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Molecular & Cellular Proteomics 1:621-649, 2002.
© 2002 by The American Society for Biochemistry and Molecular Biology, Inc.

Program

1. Opening Ceremonies

with the participation of Claudie Haigneré, French Minister of Research, and addresses by Samir Hanash, President, HUPO, Julio Celis, Chair, International Organizing Committee, and Jean Rossier, Local Organizing Committee

Thursday, November 21, 18:00–19:30, Richelieu Room

18:30

Keynote Lecture: Proteomics and Public Health

C. Brechot

19:30

Welcome Reception

2. Keynote Lecture

Friday, November 22, 9:00–9:45, Richelieu Room

9:00

The Alliance for Cell Signaling

A. Gilman

3. Plenary Session Dissecting Cellular Function: Cell Biology Meets Proteomics

Chair: A. I. Lamond

Friday, November 22, 9:50–11:20, Richelieu Room

9:50

3.1 Proteomic Analysis of Nuclear Bodies

A. I. Lamond, Y. Lam, A. Leung, A. Fox, S. Ogg, A. Vertegaal, J. Anderson, and M. Mann

10:10

3.2 Molecular Composition of the Human Centrosome

C. J. Wilkinson, J. Andersen, T. Mayor, M. Mann, and E. A. Nigg

10:30

3.3 Proteome of Organelles by LC-MS/MS

J. Rossier, D. Pflieger, P. Ducoroy, and J. Vinh

10:50

3.4 Medium Resolution Model of the Yeast Nuclear Pore Complex

F. Alber, B. T. Chait, S. Dokudovskaya, O. Karni, J. Kipper, M. P. Rout, A. Sali, C. Strambio-de-Castilla, A Suprapto, L. M. Veenhoff, R. Williams, and W. Zhang

11:20 Coffee Break, Posters, and Exhibition

12:30 Lunch and Luncheon Seminar

4. Parallel Session 1 Educational Session: Sample Preparation and Gel-based Proteomics

Chairs: T. Rabilloud and A. Görg

Friday, November 22, 14:30–16:10, Richelieu Room

14:30

4.1 2-D Electrophoresis Technology: Perfection in View?

A. Görg, G. Boguth, O. Drews, A. Köpf, G. Reil, R. Wildgruber, and W. Weiss

15:00

4.2 Proteomes and Proteomics: Current Limits and How To Push Them

T. Rabilloud, S. Luche, C. Tastet, and M. Chevallet

15:30

4.3 Protein Detection for 2-DE-based Proteomics

M. Dunn

5. Parallel Session 2 Signal Transduction

Chair: R. Taussig

Friday, November 22, 14:30–16:10, Condé Room

14:30

5.1 Alliance for Cellular Signaling—B Cell and Cardiac Myocyte Signaling

R. Taussig

14:55

5.2 High Throughput Multiplexed Analysis of Cellular Lipids

H. A. Brown

15:20

5.3 Functional Proteomic Analysis of the PKC Signaling System in Cardiac Protection Against Ischemic Injury

P. Ping, T. Vondriska, J. Zhang, C. Baines, E. Cardwell, and G. Wang

15:45

5.4 Identification of New Targets in Transforming Growth Factor-ß Signalling Using Proteomics

S. Souchelnyskyi, T. Stasyk, H. Iwahana, M. Lomnytska, U. Hellman, and T. Kanamoto

15:55

5.5 Endogenous TGF-ß Receptor-mediated Smad Signaling Complexes by Mass Spectrometry

R. Angeletti, E. Nieves, and Q. Luo

6. Parallel Session 3 Resources and Technologies

Chair: R. J. Simpson

Friday, November 22, 14:30–16:10, Lulli Room

14:30

6.1 Global Approaches to the Analysis of PTMs

H. Meyer, K. Marcus, H. Schaefer, D. Chamrad, J. Reinders, and A. Sickmann

14:55

6.2 A Novel Approach to the Quantitation of Differential Protein Expression

G. E. Reid, R. A. J. O’Hair, and R. J. Simpson

15:20

6.3 Proteomics as a Process: Using Technology Optimally

W. Blackstock

15:45

6.4 Gel-free Quantitative Proteomics

J. Vandekerkchove, J. Van Damme, M. Goethals, A. Staes, G. Thomas, L. Martens, H. Demol, M. Puype, and K. Gevaert

15:55

6.5 Flow Cytometric Isolation of Human Antibodies from a Nonimmune Saccharomyses cerevisiae Surface Display Library

M. Feldhaus

16:10 Coffee Break, Posters, and Exhibition

7. Parallel Session 4 Educational Session: Mass Spectrometry

Chair: R. Caprioli

Friday, November 22, 17:00–18:40, Richelieu Room

17:00

7.1 Profiling and Imaging of Proteins in Tissue Sections Using Mass Spectrometry as a Discovery Tool in Biological Research

R. Caprioli

17:30

7.2 A Tutorial on MALDI and ESI MS Instrumentation Used in Proteomic Studies

P. Chaurand

18:00

7.3 Mass Spectrometry Is the Key Analytical Tool in Proteomics

P. Roepstorff

8. Parallel Session 5 Microbial Proteomics

Chair: R. Van Bogelen

Friday, November 22, 17:00–18:40, Condé Room

17:00

8.1 Proteomics Applied to Antibacterial Drug Discovery

R. Van Bogelen

17:25

8.2 Microbial Proteomics—Big Lessons from Little Packages

S. Cordwell

17:50

8.3 From the Genome to Cell Physiology: Bacillus subtilis as a Model

M. Hecker

18:15

8.4 Molecular Typing of the H. pylori Clinical Isolates in Russia by Genome and Proteome Analysis

V. Govorun, K. Momynaliev, and P. Lokhov

18:25

8.5 Proteomic Identification of Proteins of Mycobacterium tuberculosis That Are Differentially Expressed in the Host

K. Pickard, J. Dhillon, D. Mitchison, P. Butcher, and C. D. O’Connor

9. Parallel Session 6 Expression Proteomics in Health and Disease (Oncology)

Chair: J. Celis

Friday, November 22, 17:00–18:40, Lulli Room

17:00

9.1 Proteomics Strategies in Cancer

J. Celis, I. Gromova, and P. Gromov

17:25

9.2 Expression Profiling of the Helicobacter pylori Clinical Isolates Obtained from Patients with Different Gastric Disorders

A. Archakov and V. M. Govorun

17:50

Serum Proteomic Patterns: Early Diagnosis of Ovarian and Prostate Cancer

L. Liotta

18:15

9.3 Proteomics of Lymphoma Cells Following Treatment with a Demethylating Drug

R. Joubert-Caron, F. Poirier, and V. Labas

18:25

9.4 Proteomics of Breast Cancer for Signal Pathway Profiling and Therapeutic Target Discovery

H. Hondermarck, I. El Yazidi-Belkoura, F. Vandermoere, E. Adriaenssens, S. Lottin, J.-J. Curgy, A.-S. Vercoutter-Edouart, and J. Lemoine

10. Keynote Lecture

Friday, November 22, 18:50–19:35, Richelieu Room

18:50

Cell Organelle Proteomics and Its Application to Cancer

J. Bergeron

11. Posters Cell Biology

Friday, November 22, 9:00–19:30, Galerie Le Notre

11.1 A Subcellular Proteomics Approach to Fish Out New Plant Chloroplast Envelope Transporters

J. Garin, M. Ferro, D. Salvi, H. Riviere-Rolland, T. Vermat, D. Seigneurin-Berny, D. Grunwald, A. Viari, and J. Joyard

11.2 What Functional Proteomics Reveals About Endoplasmic Reticulum Detergent-resistant Microdomains

E. Chevet

11.3 Reverse-proteomic Analysis of Rho GTPase Regulation in C. elegans

S. Jenna, D. T. Nguyen, J. Schrag, J. Reboul, M. Vidal, and E. Chevet

11.4 Analysis of the Mouse Brain Proteome Using 2D-LC-MS/MS

K. Marcus, R. Vetter, H. E. Meyer, and A. Sickmann

11.5 Proteomic Analysis of Mouse Embryonic Stem Cells

K. Nagano, K. Nunomura, T. Shinkawa, M. Zvelevil, A. Yang, N. Okamura, H. Miki, T. Takenawa, T. Izumi, and T. Isobe

11.6 Identification of Transglutaminase Protein Substrates

G. Marino, S. Orr, and M. Ruoppolo

11.7 Mapping of the Rat Natural Killer Cell Membrane Microdomains

P. Man, P. Novak, A. Fiserova, V. Havlicek, and K. Bezouska

11.8 Analysis of Cell Surface Proteins Using an Isotope Tagging Approach for Quantitative Mass Spectrometry

T. Oppolzer and M. Jaeger

11.9 Protein Expression in Cultured Fetal Skin

D. Crettaz, F. Vuadens, C. Scaletta, E. Servis, P. Schneider, P. Hohlfeld, J.-D. Tissot, and L. Appelgate

11.10 Proteomic Studies of Human Vascular Endothelial Cells

A. Bruneel, V. Labas, A. Mailloux, S. Sharma, M. Vaubourdolle, and B. Baudin

11.11 Proteome Analysis of U937 Cell Stimulated by Lipopolysaccharide

J. S. Ahn, N.-Y. Ha, J. Kim, S. U. Lee, B. I. Cho, Y. N. Kim, S.-J. Kang, J. W. Kim, and C.-W. Lee

11.12 Use of Quadrupole Linear Ion Trap Mass Spectrometer in Combination with Nanoscale 2D-LC for the Analysis of C. elegans Proteins

