18.20 Location Proteomics: Automated Determination of Subcellular Location Patterns by Fluorescence Microscopy
  R.F. Murphy, Carnegie Mellon University, Pittsburgh, PA, United States
18.20-18.35 Identification of Novel Lysosomal Matrix Proteins
  T. Lübke, Universität Göttingen, Göttingen, Germany
18.35-18.50 Proteomic Analysis of Liver Peroxisomes after Bezafibrate Treatment Using iTRAQ Quantification
  M. Islinger, Universität Heidelberg, Heidelberg, Germany
18.50-19.05 Proteome and Phosphoproteome Analysis of the Human Mitotic Spindle
  R. Körner, Max-Planck Institute of Biochemistry, Martinsried, Germany
19.05-19.20 Using Functional Proteomics and Lipidomics for Defining the Molecular and Cellular Mechanisms of Aging
  T. Titorenko, Concordia University, Montreal, Canada
 
17.30-19.25 NEWS CORNER I
  CHAIRS: R. Grimm & R. Westermeier
17.30-17.45 Protein Prefractionation: Passing Phase or Forward-Looking Approach?
  H.R. Hoepker, GE Healthcare Bio-Sciences, Freiburg, Germany
17.45-18.00 High-Resolution Screening of Various Biomarker Compounds by Using a New HPLC-Chip MS Technology
  R. Grimm, Agilent Technologies, Santa Clara, United States
18.00-18.15 Peptide Mapping of Biofluids by Multidimensional LC/MALDI-TOF-MS with Integrated On-Line Sample Clean-Up Using Restricted Access Materials
  F. Machtejevas, Johannes Gutenberg University, Mainz, Germany
18.15-18.25 Two-Dimensional Gel Electrophoresis/MALDI-MS Followed by iTRAQ Reagent Technology – A Powerful Tool in Toxicoproteomics for Identification and Prevalidation of Potential Early Biomarkers
  M. Kröger, Merck KGaA, Darmstadt, Germany
18.25-18.35 Biomarker Proteins in Diabetic and Normal Serum Samples Using Both Chromatographic and Preparative Electrophoretic Fractionation With 2D Gels
  A. Paulus, Bio-Rad Laboratories, Hercules, United States
18.35-18.45 Extending the Dynamic Range of Gel Based Proteomics for Biomarker Discovery
  M. Schuerenberg, Bruker Daltonik, Bremen, Germany
18.45-18.55 Improved Peptide Identification and Protein Coverage for Proteomic Samples Using Novel Alternative 2D-HPLC-MS/MS Approaches
  P. Olivova, Waters Corporation, Milford, United States
18.55-19.05 Absolute Quantitation of Proteins in Tissues by Protein Abundance Index and Isotope Dilution with Unlabeled Peptides
  Y. Ishihama, Eisai Co., Tsukuba, Japan
19.05-19.15 Nano-LC Fraction Analysis by Chip-Based Nanoelectrospray for Improved Glycopeptide Characterization
  T. Corso, Advion Biosciences, Ithaca, United States
19.15-19.25 Unique Multivariate Approach to Biomarker Discovery Using New Technology for Analysis of Proteomics Data
  D. Bramwell, Nonlinear Dynamics, Newcastle upon Tyne, UK
 
19.00-21.00 EuPA MEETING
  First GC meeting of EuPA
 

Tuesday, August 30th
 
7.00 – 8.30 Registration
 
7.00 – 8.00 INDUSTRY SYMPOSIUM
  Nonlinear Dynamics
 
8.30-10.30 HONORARY LECTURES "PIONEERS IN PROTEOMICS"
  CHAIRS: A. Görg & M. Mann
 
8.30– 9.00 A Successful Thesis?
  P. O’Farrell, University of California-San Francisco, CA, United States
9.00– 9.30 Clues to Composition and Conformation of Peptides and Proteins from Their Adduction Behaviour
  J. Fenn, Virginia Commonwealth University, Richmond, VA, United States
9.30–10.00 MALDI Mass Spectrometry in Proteomics: Past, Present and Future
  F. Hillenkamp, University of Münster, Germany
10.00– 10.30 From Sequences to Knowledge, the Role of the Swiss-Prot Component of UniProt
  A. Bairoch, Swiss Institute of Bioinformatics, Geneva, Switzerland
 
