10th Annual Proteomics...
Unraveling the Human Proteome
June 19-21, 2006 at the Fairmont Hotel, San Francisco, California

Register Here! https://commerce22.datapipe.com/chidb/2006/byg/reg.asp

Download Brochure!
http://www.beyondgenome.com/pdf_pro.asp



Pre-Conference Workshop (separate registration required):


Top-Down vs. Bottom-Up Proteome Profiling Approaches
Dr. Jim Stephenson, Senior Program Director
Mass Spectrometry Research, Research Triangle Institute

With the development of electrospray (ESI) and matrix-assisted laser desorption ionization (MALDI) in the late 1980's, mass spectrometry has played an ever increasing roll in the analysis of complex protein mixtures. Traditionally, mass spectrometry approaches are based on a bottom-up strategy that utilizes proteolytic digestion of proteins, followed by separation and detection using LC-MS/MS. The majority of MS based research to date has focused on qualitative identification, quantitation, separation strategies, sample preparation, and bioinformatic approaches of the bottom-up methodology. Within the last five years, top-down proteomics involving the analysis of intact proteins has gained increasingly popularity. The ability to characterize posttranslational modifications, reduce false positive identifications, and study protein-protein interactions make this an ideal approach for answering many questions in proteomics. In this presentation a comparison of bottom-up and top-down proteomics is discussed with particular emphasis on sample preparation, instrument selection, tandem mass spectrometry approaches, peptide/protein separations, peptide/protein identification, quantitation, analysis of posttranslational modifications, gene finding/re-annotation, SNP analysis, bioinformatics and data validation. This presentation will serve as a starting point for a group discussion of bottom-up and top-down proteomics.

Interactive Discussion:

*Instrumentation and price/performance ratio, are top-down studies worth the
investment?

*Collisional activation versus electron capture/transfer dissociation, what is the best
way to obtain sequence specific information?

*The definition of protein identification: Are one hit peptides worth the trouble in
bottom-up proteomics?

*Can false positives be kept at a minimum while datasets are mined for false
negatives?

*Top-down versus bottom up for analysis of posttranslational modifications, are these
approaches mutually exclusive?

*The elements of dynamic range in top-down and bottom-up approaches

*The current status of top-down proteomics as a routine tool for biologist

*Can top-down or bottom-up approaches make an impact in validation or discovery of
genes?

*Do top-down or bottom-up approaches provide a proteomics based approach for
analysis of single nucleotide polymorphisms?



Conference at a Glance

Array Technologies for Protein Biomarker Applications

Molecular Network Analysis Using Reverse Phase Protein Microarrays for Patient Tailored Therapy
Dr. Emanuel F. Petricoin, Co-Director, Center for Applied Proteomics and Molecular Medicine, Professor of Life Sciences, George Mason University

Antibody- and Mass Spectrometry-Based Peptide Chip Technology for Clinical Diagnostics
Dr. Christoph Borchers, Assistant Professor, Director, Biochemistry and Biophysics, University of North Carolina

An ELISA Microarray Platform for the Validation of Cancer Biomarkers
Dr. Richard C. Zangar, Senior Research Scientist, Pacific Northwest National Laboratory

Mass Spectrometry for Protein Biomarker Discovery

Tissue Proteomics-Based Cancer Biomarker Discovery
Dr. Cheng S. Lee, Associate Professor, Department of Chemistry and Biochemistry, University of Maryland

Oral Cancer Proteomics
Dr. Shen Hu, Assistant Professor, School of Dentistry, UCLA

Analysis of Serum Peptides Associated with Hepatocellular Carcinoma
Dr. Radoslav Goldman, Assistant Professor of Oncology, Georgetown University

MS Data Analysis for Biomarker Identification

Interpretation of Quantitative Shotgun Proteomic Data
Dr. Alexey I. Nesvizhskii, Assistant Professor, Department of Pathology, University of Michigan

The Proper Construction of SELDI-Based Classifiers for Early Disease Detection
Dr. Brian Luke, Senior Scientist, Advanced Biomedical Computing Center, SAIC-Frederick

Rapid Classification of Lung Diseases by Ion Mobility Spectrometry Using Biomarker Data Analysis
Dr. Joerg Ingo, Director, Department of Metabolomics, Institute for Analytical Sciences (ISAS)

Integrating Genomic and Proteomic Data
for Biomarker Discovery

Virtual Mass Spectrometry and the Discovery of Biomarkers
Dr. Paul Kearney, Executive Director, Bioinformatics, Caprion Pharmaceuticals, Inc.

Comparative Proteomics and Genomics Studies for the Discovery of HIV Biomarkers
Dr. Joyce Peng, Product Manager, Proteomics, Rosetta Biosoftware LLC

Data Fusion in Biomarker Data Analysis
Dr. Isabelle Guyon, Independent Consultant, Bioinformatics, ClopiNet

Proteomics for Target Validation

Massively Parallel Chemogenomic Assays for Target Discovery
Dr. Corey Nislow, Senior Research Scientist, Biochemistry, Stanford University

Analysis of Transiently Over Expressed Src Y527F on Phosphoproteome Signaling
Dr. Jrg von Hagen, Head of Laboratory, LSA R&D, Merck KGaA

Using a Proteomics Approach for Cancer Drug Target Identification
Dr. Tao He, Associate Director, Proteomics/Protein Therapeutics, Celera Genomics

Proteome Profiling Approaches to Study
Signaling Pathways

High-Throughput Molecular Dissection of an Age Suppressing (Klotho) Signaling Pathway Using a siRNA Kinome Library and Protein Microarrays
Dr. Kevin Rosenblatt, Assistant Professor/Associate Director, Division of Translational Pathology, UT Southwestern Medical Center

Global Profiling of Protein Tyrosine Phosphatase Activity with Ultra-Sensitive Chemical Probes
Dr. Zhong-Yin Zhang, Professor and Chair, Biochemistry and Molecular Biology, Indiana University School of Medicine

Analysis of Functional Fingerprints of Protein Interaction Hubs
Dr. Alexei Kurakin, Staff Scientist, Buck Institute for Age Research



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