G. Hopfgartner, V. Tschäppät, and E. Varesio

11.13 Metalloproteome of Normal and Copper-depleted Hep G2 Cells

E. A. Roberts, B. Sarkar, Y.-M. She, S. Narindrasorasak, and S. Yang

11.14 Influence of GSNO on the Proteome of Endothelial Cells

P. Lutter, S. Bailey, H. E. Meyer, C. Hüls, and P. Weingarten

11.15 In S. cerevisiae Unbalanced Levels of Tyrosine Phosphorylation Affect Proteome and cAMP Signalling

A. Modesti, T. Gamberi, F. Magherini, L. Bini, G. Raugei, G. Manao, and G. Ramponi

11.16 Mapping the Proteome of Primitive Hematopoietic Cells Using Protein Fluorescent Labelling

A. D. Whetton, C. A. Evans, D. Blinco, T. Holyoake, M. Alcorn, J. Melo, and S. D. Griffiths

11.17 Phosphoproteomics Analysis of Proteins from Human Fetal Liver

J. Wang, Y. Jiang, Y. Cai, F. He, and X. Qian

11.18 Identification of Substrates of Matrix Metalloproteinases in Human Plasma Using Proteomic Analysis

S.-T. Lee, I. K. Hwang, S. M. Park, and S.-J. Lee

11.19 Proteomic Analyses of the Human 20S Proteasome

S. Uttenweiler-Joseph, O. Burlet-Schiltz, S. Claverol, E. Neuhauser, B. Xu, J.-E. Gairin, and B. Monsarrat

11.20 Characterization of Tetraspanin Complexes by Immunoprecipitation and Mass Spectrometry

F. Le Naour, S. Charrin, M. Billard, V. Labas, J. P. Le Caer, C. Boucheix, and E. Rubinstein

11.21 Mass Spectrometric Characterization of Proteins Involved in the Oxidative Stress Response in Yeast

D. Pflieger, A. Delaunay, Marie-Bénédicte Barrault, M. Toledano, J. Vinh, and J. Rossier

11.22 The Final N-Terminal Trimming of a Subaminoterminal Proline-containing HLA Class I-restricted Antigenic Peptide in the Cytosol Is Mediated by Two Peptidases

F. Lévy, L. Burri, S. Morel, A.-L. Peitrequin, N. Lévy , A. Bachi, U. Hellman, B. J. Van den Eynde, and C. Servis

12. Posters Signal Transduction

Friday, November 22, 9:00–19:30, Galerie Le Notre

12.1 Characterisation of Apoptotic Nuclear Signaling Pathways by Proteomics

A. Tabbert, J. Kellermann, and E. May

12.2 Identification of Signal Transduction Proteins in Lymphocyte Membrane Microdomains

P. Pompach, P. Novak, P. Man, V. Havlicek, and K. Bezouska

12.3 Proteomic Approach to the Molecular Mechanism of Na/K-ATPase-mediated Signal Transduction

Z. Xie, Z. Yuan, and J. Tian

12.4 Functional Proteomic Analysis of Receptor Tyrosine Kinase Signaling in Swiss 3T3 Cells: Identification of Novel Differentially Regulated Downstream Effectors of Phosphoinsitide-3-Kinase

G. D. Warnasuriya, K. Nagano, R. Cramer, M. Zvelebil, J. F. Timms, A. Akpan, A. Yang, S. Corless, R. Stein, A. L. Burlingame, M. D. Waterfield, and S. Nabby-Hansen

12.5 Intracellular Analysis of Activated Cell Signalling Molecules through the Use of Phospho-specific Antibodies and Flow Cytometry

P. J. Burkett, B. J. Nelson, C. L. Pennington, A. Claxon, M. T. Wilson, J. Apgar, A. Agadir, L. Stein, and A. Stall

12.6 Sample Preparation for MALDI-TOF/TOF Protein Identification with >95% Success Rates

D. Suckau, P. Berndt, M. Schuerenberg, and H. Langen

12.7 A Transgenic Model for Muscle Gene Expression Profiling In Vivo

T. Crepaldi, P. Accornero, C. Prunotto, R. Taulli, R. Chiarle, and C. Ponzetto

13. Posters Expression Proteomics in Health and Human Disease (Oncology)

Friday, November 22, 9:00–19:30, Galerie Le Notre

13.1 Proteomic Map of the Human Cholangiocarcinoma Cell Line

C. Srisomsap, P. Subhasitanont, T. Panichakul, K. Lirdprapamongkol, S. Keeratichamroen, P. Sawangareetrakul, D. Chokchaichamnankit, J. Jai-nhuknan, and S. Sirisinha

13.2 Proteomics of Breast Cancer for Signal Pathway Profiling and Therapeutic Target Discovery

I. El Yazidi-Belkoura, E. Adriaenssens, S. Lottin, J. J. Curgy, A.-S. Vercoutter-Edouart, J. Lemoine, and H. Hondermarck

13.3 Comparative Proteome Analysis of Human Colorectal Cancer Tissues

G.-S. Ha, H.-G. Koh, K.-H. Kim, E.-B. Park, W.-J. Park, J.-Y. Lee, and Y.-S. Sohn

13.4 Parallel 2D-DIGE and Microarray Expression Profiling of a Model Breast Cancer Cell System

S. Gharbi, S. White, M. Bertani, H. L. Chan, M. D. Waterfield, and J. F. Timms

13.5 Proteomics-based Identification of PGP9.5

M. J. Nam, C. E. Schmalbach, D. E. Misek, H. Wang, R. Kuick, and S. M. Hanash

Department of Pediatrics, University of Michigan, Ann Arbor, Michigan 48109

13.6 Protein Profiling of the Human Epidermis from the Elderly Reveals Up Regulation of a Signature of IFN- Induced Polypeptides That Includes MnSOD and PI3K

P. Gromov, G. Skovgaard, H. Palsdottir, I. Gromova, M. Ostergaard, and J. Celis

13.7 Two-dimensional Molecular Profiling of Mantle Cell Lymphoma

F. Antonucci, M. Chilosi, C. Parolini, M. Hamdan, H. Astner, and P. G. Righetti

13.8 Proteome Analysis of Gastric Cancer: Overexpression of Thymidine Phosphorylase in Gastric Cancer Tissue

N.-Y. Ha, J. Kim, J. S. Ahn, B. I. Cho, Y. N. Kim, S. U. Lee, S.-J. Kang, J. W. Kim, and C.-W. Lee

13.9 Human Liver Tissue Two-dimensional Gel Electrophoresis Map and Hepatocellular Carcinoma-related Proteins

J. Kim, N.-Y. Ha, J. S. Ahn, S. U. Lee, Y. N. Kim, B. I. Cho, S.-J. Kang, C.-W. Lee, and J. W. Kim

13.10 Proteome Analysis of Gastric Cancer: Overexpression of Rho GDP Dissociation Inhibitor 1 in Human Gastric Cancer Tissues