10.30-11.15 COFFEE and POSTER BREAK
 
11.15-12.30 PLENARY LECTURES: PROTEOMICS TECHNOLOGIES
  CHAIRS: P. Roepstorff & R. Zubarev
11.15-11.40 Driving Biological Discovery using Mass Spectrometry
  J. Yates III, The Scripps Research Institute, La Jolla, CA, United States
11.40-12.05 2D Electrophoresis for Proteome Analysis
  A. Görg, Technische Universität München, Freising, Germany
12.05-12.30 Toward Error-Free Proteomics
  R. Zubarev, Uppsala University, Uppsala, Sweden
 
12.45-14.15 LUNCHEON INDUSTRY SYMPOSIA
  BD / Thermo Electron Corporation
 
14.15-15.00 POSTER SESSION II
 

PARALLEL SESSIONS

 
15.00-16.55 BIOINFORMATICS STANDARDS DATABASES
  CHAIRS: R. Apweiler & R. Appel
15.00-15.20 Towards Standardized Capturing of Proteomics Data and Proteomics Repositories
  R. Apweiler, European Bioinformatics Institute (EBI), Hinxton, United Kingdom
15.20-15.40 What’s in MS Spectra? What’s in Databases? Take the Best to Identify Active Proteins
  R. Appel, Swiss Institute of Bioinformatics, Geneva, Switzerland
15.40-15.55 An Evaluation, Comparison and Accurate Benchmarking of Several Publicly-Available MS/MS Search Algorithms: Sensitivity and Specificity Analysis
  E. Kapp, Ludwig Institute for Cancer Research, Melbourne, Australia
15.55-16.10 High-Performance Shotgun Proteomics Data Validation Using Experimental Parameters
  M. Heller, University of Bern, Bern, Switzerland
16.10-16.25 The Creation and Usage of a Human Protein Atlas Database
  E. Björling, KTH – Royal Institute of Technology, Stockholm, Sweden
16.25-16.40 Reference Libraries of Peptide Mass Spectra
  S. Stein, National Institute of Standards and Technology, Gaithersburg, MD, United States
16.40-16.55 Bioinformatics at NIAID Biodefense Proteomics Administrative Resource Center
  P. McGarvey, Georgetown University Medical Center, Washington, DC, United States
 
15.00-16.55 PROTEOMIC METHODS I
  CHAIRS: Y. Oda & F. Regnier
15.00-15.20 Activity Based and Affinity Based Approaches using Stable Isotope Labeling in Drug Discovery
  Y. Oda, Eisai Co., Tsukuba, Ibaraki, Japan
15.20-15.40 Carbonylation of Protein During Oxidative Stress
  F. Regnier, Purdue University, West Lafayette, IN, United States
15.40-15.55 Protein Quantification in Formalin Fixed Tissue Samples
  K. Becker, Technische Universität München, München, Germany
15.55-16.10 DIGE as an Analytical Tool for Quantitative Multivariable Differential-Display Proteomics
  D.B. Friedman, Vanderbilt University School of Medicine, Nashville, TN, United States
16.10-16.25 Double Standards in Quantitative Proteomics: Direct Comparative Assessment of Difference Gel Electrophoresis and Metabolic Stable Labeling
  A. Kolkmann, Utrecht University, Utrecht, The Netherlands
16.25-16.40 Multi-Dimensional Capillary Electrophoresis Separation Interfaced with Mass Spectrometry for Bioanalytical Drug Characterization
  N. Guzman, Johnson & Johnson, Raritan, NJ, United States
16.40-16.55 Molecular Tools for the Detection and Enrichment of Protein Families in Functional Proteomics
  N. Sewald, Bielefeld University, Bielefeld, Germany
 
15.00-17.00 POST-TRANSLATIONAL MODIFICATIONS
  CHAIRS: P. Roepstorff & N. Taniguchi
15.00-15.20 Modification Specific Proteomics, a Concept for Subproteomics
  P. Roepstorff, University of Southern Denmark, Odense, Denmark
15.20-15.40 Role of Branching N-Glycans and the Functional Glycomics
  N. Taniguchi, Osaka University Graduate School of Medicine, Osaka, Japan
15.40-16.00 Quantitation of Post-Translational Modifications in Proteomics by Mass Spectrometry
  O.N. Jensen, University of Southern Denmark, Odense, Denmark
16.00-16.15 Detection of Phosphopeptides from Complex Mixtures using Titanium Oxide Pre-Columns and FT-ICR Mass Spectrometry
  M. Pinkse, Utrecht University, Utrecht, The Netherlands
16.15-16.30 Phosphorylation as a Regulatory Mechanism in the Spindle Assembly Checkpoint
  A. Kettenbach, Harvard Medical School, Boston, MA, United States
16.30-16.45 Revival of Negative Ion Electrospray Tandem Mass Spectrometry in Protein Phosphorylation Analysis
  W. Lehmann, German Cancer Research Center, Heidelberg, Germany
16.45-17.00 Peptoscope: Automatic Detection of Post-Translational Modifications Driving a Search Engine
  F. Potthast, Uni/ETH Zürich, Zürich, Switzerland
 
15.00-16.55 CLINICAL PROTEOMICS II
  CHAIRS: M.J. Dunn & P. Ping
15.00-15.20 Myocardial Ischemic Injury and Proteasome Function
  P. Ping, Geffen School of Medicine at UCLA, Los Angeles, CA, United States
15.20-15.40 Proteomics of the Transplanted Heart
  M.J. Dunn, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
15.40-15.55 Integrated Proteomic and Metabolomic Analysis Reveals Metabolic Remodelling in Human Persistent Atrial Fibrillation
  U. Mayr, St. George’s University of London, London, United Kingdom
15.55-16.10 Potential Rational Disease Biomarkers for Chronic Obstructive Pulmonary Disease (COPD) from Human Plasma
  J. Bandow, Pfizer Inc., Ann Arbor, MI, United States
16.10-16.25 Characterization of the Multiple Sclerosis Cerebrospinal Fluid Proteome by Gel-Based and Gel-Free Proteomic Approaches
  D. Dumont, Limburgs Universitair Centrum, Diepenbeek, Belgium
16.25-16.40 Quantitative Cellular Proteomics of Presynaptic Active Zone and Postsynaptic Density of Mouse Hippocampus – Effect of Morphine Treatment
  R. Wang, Mount Sinai School of Medicine, New York, NY, United States
16.40-16.55 Vaccine Discovery and Proteomics
  G. Grandi, Chiron Vaccines, Siena, Italy
 