Y. N. Kim, B. I. Cho, N.-Y. Ha, J. Kim, J. S. Ahn, S. U. Lee, S.-J. Kang, J. W. Kim, and C.-W. Lee

13.11 Proteome Analysis of Gastric Cancer: Overexpression of Galectin-1 in Human Gastric Cancer Tissue

B. I. Cho, Y. N. Kim, N.-Y. Ha, J. Kim, J. S. Ahn, S. U. Lee, S.-J. Kang, J. W. Kim, and C.-W. Lee

13.12 A New Look at the Tumor Proteome by Large-scale Analysis of MHC Peptides

A. Admon, E. Barnea, I. Beer, L. Dassau, and T. Ziv

13.13 Proteomic Analysis of Tyrosine Phosphorylated Proteins in Human MCF-10A Mammary Epithelial Cells Treated by HGF/SF

J. Deheuninck, S. Reveneau, D. Tulasne, C. Leroy, B. Vandenbunder, Y. de Launoit, and V. Fafeur

13.14 Database for Fluorescence 2D Difference Gel Electrophoresis (2D-DIGE)

Y. Mori, T. Kondo, T. Yamada, and S. Hirohashi

13.15 Clustering Analysis of Human Cancer Cell Lines Based on Quantitative 2D

M. Seike, T. Kondo, T. Yamada, and S. Hirohashi

13.16 Protein Expression Fingerprints of Normal Segments of the Colon

I. Gromova, P. Gromov, and J. Celis

13.17 Mass Spectrometry-based Analysis of Tubulin Isoforms in Taxol-sensitive and -resistant Human Cancer Cell Lines

P. Verdier-Pinard, F. Wang, B. Burd, S. Horwitz, and G. Orr

13.18 Proteomic Studies on Hepatocellular Carcinoma

Q.-c. Xia, R. Zeng, Z.-y. Tang, and H.-y. Wang

13.19 New Differentially Expressed Stomach Cancer Markers Identified through Extended Proteomics Analysis on Highly Selected Tumor Samples

M. L. Fogeron, S. Lamer, S. Heim, Ch. Röcken, M. Ebert, and P. von Hoegen

13.20 Cell Surface Expression of Heat Shock Proteins in Human Leukemia Cell Lines

J. H. Jang, B. K. Shin, D. E. Misek, and S. M. Hanash

13.21 Proteome Analysis of Gastric Cancer: Characterization of Proteome Analysis Data and Comparison of Pre-processing Methods for the Differential Expression Analysis

J. W. Kim, S. J. Ahn, E. H. Suh, J. M. Bae, and C.-W. Lee

13.22 Proteomics-based Microarray Technology for the Identification of Tumor Antigens

J. Madoz-Gurpide, D. E. Misek, H. Wang, and S. M. Hanash

13.23 Comprehensive Profiling of Surface Membrane Proteins of Cancer Cells

B. K. Shin, J. H. Jang, D. E. Misek, R. Zhao, H. Wang, R. Kuick, and S. M. Hanash

13.24 Differential Expression of Sub-proteome Between Human Liver Cancer HepG2 and Hep3B Cell Lines

C.-Y. Wu, S.-P. Wu, C.-L. Lee, S.-Y. Huang, C.-L. Chen, Y.-T. Wu, K.-H. Khoo, S.-T. Chen, and A. H.-J. Wang

13.25 Strategic Experimental Approach Towards Establishing Model Hepatoma Cell Lines for the Global Human Liver Proteome Initiatives

C.-L. Lee, W.-T. Shyu, C.-Y. Lin, H.-H. Hsiao, C.-L. Chen, C.-Y. Wu, Y.-T. Wu, K.-H. Khoo, and A. H.-J. Wang

13.26 Proteomic-based Identification of Tumor Antigens in Pancreatic Cancer

S.-H. Hong, D. E. Misek, H. Wang, R. Zhao, C. Logsdon, and S. M. Hanash

13.27 Proteome Mapping of Chronic Lymphocytic Leukemia

C. A. Evans, D. A. E Cochran, D. Blinco, J. Burthem, S. K. Stevenson, S. J. Gaskell, and A. D. Whetton

13.28 Identification of Metastasis-associated Proteins by Proteomic Analysis and Functional Exploration of IL-18 in Metastasis

D. Jiang, W. Ying, Y. Lu, J. Wan, Y. Zhai, W. Liu, Z. Qiu, X. Qian, and F. He

13.29 Using Antibody Microarray for Proteomic Analysis of Esophageal Squamons Cell Carcinoma

X. Zhao, Y. Liu, Y. Mao, H. Wang, X. Ni, F. Liu, and M. Wu

13.30 Metabolic Proteome Analysis of Hepatocellular Carcinoma

K.-S. Park, H. Kim, and Y.-K. Paik

13.31 Complementary Proteome Analysis of a Human Cancer Cell Line by MALDI-MS and MALDI-MS/MS

E. Claude, A. Wallace, D. Gostick, A. Alaiya, G. Auer, and J. Langridge

13.32 Human 20S Proteasome: Reference Map, Post-translational Modifications, and Comparative Cancer Cell Lines Analyses

S. Uttenweiler-Joseph, O. Burlet-Schiltz, S. Claverol, E. Neuhauser, B. Xu, J. E. Gairin, and B. Monsarrat

13.33 Differntial Cell Surface Protein Expression on Normal and Neoplastic Humal Prostate Cells and Their Regulation by Interferons

S. Naaby-Hansen, C. Hastie, A. Akpan, M. Saxton, R. Cramer, K. Nagano, and J. R. Masters

13.34 Identification of Tumor Antigens That Elicit a Humoral Response to Dendritic Cell-based Immunotherapy in Patients with Melanoma

K. Dua, H. Wang, F. Le Naour, J. Mule, S. M. Hanash, and L. Beretta

13.35 Proteomic-based Approach for the Identification of Early Tumor Markers Associated with Hepatocellular Carcinoma

K. Dua, F. Le Naour, J. A. Marrero, D. E. Misek, C. Bréchot, S. M. Hanash, and L. Beretta

13.36 Proteomic Characterization of the HCV NS5A Natural Mutants Isolated from Interferon Responder Versus Non-responder Patients with HCV

A. Elafros, C. Bréchot, S. M. Hanash, and L. Beretta

13.37 Proteome Differential Display of MCF-7 Cell Lines with High Capability for Active Dissociation of Hoechst 33342 and Wild Type

O. V. Tikhonova and V. V. Levina

13.38 BD PowerBlot Western Array Analysis of Protein Expression in Differentiated SH-SY5Y Neuroblastomas

M. T. Wilson, J. K. Stevenson, E. B. Heywood, A. M. Siemers, A. L. Claxon, B. J. Nelson, C. H. Keith, and R. Campos-Gonzalez

13.39 Two-dimensional Gel Electrophoresis Map for Human Stomach Tissue

S. U. Lee, N.-Y. Ha, J. Kim, J. S. Ahn, Y. N. Kim, B. I. Cho, S.-J. Kang, J. W. Kim, and C. W. Lee

13.40 Proteome Analysis of Gastric Cancer: Overexpression of Nucleoside Diphosphate Kinase A in Human Gastric Cancer Tissue

S.-J. Kang, N.-Y. Ha, J. Kim, J. S. Ahn, Y. N. Kim, B. I. Cho, S. U. Lee, J. W. Kim, and C. W. Lee

13.41 Application of Fluorescence Dyes in a Linkage of Laser Microdissection and Two-dimensional Gel Electrophoresis: As a Tool for Cancer Proteomic Study

T. Kondo, M. Seike, Y. Mori, K. Fujii, T. Yamada, and S. Hirohashi

13.42 Proteomics of Renal Disorders: Urinary Proteome Analysis by Two-dimensional Electrophoresis and MALDI-TOF Mass Spectrometry

Y. Kumar, N. R. V. Uppuluri, K. Babu, K. Phadke, P. Kumar, S. Ballal, and U. Tatu

13.43 Isolation of Rheumatoid Arthritis-specific Proteins Using Proteomic Analysis

D. R. Kim, Y.-S. Hah, E.-H. Cho, Y. J. Lee, and C. W. Kim

13.44 Discovery, Purification, and Identification of Biomarkers from Complex Samples by Combining ProteinChip® Array Analysis with Micropurification Strategies

R. I. Viner, S. Fu, N. Tang, and S. R. Weinberger

13.45 Post-translational Modification of Serum Proteins Underlies the Mass Spectral Fingerprinting of Disease

J. Marshall, P. Kupchak, W. Zhu, J. Yantha, T. Vrees, S. Furesz, K. Jacks, C. Smith, I. Kireeva, R. Zhang, M. Takahashi, E. Stanton, and G. Jackowski

13.46 Analysis of Complex Autoantiboy Repertoires by SELDI-TOF

F. H. Grus, S. C. Joachim, and N. Pfeiffer

14. Posters Microbial Proteomics

Friday, November 22, 9:00–19:30, Galerie Le Notre

14.1 Proteomic Analysis of Acholeplasma laidlawii Mutants Resistant to Tetracycline and Fluoroquinolone

S. Moshkovskii, V. Govorun, and E. Goufman

14.2 Towards Proteomic Maps of Listeria monocytogenes EGDe

P. Folio, I. Chafsey, A. Belkorchia, C. Chambon, and M. Hébraud

14.3 The Carbon Flux Distribution and Proteome Analysis of the E. coli Strain with Thermo-regulated Expression of the Thr-Operon

M. S. Benevolensky, I. V. Manukhov, A. D. Kivero, V. M. Govorun, A. S. Arseniev, S. V. Mashko, and V. G. Debabov

14.4 2D Gel Analysis of Soluble Proteins Associated to the Cell Membrane of Lactococcus lactis, a Streptococcacae