17.00-17.30 COFFEE and POSTER BREAK
 

PARALLEL SESSIONS

 
17.30-19.30 NEWS CORNER II
  CHAIR: H.E. Meyer
17.30-17.40 Mild Tissue Dissociation and Subcellular Fractionation Sample Preparation Tools, Facilitating Functional Investigations of Proteins
  R. Hendricks, Merck KgaA, Darmstadt, Germany
17.40-17.50 Strategies for Selective Isolation and Identification of Proteins from Complex Clinical Samples by Magnetic Bead-Based MALDI-TOF/TOF
  M. Kostrzewa, Bruker Daltonik, Bremen, Germany
17.50-18.00 Cost-Efficient and High Capacity Depletion of Abundant Serum Proteins
  M. Palm, Affibody AB, Bromma, Sweden
18.00-18.10 Developments in TOF/TOF Technology Applied to Proteomics
  M. Hornshaw, Applied Biosystems, Warrington, United Kingdom
18.10-18.20 Dynamic Analysis of Nucleolar Proteome by i-PROT Technology
  B. Xie, Agilix,Corporation, New Haven, CT, United States
18.20-18.30 Reversible Covalent Binding of the Fluorophore Epicoccone to Proteins Provides a Novel Approach to the Sensitive Quantification of Proteins Across a Wide Variety of Different Platforms
  D. Veal, Fluorotechniques, Sydney, Australia
18.30-18.40 EpiTags: A Scalable Approach for Building Binders and Assays to Study the Proteome
  J. Tonkinson, Epitome Biosystems, Waltham, MA, United States
18.40-18.50 Array-Based Systems for High Information Protein Interaction Analysis in Proteomics
  B. Persson, Biacore AB, Uppsala, Sweden
18.50-19.00 Discover Multiple Facets of the Innovative Phenyx Platform and Achieve Increased Confidence in Protein Identification
  P.-A. Binz, Geneva Bioinformatics (GeneBio SA), Geneva, Switzerland
19.00-19.10 Integration of Databases, TRANSFAC, TRANSPATH and Proteome, is the Comprehensive Resource to Study Protein Functions
  A. Kel, Biobase GmbH, Wolfenbüttel, Germany
19.10-19.20 Fourier Transform Mass Spectrometry Based Comparative Proteomics for Plasma Profiling
  C. Paweletz, Merck Research Laboratories, Rahway, NJ,United States
19.20-19.30 Protein Biomarkers for Inflammatory Disease Dissection
  C. Labeur, Peakadilly, Zwijnaarde, Belgium
 
17.30-19.30 DOCTORS’ OFFICE I: Two-Dimensional Electrophoresis & DIGE
  CHAIRS:
T. Rabilloud, CEA-INSERM, Grenoble, France
R. Westermeier, GE Healthcare, Freiburg, Germany
D. Friedman, Vanderbilt University, Nashville, TN, United States
W. Weiss, Technische Universität München, Freising, Germany
 
17.30-19.30 DOCTORS’ OFFICE II Mass Spectrometry
  CHAIRS:
P. Roepstorff, University of Southern Denmark, Odense, Denmark
K. Hjernœ, University of Southern Denmark, Odense, Denmark
O.N. Jensen, University of Southern Denmark, Odense, Denmark
M. R. Larsen, University of Southern Denmark, Odense, Denmark
 
17.30-19.30 DOCTORS’ OFFICE III : Bioinformatics
  CHAIRS:
R. Appel, Swiss Institute of Bioinformatics, Geneva, Switzerland
H. Hermjakob, European Bioinformatics Institute, Hinxton, United Kingdom
P.-A. Binz, Geneva Bioinformatics, Geneva, Switzerland
F. Lisacek, Swiss Institute of Bioinformatics, Geneva, Switzerland
 

Wednesday, August 31st
 
7.00 – 8.30 Registration
 
7.00 – 8.00 INDUSTRY SYMPOSIUM
  Agilent Technologies
 
8.30-10.20 PLENARY LECTURES: SUBPROTEOMES
  CHAIRS: R. Aebersold & R. Simpson
8.30– 9.00 Proteomics of the Early Secretory Pathway
  J.J.M. Bergeron, McGill University, Montreal, QC, Canada
9.00– 9.30 Cell Fate Decisions Revealed by Quantitative Phosphoproteomics
  M. Mann, Max-Planck-Institute of Biochemistry, Martinsried, Germany
9.30– 9.55 Combined Fractional Diagonal Chromatography (COFRADIC): A Multi-Purpose Tool for Peptide-Centric Proteomics
  J. Vandekerckhove, University of Gent, Gent, Belgium
9.55– 10.20 Quantitative Proteomics by Metabolic Stable Isotope Labeling and Mass Spectrometry
  A. Heck, Utrecht University, Utrecht, The Netherlands
 
10.20-10.50 COFFEE and POSTER BREAK
 
10.50-12.40 PLENARY LECTURES: MODEL ORGANISMS
  CHAIRS: J. Bergeron & J. Vandekerckhove
10.50-11.20 Analysis of the Budding Yeast Proteome
  E. O’Shea, Howard Hughes Medical Institute, San Francisco, CA, United States
 
11.20-11.50 Towards a Comprehensive Understanding of Bacterial Physiology by Proteomics
  M. Hecker, University of Greifswald, Greifswald, Germany
11.50-12.15 Deciphering Membrane Proteomes in the Model Plant Arabidopsis thaliana
  H. Barbier-Brygoo, CNRS, Gif-sur-Yvette Cedex, France
12.15-12.40 A Novel Cell Signalling Pathway in Arabidopsis Revealed by Proteomics
  A. Slabas, University of Durham, Durham, United Kingdom
 
12.45-14.15 LUNCHEON INDUSTRY SYMPOSIA
  GE Healthcare / Waters Corporation
 
14.15-15.00 POSTER SESSION III
 

PARALLEL SESSIONS

 
15.00-17.00 HUPO INITIATIVES I
  CHAIRS: J. Bergeron & Y.K. Paik
15.00-15.30 HUPO Human Liver Proteome Project
  F. He, Beijing Institute of Radiation Medicine, Beijing, China
15.30-16.00 HUPO Plasma Proteome Project
  G. Omenn, University of Michigan, Ann Arbor, MI, United States
16.00-16.30 HUPO Brain Proteome Project
  H.E. Meyer, Ruhr University Bochum, Bochum, Germany
16.30-16.45 Quantitative Proteomics of Membrane Proteins for Studying Brain and its Diseases
  J. Wisniewski, Protana Inc., Toronto, Canada
16.45-17.00 Identification of Hepatocellular Carcinoma-Associated Serum Glycoproteins by Lectin Affinity Purification and 2D Gel Analysis
  I. Ang, Chinese University of Hongkong, Hong Kong, P.R. China
 
15.00-16.55 CLINICAL PROTEOMICS III & TOXICOLOGY
  CHAIRS: L. Bini & G. Schmitz
15.00-15.20 Proteomic Approach to Define Multivariate Protein Markers in Lung Diseases
  L. Bini, University of Siena, Siena, Italy
15.20-15.40 Plasma Proteomics – Challenges and Windows of Opportunities
  G. Schmitz, University of Regensburg, Germany
15.40-15.55 A Proteomic Approach to Human Muscle Plascity and Function: From Physiology to Pathology
  C. Gelfi, National Research Council, Segrate, Italy
15.55-16.10 Proteome Analysis of the Red Blood Cell: What More Can be Learned?
  E. Pasini, Biomedical Primate Research Center, Rijswijk, The Netherlands
16.10-16.25 Overexpression of Angiopoietin-like Protein 4 Alters the Protein Expression Profiles of the Liver Tissue in DB/DB Diabetic Mice
  Y. Wang, University of Hong Kong, Hong Kong, P.R. China
16.25-16.40 Identification and Purification of Sperm Surface Proteins Related to Sperm Maturation
  C. Belleanne, INRA, Nouzilly, France
16.40-16.55 Proteomics in Predictive Toxicology
  H. Platsch, BASF, Ludwigshafen, Germany
 