A. Guillot, C. Gitton, and M.-Y. Mistou

14.5 Metabolic Adaptation of Lactococcus lactis Cultivated in a Milk Microfiltrate

C. Gitton, A. Guillot, and M.-Y. Mistou

14.6 Global and Functional Proteomic Analysis of the Pathogen Leptospira interrogans

R. Zeng and Q.-c. Xia

14.7 A Two-dimensional Map of Cytosolic Proteins of Agrobacterium tumefaciens

R. Rosen, A. Sacher, K. Büttner, D. Becher, M. Hecker, and E. Z. Ron

14.8 Proteomic Analysis of Osmotic Stress Responses in Salmonella

B. Cochrane and C. D. O’Connor

14.9 Differential Proteomic Analysis of Bacillus subtilis by 2D Gels, MALDI-TOF MS and LC-MSMS

V. Labas, J. Vinh, E. Turlin, and A. Sekowska

14.10 Prediction of Essential Bacterial Genes: Machine Learning in Functional Proteomics

G. Rajeev and S. Ashutosh

15. Posters Resources and Technology

Friday, November 22, 9:00–19:30, Galerie Le Notre

15.1 AFM and Optical Biosensors in Proteomics

Y. Ivanov, V. Kuznetsov, and A. Archakov

15.2 Isolation of Group-specific (Phospho-, Methionine-, and Tryptophan-containing) Peptides for Mass Spectrometric and Proteomic Analysis

P. Haney, C. Draveling, and W. Qoronfleh

15.3 Resources for Functional Research: Repository and Application

B. Korn, U. Radelof, S. Schulze-Kremer, and J. Maurer

15.4 Antiseromics: High Throughput Production of Antibodies Against Proteins Encoded by the Human Genome

N. Barclay, N. Hutchings, R. Adhikari, and R. Sapkota

15.5 Microfluidic Technology Applied to Protein Sizing and Quantitation

M. Kuschel, T. Neumann, M. Kratzmeier, and P. Barthmaier

15.6 Preliminary Trial of Monoclonal Antibody Based Microarray Using Radioactive Probes

Y.-j. Park, J. H. Park, Y. H. Park, D. H. Kim, D. Y. Lee, S. H. Ryu, C. J. Choi, H. J. Choo, and M.-k. Kim

15.7 High-throughput Visualisation and Selection of GFP-expressing Colonies

S. Stephens, R. Woodrough, T. Nestor, R. Atkinson, C. Mann, and A. Figg

15.8 Scaling Up Automated Protein Excision from 1D and 2D Gels

C. Mann, A. Board, J. Colehan, R. Woodrough, S. Richmond, and S. Stephens

15.9 Temperature-controlled High-speed Printing of Functional Protein Arrays

C. Mann, D. Hart, J. Boutell, B. Godber, and S. Stephens

15.10 Analysis of Phosphorylated Platelet Proteins Using 2D-PAGE, Immunoprecipitation, and Mass Spectrometry

K. Marcus, J. Moebius, and H. E. Meyer

15.11 Large-scale Subcellular Localisation and Functional Analysis of Novel Proteins

J. Simpson, U. Liebel, V. Starkuviene, H. Erfle, A. Poustka, S. Wiemann, and Rainer Pepperkok

15.12 Affinity Annotation Proteomics of Proteins Encoded by the Human Chromosome 21

C. Agaton, J. Galli, I. H. Guthenberg, L. Janzon, M. Hansson, C. Höög, J. Lundeberg, S. Ståhl, F. Pontén, and M. Uhlén

15.13 Protein Characterization Using AP-MALDI/Ion Trap and 2D-Nano-LC/Ion Trap Mass Spectrometry

R. Grimm, F. Mandel, R. Sample, and C. Sauber

15.14 Desorption/Ionisation on Silicon (DIOS): Highly Reproducible, Enhanced Surfaces for Proteomics

P. Skipp, M. Farooqui, A. Evans, and C. D. O’Connor

15.15 Optimization of Enzyme Immobilization Techniques and Miniaturized Peptide Mapping Devices for Structural Proteomics Applications

K. C. Waldron, C. Dartiguenave, H. Hamad, J. Vinh, V. Labas, and J. Rossier

15.16 Optimization of a Method for Trypsin Immobilization by Cross-linking with Glutaraldehyde for Peptide Mapping

I. Migneault, H. Abouchakra, K. C. Waldron, and M. J. Bertrand

15.17 A Novel C-terminal Sequencing Method for Proteome Study

K. Miyazaki and A. Tsugita

15.18 NIST SRM 1951a as a Prototype Serum Standard for Human Proteomics

Y. Xiao, M. Welch, O. J. Semmes, and P. E. Barker

15.19 Fractionation of Proteins with Aqueous Two-phase Systems for Enhanced Resolution of Membrane Proteins in Proteomic Studies

H. Everberg and F. Tjerneld

15.20 Application of 2-D Protein Chromatography Coupled with ESI-TOF MS for Non-Gel Based Proteomic Analysis

Steven A. Cohen, Scott J. Berger, Asish B. Chakraborty, and Hongji Liu

15.21 FFE–Sample Processing by Hydrophilic Interaction Solid Phase Extraction (HILISP): Concentration Effects and Compatible Recovery for FFE-2D PAGE and FFE-HPLC

U. Schneider, A. Posch, G. Weber, P. J. A. Weber, M. Nissum, C. Obermaier, R. Wildgruber, S. Kuhfuss, and C. Eckerskorn

15.22 Depletion of Highly Abundant Proteins by Free-Flow Electrophoresis

P. J. A. Weber, G. Weber, R. Kussian, C. Obermaier, M. Mast, M. Hauptmann, A. Posch, and C. Eckerskorn

15.23 Parallel and Real-time Interactions Monitoring Using Protein Microarrays

P. Guédon and T. Mercey

15.24 Simplified Spot Patterns and Improved Reproducibility in 2-D Electrophoresis with the Aid of DeStreak^TM

I. Olsson, K. Larsson, J. J. Hedberg, J. Öhman, S. Cetinkaya, and B. Bjellqvist

15.25 Ultra Sensitive Detection of Unstained Proteins in Acrylamide Gels by Native UV Fluorescence

J. Roegener, P. Lutter, R. Reinhardt, M. Blueggel, H. E. Meyer, and D. Anselmetti

15.26 Integrated Miniaturized 2D Protein Mapping Using the Digital ProteomeChip^TM

S. Bukshpan, G. Zilberstein, O. Kagan, G. Isabelle, and R. Garlick

15.27 A Novel, Automated 2-Dimensional Electrophoresis System for Protein Profiling

L. E. Cammish

15.28 Protein Microarrays: Resolving the Problems for Use in Breast Cancer Studies

L. E. Cammish

15.29 Improved Proteome Analysis of Saccharomyces cerevisiae Mitochondria by Free-Flow Electrophoresis

A. Posch, P. J. A. Weber, G. Weber, C. Eckerskorn, U. Schneider, M. Nissum, M. Ueffing, T. Meitinger, and H. Zischka

16. Posters Sample Preparation and Gel-based Proteomics

Friday, November 22, 9:00–19:30, Galerie Le Notre

16.1 Novel 2-D Sample Preparation of Nuclear and Membrane Proteins

M. Benton, P. Haney, R. Ignacio, K. Romanowich, and W. Qoronfleh

16.2 Reproducibility of Two-dimensional Gel Analyses

K. K. Challapalli, C. Zabel, N. Steireif, J. Schuchhardt, J. Klose, and H. Herzel

16.3 Proteomic Analysis of Rat Brain Tissue: Comparison of Methods for Two-dimensional Gel Electrophoresis

C. Piubelli, L. Carboni, B. Jansson, P. G. Righetti, and E. Domenici

16.4 A New Integrated Statistical Approach to the Diagnostic Use of Two-dimensional Maps

D. Cecconi, E. Marengo, E. Robotti, V. Gianotti, P. G. Righetti, and E. Domenici

16.5 High Sensitivity Detection of Proteins in Two-dimensional Gels by Fluorophore Labelling Prior to First Dimension Isoelectric Focusing

P. Jackson, S. Kramer, D. Sissors, T. Erickson, J. Trometer, and M. Bobrow

16.6 Quantitative Proteome Analysis: Comparison of Ettan DIGE with Conventional "One Sample Per Gel" Studies

J. Prime, A. Alban, B. Hughes, and S. Fowler

16.7 Screening and Identification of Hypoxic Proteins by Two-dimensional Polyacrylamide Gel Electrophoresis and SELDI Mass Spectrometry

G. Shi, Y. Chen, Q.-T. Le, A. Giaccia, and A. Koong

16.8 Protein Staining Methods: Comparison of Sensitivity and Compatibility with Mass Spectrometry

N. Gustavsson, P. Giavalisco, J. Klose, H. Lehrach, and J. Gobom

16.9 Cysteine Labelling of Protein Samples with Fluorescent CyDyes: Application to 2D-DIGE and Use of Affinity-tagged Dyes for Sample Enrichment

T. John, S. Gharbi, H.-L. Chan, P. Gaffney, and M. Waterfield

17. Posters Mass Spectrometry

Friday, November 22, 9:00–19:30, Galerie Le Notre

17.1 Miniaturized TOF Mass Spectrometers for Proteomics-based Diagnostics

R. Cotter, R. English, B. Gardner, A. Hardy, and B. Warscheid

17.2 Comprehensive 2D Capillary LC as Front End Separation Technique in MS Proteomics

M. Smoluch, G. Mitulovic, and R. Swart

17.3 MALDI-TOF Sample Preparation for High Success Proteomics

D. Suckau, P. Berndt, M. Schuerenberg, and H. Langen

17.4 Error Tolerant Database Matching of Uninterpreted MS/MS Data

D. Creasy and J. Cottrell

17.5 Ettan DIGE—Accurate and Quantitative Proteome Analysis

F. Ghouze, A. Alban, and I. Currie

17.6 Application of QTRAP Technology for Proteomic Analysis

A. Podtelejnikov, J. Bunkenborg, B. Pilch, I. Stewart, J. C. Y. Le Blanc, J. Wisniewski, and M. Mann

17.7 Analysis of Complex Proteomes Using Two Dimensional Liquid Chromatography Prior to Mass Spectrometry

U. Schweiger-Hufnagel, M. Lubeck, and C. Baessmann

17.8 Improved Enrichment of Phosphopeptides by IMAC with On-resin ß-elimination and Michael Addition

A. Thompson, S. Hart, K. Barnouin, and R. Cramer

17.9 Visual Comparison of Peptide Mixtures Using Two-dimensional Mass Spectrometry-based Maps

I. Beer, E. Barnea, I. Maman, and A. Admon

17.10 Pep-Miner: High-throughput Proteomics Made Easy

I. Beer, E. Barnea, G. Korland, M. Lechtman, and A. Admon

17.11 Novel Nanobore HPLC Columns for Protein Identification Using Pre-column Enrichment 2D-NanoLC Ion Trap Mass Spectrometry

A. Wenner, F. Mandel, C. Sauber, and R. Sample

17.12 Two-dimensional Chromatographic/Electrophoretic On-line Pre-concentration of In-gel Digest for Protein Identification by Electrospray Ionization Tandem Mass Spectrometry

G. Zhang, X. Wang, H. Fan, C. Xu, H. Bao, and P. Yang

17.13 Optimizing Protein Sequence Coverage from Peptide Mixtures Using Micro-columns Packed with Increasingly More Hydrophobic Chromatographic Material

M. R. Larsen, S. J. Cordwell, and P. Roepstorff

17.14 Performance Characteristics of Atmospheric Pressure MALDI Ion Trap Mass Spectrometry for Protein and Peptide Identification

R. Sample, V. Carlesso, F. Mandel, and C. Sauber

17.15 NanoLC-MALDI MS for the Analysis of Complex Peptide Mixtures

E. Mirgorodskaya, T. Kreitler, N. Gustavsson, D. Theiss, H. Lehrach, and J. Gobom

17.16 A New Calibration Method Improves Protein Identification by MALDI-TOF MS Peptide Mapping

J. Gobom, T. Kreitler, E. Nordhoff, and H. Lehrach

17.17 True MS/MS and MSon a MALDI QIT TOF MS

C. Sutton, E. Raptakis, R. Edward, and R. Martin

17.18 Applications of LC/MS and LC/MALDI Workflows in Proteomics Using the QSTAR^TMXL, Q Trap Mass Spectrometry Systems

J. Torpey

17.19 Nanoelectrospray MS and MS/MS of Non-covalent Protein-DNA Complexes

C. Vreuls, V. Gabelica, P. Filée, V. Duval, B. Joris, and E. De Pauw

17.20 Differential Proteomics: Comparison of DIGE and ICAT—Application to the Study of Human Macrophages

C. Tokarski, C. Cren-Olivé, N. Bencherif, F. Pinet, and C. Rolando

17.21 A Fully Automated De Novo Sequencing Strategy for Whole Q-Tof Electrospray LC-MS/MS Datasets

J. Langridge, A. Wallace, K. Compson, A. Millar, P. Young, R. O’Malley, N. Swainston, J. Skilling, and J. Hoyes

17.22 The Use of an Alternative Approach for Protein Expression Profiling by an Isotope-coded Affinity Tag (ICAT) LC-MS Strategy

S. Leicester, P. Young, R. O’Malley, A. Millar, A. Wallace, K. Compson, D. Goodlett, S. Purvine, and J. Langridge

17.23 The Use of a "Self-Calibration" Method for Improving Protein Identification by Peptide Mass Fingerprinting with MALDI-TOF-MS

J. Brown, A. Wallace, K. Compson, and D. Gostick

17.24 Direct Epitope Mapping on Protein Biochip Array Using LDI-QqTOF Mass Spectrometry

N. Tang and S. R. Weinberger

18. Keynote Lecture

Saturday, November 23, 9:00–9:45, Richelieu Room

9:00

Systems Biology: Integrating Genomics, Proteomics, and Computation

L. Hood

9:45 Coffee Break, Posters, and Exhibition

19. Plenary Session The Human Proteome Initiatives

Chair: S. Hanash

Discussion leaders: C. Merril, G. Omenn, R. Ruddon, and G. Siest

Saturday, November 23, 10:10–11:20, Richelieu Room

10:10

19.1 Current Status of HUPO Initiatives

S. Hanash

20. Round Table Discussion Human Proteome Effort Throughout the World

Chair: Y.-K. Paik

Discussion leaders: R. Apweiler, A. Archakov, A. Bairoch, R. Bradshaw, J. E. Celis, M. Dunn, A. Görg, F. He, I. Humphery-Smith, P. James, M. Mann, S. Old, T. Rabilloud, R. J. Simpson, and A. Tsugita

Saturday, November 23, 11:20–13:00, Richelieu Room

11:20

20.1 Human Proteome Effort Throughout the World

Y.-K. Paik

13:00 Lunch and Luncheon Seminar

21. Parallel Session 7 Clinical Applications of Proteomics

Chair: D. Hochstrasser

Saturday, November 23, 14:30–16:10, Richelieu Room

14:30

21.1 Vaccine Candidates by Classical Proteomics: Breakthrough for the Development of a New Vaccine Against Tuberculosis?

P. R. Jungblut, J. Mattow, L. Grode, U. Schaible, and S. H. E. Kaufmann

15:00

21.2 Plasma Analysis by Proteomics

K. Rose, G. Argoud-Puy, T. Baussant, G. Böhm, P. Botti, L. Bougueleret, J. Colinge, I. Cusin, H. Gaertner, S. Jimenez, A. Johnson, M. Kussmann, L. Menin, C. Menzel, F. Ranno, P. Rodriguez-Tomé, J. Rogers, M. Villain, and D. Wetmore

15:30

21.3 Molecular Profiling of Ischemia-Reperfusion in Human Liver

A. Emadali, E. Chevet, and P. Metrakos

15:45

21.4 Combined Transcriptome and Proteome Approaches to Elucidate Gene Expression Patterns of Synovial Tissues from Patients with Rheumatoid Arthritis Versus Osteoarthritis

M. O. Glocker, P. Lorenz, A. Francke, D. Koczan, M. Bantscheff, S. Mikkat, S. Möller, P. Ruschpler, and P. Stiehl

22. Parallel Session 8 Protein Interactions

Chair: P. Legrain

Saturday, November 23, 14:30–16:10, Condé Room

14:30

22.1 From Protein Interactions to Pathway Annotation for Validation of Drug Targets

P. Legrain

14:50

22.2 The Contribution of Small Conserved Domains to the Establishment of Protein Interaction Networks

G. Cesareni

15:20

22.3 Protein Complexes and Molecular Networks

G. Superti-Furga

15:40

22.4 Monitoring of Protein-Protein Interactions in P450-containing Systems in Real Time

Y. Ivanov, S. Usanov, and G. H. B. Hoa

15:50

22.5 High-throughput Mapping of Protein-Protein Interactions: Automation of the Yeast Two-Hybrid System

S. A. Richmond, K. Gregan, K. Russell, C. Mann, and J. F. Burke

23. Parallel Session 9 Bioinformatics in Proteomics

Chair: R. Apweiler

Saturday, November 23, 14:30–16:10, Lulli Room

14:30

23.1 Database Resources for Proteome Research: SWISS-PROT, TrEMBL, InterPro

R. Apweiler

14:50

23.2 New Developments in Proteomatics at the Swiss Institute of Bioinformatics

R. D. Appel, P. Hernandez, M. Tuloup, D. Walther, R. Gras, M. Müller, C. Hoogland, P.-A. Binz, G. L. Corthals, J.-C. Sanchez, and D. F. Hochstrasser