15.00-16.45 PROTEOMIC METHODS II
  CHAIRS: J. Vandekerckhove & D. Fenyö
15.00-15.15 ICPL, a Technique for Comprehensive and Quantitative Proteome Analysis
  F. Lottspeich, Max-Planck Institute of Biochemistry, Martinsried, Germany
15.15-15.30 Non-Labeling Liquid Chromatography-Mass Spectrometry-Based Quantitative Proteomics
  X. Li, Institute for Systems Biology, Seattle, United States
15.30-15.45 Comparison of Time-Course and Steady-State Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) to Investigate the Function and Dynamics of a Large Multi-Protein Complex
  J. Andersen, University of Southern Denmark, Odense, Denmark
15.45-16.00 Fluorous Proteomics: Enrichment and Analysis of Peptide Subsets Using Fluorous Affinity Tags and Mass Spectrometry
  E. Peters, Genomics Institute of the Novartis Research Foundation, San Diego, CA, United States
16.00-16.15 New Approaches to Full Characterization of Cancer Biomarkers at the Trace Level – Epidermal Growth Factor Receptor
  S. Wu, Northeastern University, Boston, MA, United States
16.15-16.30 2-Dimensional-Image-Converted Analysis of Nano-Flow Liquid Chromatography and Mass Spectrometry
  M. Ono, National Cancer Research Institute, Tokyo, Japan
16.30-16.45 Predicting the Success Rate of Proteome Analysis by Modelling Protein Abundance Distributions and Experimental Designs
  D. Fenyö, Rockefeller University, New York, United States
 
15.00-17.00 MICROBIAL AND OTHER NON- MAMMALIAN PROTEOMES
  CHAIRS: M. Hecker & A. Nordheim
15.00-15.15 Proteomic Identification of Proteins Associated With Biofilm Growth of the Pathogen Staphylococcus aureus
  A. Nordheim, University of Tübingen, Tübingen, Germany
15.15-15.30 Mining Quorum Sensing Regulated Proteins – Role of Bacterial Cell Communication in Global Gene Regulation as Assessed by Proteomics
  K. Riedel, Institute of Plant Biology, University of Zürich, Zürich, Switzerland
15.30-15.45 Syntrophic Microbes Examined With Virtual and Classical 2-D Gels
  R. Loo, University of California – Los Angeles, Los Angeles, United States
15.45-16.00 Proteomic Profiling of Bacterial Strains
  V. Govorun, Research Institute for Physico-Chemical Medicine, Moscow, Russia
16.00-16.15 Monitoring the Dynamic of Transcription and Translation Within the Time Course of Recombinant E. coli Cultivations
  K. Dürrschmid, University of Natural Resources and Applied Life Sciences, Vienna, Austria
16.15-16.30 Proteome Analysis of Corynebacterium glutamicum
  A. Poetsch, Ruhr University Bochum, Bochum, Germany
16.30-16.45 Proteomic Analysis of the Membrane Proteins in Alkalimonas amylolytica
  B. Meng, Beijing Genomics Institute, CAS, Beijing, China
16.45-17.00 FLYCAT – Towards a Drosophila Proteome Database
  E. Brunner, University of Zürich, Zürich, Switzerland
 
17.00-17.30 COFFEE and POSTER BREAK
 

PARALLEL SESSIONS

 
17.30-19.30 HUPO INITIATIVES II
  CHAIRS: R. Simpson & G. Omenn
17.30-17.45 Quantitation and Resolution of Proteins in Complex Specimens
  M. Mann, Max-Planck Institute of Biochemistry, Martinsried, Germany
17.45-18.00 Priority Proteins from Each Initiative for HUPO Antibodies Production
  M. Uhlen, Royal Institute of Technology (KTH), Stockholm, Sweden
18.00-18.15 Organ-Based Additional Proteomes and Annotation
  P. Ping, Geffen School of Medicine at UCLA, Los Angeles, CA, United States
18.15-18.30 Bioinformatics Annotations and Cross-Comparisons of Proteomics Findings in Plasma, Liver and Brain
  R. Apweiler, European Bioinformatics Institute (EBI), Hinxton, United Kingdom
18.30-18.45 High Throughput Analysis of Plasma Proteins
  R. Aebersold, Swiss Federal Institute of Technology ETH, Zürch, Switzerland
18.45-19.00 Feasibility of Clinical Proteomics
  D. Hochstrasser, Geneva University Hospital, Geneva, Switzerland
19.00-19.15 Proteomics of Protein Biomarkers for Liver Diseases
  L. Beretta, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
19.15-19.30 General Discussion
 
17.30-19.25 CLINICAL BIOMARKER DISCOVERY
  CHAIRS: S. Pennington & H. Hondermarck
17.30-17.50 Discovery, Validation and Quantification of Potential Biomarkers and Therapeutic Targets
  S. Pennington, Conway Institute, University College Dublin, Dublin, Ireland
17.50-18.10 Proteomics of Breast Cancer for Signal Pathway Profiling and Target Discovery
  H. Hondermarck, University of Sciences and Technologies, Lille, France
18.10-18.25 The Multi-Dimensional µLC-MALDI-MS Differential Peptide Profiling System for Identification of Cancer Biomarker
  K. Uchida, Graduate School of Comprehensive Human Sciences, Tsukuba, Japan
18.25-18.40 Biomarker Discovery in Human Cerebral Spinal Fluid for Neurodegenerative Diseases
  C. Pan, University of Washington, Seattle, WA, United States
18.40-18.55 Focused Mass Spectrometric Proteomics for Discovery of Novel Diagnostic Targets in Biofluids
  N. Heegaard, Statens Serum Institut, Copenhagen, Denmark
18.55-19.10 Discovery of Biomarkers in Type 2 Diabetes Urine: Potential for a Non-Invasive Early Diagnostic
  B. Walsh, Minomic Pty Ltd., Harbord, Australia
19.10-19.25 Developing Peptide MRM-Based Assays for Cardiovascular Biomarker Proteins in Plasma Using a Hybrid Triple Quadrupole Linear Ion Trap Mass Spectrometer
  C. Hunter, Applied Biosystems, Foster City, Untied States
 
17.30-19.30 FUNCTIONAL PROTEOMICS
  CHAIRS: B. Küster & D. Figeys
17.30-17.45 A Proteomic Screen for Host Cell Proteins Interacting With Tyrosine Phosphorylated Bacterial Effectors
  M. Selbach, Max-Planck Institute of Biochemistry, Martinsried, Germany
17.45-18.00 Analysis of Protein Kinases by Chemical Proteomics
  H. Daub, Max-Planck Institute of Biochemistry, Martinsried, Germany
18.00-18.15 Cell Cycle Dynamics of Chromatin Proteome in Xenopus Egg Extract
  G. Khoudoli, University of Dundee, Dundee, United Kingdom
18.15-18.30 Targeted Proteomic and Structural Analysis of 14-3-3sigma, a p53 Effector Commonly Silenced in Cancer
  H. Hermeking, Max-Planck Institute of Biochemistry, Martinsried, Germany
18.30-18.45 Systematic Analysis of Uncharacterized Protein Complexes From Saccharomyces cerevisiae
  K. Breitkreuz, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Ontario, Canada
18.45-19.00 Mapping Protein-Protein and Protein-DNA Interactions
  D. Figeys, University of Ottawa, Ottawa, Canada
19.00-19.15 Functional Knockouts of Specific Protein Interactions
  M. Fear, Institute for Child Health Research, Perth, Australia
19.15-19.30 Proteomic Mapping of Dynamic Protein-Protein Interactions in Mammalian Cells
  M. Barrios-Rodiles, Samuel Lunenfeld Research Institute, Toronto, Canada
 