15:10

High Throughput Genomics and the Grid

P. E. Bourne

15:30

23.3 Unity and Diversity of Protein Superfamilies

S. Gusev and A. Archakov

15:40

23.4 Statistical Standards for High Throughput Proteomics

A. I. Nesvizhskii, A. Keller, J. K. Eng, E. Kolker, and R. Aebersold

15:50

23.5 Study of Spot Overlapping in 2D-PAGE Maps by Bidimensional Autocovariance Function

N. Marchetti, M. C. Pietrogrande, F. Dondi, A. Felinger, and P. G. Righetti

16:10 Coffee Break, Posters, and Exhibition

24. Parallel Session 10 Educational Session: Bioinformatics

Chair: M. Mann

Saturday, November 23, 17:00–18:40, Richelieu Room

17:00

Overview of Different Algorithms for Protein Identification Via Mass Spectrometric Data

M. Mann

17:30

24.1 Proteomics Databases: Navigating the Archipelago

H. Hermjakob

18:00

24.2 A Tutorial on Systematic Proteomics Analyses

S. Schandorff

25. Parallel Session 11 Biotechnology Perspectives

Chair: I. Humphery-Smith

Saturday, November 23, 17:00–18:40, Lulli Room

17:00

25.1 Protein Chips and Bioinformatics: Essential Tools for Biomarker Discovery

D. Chan

17:15

25.2 Proteomic Analyses Using a Fully Automated Chip-based Nanoelectrospray System

C. K. Van Pelt, S. Zhang, X. Huang, G. Williams, and M. H. Allen

17:30

25.3 A Sample Preparation Platform Technology for Proteomic Applications

W. Qoronfleh

17:45

25.4 Prioritising the Proteome: Identifying Pharmaceutically Relevant Targets by Linking Sequence to Function Through 3D Structure

J. Overington

18:00

Use of Protein Profiling Chips for Biomarker Discovery to Guide Medical and Drug Development Decision Making

S. Kingsmore

18:15

25.5 From Gene Products to Disease Phenotype: Antibody Chips for Predictive Medicine in Cancer

M. Jendoubi, C. Chavany, J.-F. Martini, Y. Xu, and R. Valle

18:25

25.6 From Cell to Gel to Well: A Modular Automated Platform for Proteomics Assays

C. Eckerskorn

18:35

32.4 ZOOM® Proteomics: Rapid Methodology for 2D Protein Profiling

M. Pisano, B. Allen, and R. Nunez

26. Parallel Session 12 High-throughput Proteomics

Chair: C. Fenselau

Saturday, November 23, 17:00–18:40, Condé Room

17:00

26.1 Comparative Proteomics: New Methods and Applications

C. Fenselau, Y. Hathout, M. Gehrmann, A. Rahbar, K. Shefcheck, and K. Reynolds

17:25

26.2 The Role of Proteomics in Disease Discovery

W. Hancock

17:50

26.3 High Throughput Proteomic Studies and Their Integration with Genomics

A. Moseley, B. Hollingsworth, I. Gloger, and P. Cutler

18:15

26.4 High-throughput Proteomic Antibody Production Using MAPs as Immunogens and Hens as Hosts

S. C. Huang, P. Snyder, S. Zhang, P. Wang, and J. Jiang

18:25

26.5 High-stringency Proteomics Concepts Aimed for High-throughput Generation of Monospecific Antibodies for cDNA-encoded Proteins

R. Falk, S. Gräslund, M. Eklund, S. Ståhl, and S. Hober

27. Keynote Lecture

Saturday, November 23, 18:50–19:35, Richelieu Room

18:50

Mass Spectrometry-based Proteomics in Molecular Cell Biology

M. Mann (EMBO lecturer)

28. Posters Pharmacogenomics and Proteomics in the Pharmaceutical Industry

Saturday, November 23, 9:00–19:30, Galerie Le Notre

28.1 Development of Cytochrome P450 Knowledgebase

A. Lisitsa and A. Archakov

28.2 Proteome Differential Display of MCF-7 Cell Lines with High Capability for Active Dissociation of Hoechst 33342 and Wild Type

O. Tikhonova and V. Levina

28.3 Computer-aided Selection of Targets for Antimicrobial Drug Design Based on Comparative Analysis of Genomes

A. Dubanov and A. Ivanov

28.4 Proteomic Analysis of the Pancreas in TGZ-treated ZDF Rats

K. H. Choi, D. K. Kim, J. Y. Park, K. J. Roh, E.-S. Park, C. H. Han, Y. H. Ahn, and J. K. Seong

28.5 Chronic Nicotine Administration in Rat Induces Proteomic Changes on Polymorphonuclear and Mononuclear Leukocytes

C. Piubelli, H. Astner, L. Carboni, F. Caldara, B. Jansson, M. Hamdan, E. Domenici, and P. G. Righetti

28.6 Proteomic Analysis of Human Hepatic Drug-metabolizing Enzymes

M. Alterman and T. Duzhak

28.7 Application of Toxicoproteomics to Drug Development: Effects of a Kinase Inhibitor on Protein Expression in Rat Liver

J.-F. Leonard, E. Boitier, M. Courcol, M. Duchesne, F. Parker, R. Roberts, Z. Jayyosi, P. Rao, and J.-C. Gautier

28.8 New Lead Compounds Via Smart Proteomics Approach

C. Huels, S. Muellner, E. Eigenbrodt, S. Mazurek, H. Grimm, H. Stark, and H. E. Meyer

28.9 Proteomics Identification of Beneficial Actions of Grape Seed Extract on AD-linked Protein Targets

J. Deshane, L. Chaves, L. Wilson, M. Kirk, S. Barnes, S. Meleth, and H. Kim

28.10 Proteomics Applied to Antibacterial Drug Discovery

R. A. Van Bogelen

29. Posters Bioinformatics

Saturday, November 23, 9:00–19:30, Galerie Le Notre

29.1 A High Throughput Protein Identification Expert System for 1D PAGE—MALDI-TOF MS Proteome Inventory Technique

P. Lokhov and V. Govorun

29.2 An Integrated Data Management System for Protein Informatics

A. Pervez, D. Heath, O. Sauer, A. Elbaggari, B. Sadownick, and T. Slyker

29.3 PATIKA: An Integrated Visual Environment for Collaborative Construction and Analysis of Cellular Pathways

E. Demir, O. Babur, U. Dogrusoz, A. Gursoy, G. Nisanci, R. Cetin-Atalay, and M. Ozturk

29.4 ProteinScape: An Integrated Bioinformatics Platform for Proteome Analysis

H. Thiele and M. Blüggel

29.5 PROCSY—PROtein Characterization SYstem

O. Sella-Tavor, A. Wool, and Z. Smilansky

29.6 The Proteome Analysis Database

M. Pruess, A. Kanapin, Y. Karavidopoulou, P. Kersey, V. Mittard, I. Phan, F. Servant, and R. Apweiler

29.7 Quantitative Analysis of Two-dimensional Gel-separated Proteins Using Isotopically Marked Alkylating Agents and Matrix-assisted Laser Desorption/Ionisation Mass Spectrometry

D. Cecconi, S. Gehanne, L. Carboni, P. G. Righetti, E. Domenici, and M. Hamdan

29.8 A New Approach Based on Fuzzy Logic and Principal Component Analysis for the Classification of 2D Maps: Application to a Lymphoma Case Study

F. Antonucci, E. Marengo, E. Robotti, and P. G. Righetti

29.9 Knowledge Discovery to Understand and Predict Peptide Mass Fingerprinting Spectra

P.-A. Binz, S. Gay, D. F. Hochstrasser, and R. D. Appel

29.10 A Proteomic Approach in the Analysis of Thyroid Hyperplastic Goiter

M. E. Schininà, G. Mignogna, A. Giorgi, F. Cancellario d’Alena, S. Scarpino, and M. Simmaco

29.11 Proteome-related Activities of the EBI Sequence Database Group

A. van den Broek and R. Apweiler

29.12 InterPro Database

M. Krestyaninova, N. J. Mulder, R. Apweiler, and InterPro Consortium

29.13 Metabolic Network from Proteomic Data Using Graph Theory

A. Joulie, C. Gitton, A. Guillot, S. Corteel, M. Y. Mistou, and D. Barth

29.14 KAST: A Protein Network Analysis System for the Spots in Two-dimensional Electrophoresis Gel Image

M.-S. Kwon, S. Y. Cho, L. H. Lee, S. Y. Ha, and Y.-K. Paik

29.15 YPRC-PDB: An Integrated Proteome Database for Two Dimensional Electrophoresis (2-DE) Data Analysis and Laboratory Information Management System

S. Y. Cho, K.-S. Park, J. E. Shim, M.-S. Kwon, G. H. Joo, W. S. Lee, J. Chang, H. Kim, and Y.-K. Paik

29.16 Advanced Proteome Data Analysis for High Throughput Proteomics—Towards a Brain Proteome Database

M. Blüggel, J. Gobom, A. Wattenberg, S. Bailey, C. Scheer, G. Körting, D. Chamrad, H. E. Meyer, and J. Klose

29.17 Comparison of Mass Spectral Data Search Results for Several Search Programs Using EST Database

K.-H. Kwon, S. I. Kim, M. Kim, J. S. Yoo, and Y. Mok Park

29.18 Beyond Data: DiBase^TM Bridges the Information Gap—Getting the Picture, not the Pixels

W. Farag

29.19 Using Image Fusion and Positional Indexing to Create Proteome Maps from Collections of 2D Gel Images

S. Luhn, M. Berth, M. Hecker, and J. Bernhardt

29.20 Laboratory Workflow System (LWS) for Proteomics, a Database System Managing Samples from 2D Electrophoresis to MALDI-MS Protein Identification Results

A. Jorsback, M. Degerman, and G. Jacobson

30. Posters Biotechnology Perspectives

Saturday, November 23, 9:00–19:30, Galerie Le Notre

30.1 Result Driven Strategies for Protein Identification and Quantitation

A. Graber, N. Khainovski, D. Patterson, P. Juhasz, and S. Martin

30.2 Monolithic Capillary Columns for High-speed Protein/Peptide Separations

G. Mitulovic, R. Swart, and J.-P. Chervet

30.3 ECL Advance: A New Chemiluminescent Substrate for Western Blotting

K. Tate, S. Cottrell, P. Jones, and C. Wheeler

30.4 High Throughput Dialysis of Small Volume Protein Samples

T. Haq and M. Perreault

30.5 CALI—An Innovative Approach for the Identification and Validation of Novel Drug Targets

S. Rubenwolf

30.6 High-speed Protein Digestion and Sample Preparation for MALDI-MS on a Microfluidic CD

M. Holmquist, J. Engström, U. Selditz, and P. Andersson

30.7 Protein Quantification in Microfluidic Protein Arrays Using Affibody Affinity Binders in a CD Microlaboratory

M. Inganäs, S. Lindman, E. Landström, and E. Forsberg

30.8 Preparing Samples in Parallel in a CD Microlaboratory Improves Sensitivity of MALDI Analysis to Facilitate Successful Protein Identification

M. Gustafsson, E. Togan-Tekin, G. Ekstrand, R. Kange, P. Andersson, and S. Wallenborg

30.9 UltraPlex Barcodes Molecules

R. Booth, W. Bowen, D. Onley, and P. Swarbrick

30.10 eTag^TMReporter Assay System for Solution-phase Multiplexing of Gene Expression and Protein Analysis

S. Singh

30.11 Differential Protein Expression on Protein Arrays

S. Evans, C. Wheeler, P. Easton, A. Moody, A. Bamford, T. Cross, and C. Smith

30.12 Detection and Identification by MALDI MS of Alzheimers Brain Proteins in 2-D Gels Using a Novel, High Sensitivity Fluorophore

M. F. Lopez, S. Melov, D. Bennett, E. Chernokalskaya, P. Jackson, S. Kramer, D. Sissors, T. Erickson, and J. Trometer

30.13 Applications of Magnetic Particles in Proteomics Using PickPen Technology with QuickPick Products

P. Mattsson, T. Tenhunen, and M. Korpela

30.14 Phenotyping of a Diabetes Animal Model by Peptidomics

M. Schrader, I. Schulte, A. Appelt, S. Neitz, and R. Hess

30.15 Automated Purification of Recombinant Proteins in a 96-well Format: No Centrifugation Required

J. Tilghman, A. Grabski, M. Mehler, D. Drott, and J. Van Dinther

30.16 Staccato—Automation for High Throughput Proteomics

T. Stelzer

30.17 Integrated Sample Preparation Platform for In-Gel Protein Digestion

E. Chernokalskaya, A. Dedeo, P. Clark, M. Emerick, D. Brewster, I. Smirnov, J. Campbell, C. Murphy, V. Tisdale, and W. Kopaciewicz

30.18 Uniform Labeling of Proteins Using Universal Linkage System ULS®

P. van der Hoeven

31. Posters Protein Interactions

Saturday, November 23, 9:00–19:30, Galerie Le Notre

31.1 High-throughput Approaches for the Identification of Carbohydrate-Protein Interactions in Functional Glycomics

K. Bezouska, P. Mader, L. Kriz, P. Novak, P. Man, and V. Havlicek

31.2 Fast Topological Analysis of a Supramolecular Protein Complex by MALDI Mass Spectrometry and Hydrogen/Deuterium Exchange

J.-M. Schmitter, A. Nazabal, J. Vaillier, S. Chaignepain, and J. Velours

31.3 Cloning, Expression, and Characterisation of Human Brain Proteins

U. Borgmeier, C. Gotthold, M. Krause, and H. Seitz

31.4 Heteromeric MAPPIT: A New Tool to Study Modification-dependent Protein-Protein Interactions

I. Lemmens, S. Eyckerman, D. Catteeuw, A. Verhee, K. Verschueren, D. Huylebroeck, J. Vandekerckhove, and J. Tavernier

31.5 Protein Profiles of Calmodulin-binding Proteins in Focal Ischemic Rat Brains: Affinity Chromatography-based Functional Proteomics

D. H. Kang, H.-S. Jung, D. J. Lee, T. H. Kang, M. H. Kim, N.-W. Sohn, and C. Kang

31.6 Protein Microarrays as Tool to Identify Novel Protein-Protein Interactions

U. Korf, B. Guilleaume, D. Bossemeyer, T. Kohl, R. Zahn, M. Schnölzer, B. Ueberle, W. Huber, and S. Wiemann

31.7 Ligand Fishing, Identification, and Interaction Analysis Using Combined Surface Plasmon Resonance and Mass Spectrometry

A. McWhirter, Ö. Jansson, D. Suckau, J. Buijs, A. Zhukov, and E. L. Filonzi

31.8 Evidence for Preferential Protein Targets of Age-related Glycation in Peripheral Blood Lymphocytes

S. Poggioli, H. Bakala, and B. Friguet

31.9 Characterization of the Stoichiometry of Protein Complexes

E. O. Hochleitner and F. Lottspeich

32. Posters High-throughput Proteomics

Saturday, November 23, 9:00–19:30, Galerie Le Notre

32.1 Data Analysis and Quality Management in High-throughput Proteomics

M. Markmann, B. Winkler, C. Ribeaux, and P. Haberl

32.2 Interfacing Capillary/Nano LC with MALDI/MS for High Throughput Proteomics

J.-P. Chervet, G. Mitulovic, M. Smoluch, and R. Swart

32.3 High Throughput Proteomics: Nucleoporin Networks Using Automated MALDI-TOF/TOF MS

L. Huang, R. Chalkley, N. Allen, M. Rexach, and A. L. Burlingame

32.5 Automation of In-Gel Digestion for Protein Identification

J. Van Dinther, A. Pitt, L. Kellard, J. Tilghman, S. Gutierrez, C. Hapenney, V. Tisdale, and M. Engelstein

32.6 A Plate-based Array for Multiplexed, High-throughput Quantification of Proteins

S. Van Arsdell, C. Vietz, R. Pande, and C. Burns

32.7 Development of a Modular High Content Screening Platform for the Systematic Functional Characterisation of Novel Human cDNAs

U. I. Liebel, D. Arlt, H. Erfle, J. C. Simpson, V. Starkuviene, S. Wiemann, and R. Pepperkok

32.8 Protein Sequence Tags (PST)—A New High Throughput Protein Profiling Technology

K. Kuhn, T. Prinz, J. Schwarz, U. Bauer, C. Hamon, and T. Neumann

32.9 Microfluidic Device for High-throughput Proteomic ESI-MS Analysis

S. Le Gac and C. Rolando

32.10 Automated High Throughput Techniques for Proteome Analysis the Proteomics Street

S. Bailey, A. Wattenberg, C. Koester, P. Hufnagel, D. Suckau, and M. Blueggel

32.11 Proteomics Profiling After Spinal Cord Injury: Early Detection of a Neuroprotection Signature

J. F. Cornuel, C. Delalande, P. Y. Simonin, and S. Feldblum

32.12 A Unique Approach to Automated, Parallel, High Throughput Protein Expression and Purification

L. E. Cammish

33. Posters Clinical Applications

Saturday, November 23, 9:00–19:30, Galerie Le Notre

33.1 Analysis of Posttranslational Modifications of -A-Crystallin During Aging of the Eye Lens

H. Schaefer, A. Sickmann, M. Herrmann, J. Klose, and H. E. Meyer

33.2 Computer-assisted Mapping of Antigenic and Functional Regions in Hepatitis C Virus Proteins

B. Sobolev and L. Olenina

33.3 Protein Changes Induced by IL-1ß in Islets of Langerhans In Vitro Followed In Vivo During Development of Diabetes in Diabetes Prone BB Rats