17.30-19.30 PLANT PROTEOMES AND METABOLOMES
  CHAIRS: J. Jorrin & L. Willmitzer
17.30-17.50 Integrative Analysis of the Metabolome and Transcriptome
  L. Willmitzer, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, Germany
17.50-18.10 Proteomics of Plant Responses to Biotic Stresses: Progress, Problems and Challenges
  J. V. Jorrín, University of Córdoba, Córdoba, Spain
18.10-18.25 Using Proteomics Approaches to Help the Rice Genome Annotation
  J. Wang, Beijing Genomics Institute, Beijing, P.R. China
18.25-18.40 Hiding Behind Hydrophobicity – Transmembrane Segments in Mass Spectrometry
  L. Eichacker, Ludwig-Maximilians-Universität München, Munich, Germany
18.40-18.55 Membrane Proteomics of Arbuscular Mycorrhiza
  E. Dumas-Gaudot, INRA, Dijon, France
18.55-19.10 Tracing Altered Metabolic States in the Thylakoid Membrane
  H. Seelert, Darmstadt University of Technology, Darmstadt, Germany
19.10-19.25 Extracellular Matrix Proteome of Chickpea (Cicer arietinum) Illustrates Pathway Abundance, Novel Protein Functions and Evolutionary Perspect
  N. Chakraborty, National Centre for Plant Research, New Delhi, India
 
20.00–23.00 CONGRESS DINNER
 

Thursday, September 1st

 
7.00 – 8.30 Registration
 
08.30-10.00 PLENARY LECTURES: INTERACTION PROTEOMICS
  CHAIRS: E. O’Shea & O.N. Jensen
08.30– 09.00 The EU Interaction Proteome Project
  F.U. Hartl, Max-Planck Institute of Biochemistry, Martinsried, Germany
09.00- 09.30 Funtional and Chemical Proteomics for Drug Discovery
  B. Küster, Cell Zome, Heidelberg, Germany
09.30-10.00 Regulation of the Raf Signalling Pathway by Protein Interactions
  W. Kolch, Beatson Institute for Cancer Research, Glasgow, United Kingdom
 
10.00-10.30 COFFEE BREAK
 
10.30–12.15 ROUND TABLE: EUROPEAN AND INTERNATIONAL COLLABORATION IN PROTEOMIC RESEARCH
 
Topic Keynote Speaker Organisation
  A. Abbott, Moderator, Science Journalist Nature Publishing Group
Building the EU’s knowledge economy O. Quintana Trias, Director, DG Research, Directorate Health European Commission
Future vision for proteomics research M. Mann, Head, Max-Planck Institute for Biochemistry Max - Planck Institute
Funding Proteomics and Systems Biology Research: Experiences from both sides of the Atlantic R. Aebersold, Head, Institut für Molekulare Systembiologie Swiss Federal Institute of Technology ETH
Applications of proteomics research: the industry view H. Langen, Head of Proteomics, Roche Center for Medical Genomics F. Hoffmann-La Roche Ltd.
Roundtable and Q&A All speakers, in presence of J. Fenn, Nobel Prize Laureate (Virginia Commonwealth University Richmond, VA, USA)  
 
12.15-13.30 LUNCHEON INDUSTRY SYMPOSIUM
  Applied Biosystems
 
13.30-15.00 PLENARY LECTURES: SYSTEMS BIOLOGY
  CHAIRS: A. Heck & B. Küster
13.30–14.00 Proteomics as a Genomic Science
  R.H. Aebersold, Swiss Federal Institute of Technology ETH, Zürch, Switzerland
14.00-14.30 Integration of Experimental Data on Gene Expression and Protein-Protein Interaction with Predicted Functional Associations
  S. Brunak, Technical University of Denmark, Lyngby, Denmark
14.30-15.00 SmartCell: A Cell Network Simulation Program
  L. Serrano, EMBL Heidelberg, Germany
 
15.00-15.30 CLOSING CEREMONY
  Poster Awards and HUPO Distinguished Awards
 
15.30-16.00 CLOSING LECTURE
  Equalizer Beads: The Quest for a “Democratic Proteome”
  P.G. Righetti, University of Verona, Verona, Italy