T. Sparre, U. B. Christensen, P. M. Larsen, S. Fey, C. Gotfredsen, P. Roepstorff, A. E. Karlsen, F. Pociot, and J. Nerup

33.4 Exploring the Cardiovascular Pathology by Functional Genomics Techniques

P.-W. Wang and T.-L. Pan

33.5 Exploring the Pathophysiology of Liver Fibrosis by Proteomics

T.-L. Pan

33.6 Novel Affinity Ligands for Complexity Reduction of Serum or Plasma Samples Prior to High Resolution Proteomic Analysis

M. R. Kavonian, E. Chernokalskaya, M. G. Pluskal, M. Robinson, S. Gutierrez, and A. M. Pitt

33.7 Proteins Involved in Recruitment of Renin-expressing Cells During Renovascular Hypertension Identified by Proteomic Analysis

F. Pinet, F. Poirier, N. Imam-Sghiouar, J.-P. LeCaer, M. Caron, R. Joubert-Caron, and P. Corvol

33.8 An Orthogonal High Resolution Three-Dimension Separation System Coupled with DIGE for Quantitative Analysis of Serum Proteins

H. Wang, R. Zhao, R. Hinderer, D. Misek, and S. Hanash

33.9 Two-dimensional Mapping of Cellular Prion Protein from Cerebrospinal Fluid and Central Nervous System: Immunoblotting and Purification Via Dedicated Antibodies

N. Campostrini, A. Castagna, A. Farinazzo, G. Zanusso, S. Monaco, and P. G. Righetti

33.10 Isoenzyme Forms and Catalytic Activity of Brain Na-K-ATPase During Ageing

R. F. Villa and A. Gorini

33.11 Characterization of the N-linked Oligosaccharides of an Immunoglobulin M 12A1 Protective Against Crytococcus neoformans

R. Angeletti, F. Wang, A. Nakouzi, and A. Casadevall

33.12 Identification of Proteins Expressed in Human Plasma Exposed with Benzene by 2D Gel Electrophoresis

W.-A. Joo, W.-k. Son, K. Choi, H.-J. Lee, D.-Y. Lee, and C.-W. Kim

33.13 Metabolic Syndrome and Monocyte Activity

P. Tretjakovs, U. Kalnins, I. Dabina, A. Erglis, I. Dinne, A. Jurka, and V. Pirags

33.14 Serum and Urine Proteomics: Protein Profiling and Identification of Ovarian Cancer Biomarkers Using Mass Spectrometry and Liquid Chromatography

B. Ye, S. Mok, S. Skates, S. Gygi, L. Fu, R. Berkowitz, and D. Cramer

33.15 Proteomic Analysis of a Mammalian Model of Parkinson’s Disease Using 2D-DIGE-MS

J. Pickering, V. Godbole, S. Fowler, S. Lewis, K. Sköld, M. Svensson, and P. Andren

33.16 Comparative Proteomic Exploration of a Human Mitochondrial tRNA Disorder

P. Tryoen-Toth, S. Richert, B. Sohm, A. Van Dorsselaer, E. Leize, and C. Florentz

33.17 Proteomic and Glycomic Analyses of Mouse Uterine Luminal Fluid

C.-W. Kuo, H.-H. Hsiao, W.-T. Shyu, C.-M. Chen, Y.-C. Lee, S.-T. Chu, and K.-H. Khoo

33.18 Comparative Proteomic Investigations of the Human Olfactory Mucus Give Evidence of Secreted Odorant-binding Proteins

L. Briand, B. Sarazin, C. Henry, J.-C. Huet, C. Eloit, D. Trotier, and J.-C. Pernollet

33.19 Altered Protein Profiles of Postsynaptic Density (PSD) by Ischemic Insults on Rat

M. H. Kim, D. H. Kang, T. H. Kang, E. S. Seo, N.-W. Sohn, M. Suh, and C. Kang

33.20 Proteomics Study on the Function of Simvastatin to the Artery of Atherosclerotic Rabbit

Y.-l. Yu, P.-y. Yang, H.-z. Fan, Z. Huang, Y.-c. Rui, and P.-y. Yang

33.21 Protein Changes in Thyroid Diseases

J. Svasti, C. Srisomsap, P. Subhasitanont, and P. Punyarit

33.22 Identification of Cardiac Protein Expression Abnormalities in Diabetes Mellitus by LC-MS/MS

L. Stuart, A. Clermont, X. Chen, and E. Feener

33.23 Tools for High-throughput Proteomics—Expression Profiling for Diabetes Research

M. Macht, S. Deininger, S. Lehr, P. Palloch, S. Müller, M. Brodacki, A. Herkner, J. Kotzka, and D. Müller-Wieland

33.24 PARIS: An Proteomic Analysis and Resource Indexation System

J. Wang, C. Caron, A. Trubuil, M.-Y. Mistou, and C. Gitton

33.25 The Analysis of Plasma Proteomics in Trauma Mouse

J. Yin, Y. Xu, X. Gu, J. Wang, R. Wang, and S. Liu

33.26 Spinal Cord Injury-associated Proteins in Adult Rats Separated by Two-dimensional Gel Electrophoresis and Identified by Mass Spectrometry and Immunoblotting

Q. Ding, L. Xiao, Y. Guo, F. Kong, S. Xiong, S. Jing, and S. Liu

33.27 Proteome Study of the Protective Effect Against Liver Ischemia/Reperfusion Injury by Lidocaine Injection into Hepatoduodenal Ligament in Rats

M. Chen, C. Li, Q. Ding, S. Liu, and Z. Huang

33.28 Peptidomics-based Discovery of Novel Neuropeptides: Proteomics and Peptidomics of a Parkinson’s Disease Model

P. Andren, M. Svensson, K. Skold, J. Pickering, S.-E. Skold, and P. Svenningsson

33.29 Global Proteomics for Human Blood Serum I: Multidimensional Separation of Peptides Coupled with Mass Spectrometry

J. Adkins, S. Varnum, K. Auberry, R. Moore, N. Angell, D. Wunschel, R. Smith, D. Springer, and J. Pounds

33.30 Alterations to the Myocardial Protein Profile as a Consequence of Ischemia/Reperfusion Injury

M. Y. White, S. J. Cordwell, H. C. K. McCarron, G. Craft, A. S. Tchen, B. D. Hambly, and R. W. Jeremy

33.31 Significant Coverage of the Normal Human Serum Proteome by Gel-Less LC-ESI-ION TRAP

J. Marshall, C. Smith, W. Zhu, L. Ingratta, L. Barker, D. Pinchev, R. Zhang, and G. Jackowski

33.32 Functional Proteomic Platform for Mapping Cardiac Subproteomes in the Mouse: A Strategy for the Human Cardiac Proteome Project

T. M. Vondriska, G.-W. Wang, J. Zhang, X. J. Qiao, E. M. Cardwell, and P. Ping

34. Keynote Lecture

Sunday, November 24, 9:00–9:45, Richelieu Room

9:00

Contributions of Proteomic Profiling to Drug Discovery and Development

S. Hefta

35. Plenary Session Pharmacogenomics and Proteomics in the Pharma Industry

Chair: C. DeBouck

Sunday, November 24, 9:50–11:20, Richelieu Room

9:50

35.1 Proteomics in Biomarker Discovery

S. Carr

10:20

35.2 Selecting Targets for Therapeutic Validation Through Differential Protein Expression Using Chromatography-Mass Spectrometry

S. D. Patterson, T. E. Ryan, M. D. Bond, B. M. Domon, and I. N. McCaffery

10:50

Proteomics in Target Discovery—From ID to Function

J. Voshol

36. Round Table Discussion Collaboration Between Industry and Academia

Chair: H. Langen

Discussion leaders: J. E. Celis, M. Dunn, S. Hefta, L. Segal, R. Van Bogelen, and J. Voshol

Sunday, November 24, 11:20–13:00, Richelieu Room

FOOTNOTES

Numbers prior to titles correspond to abstract numbers (see p. #).

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