Day 1, Tuesday, October 28, 2008
7:30 a.m. - 8:00 a.m.	Registration and Morning Break
8:00 a.m. - 8:10 a.m.	Welcome and Introduction Henry Rodriguez, Ph.D., M.B.A. Director, Clinical Proteomic Technologies for Cancer National Cancer Institute, National Institutes of Health
8:10 a.m. - 8:50 a.m.	Keynote Lecture: Genomic Variation and Disease David Altshuler, M.D., Ph.D. Professor of Genetics and Medicine Harvard Medical School/Massachusetts General Hospital Director Program in Medical and Population Genetics Broad Institute of MIT and Harvard
8:50 a.m. - 12 noon	Clinical Proteomic Technologies for Cancer (CPTC) and Innovative Molecular Analysis Technologies (IMAT) Program Joint Session: Fostering Collaborative Efforts Co-Chairs:    Christopher Kinsinger, Ph.D.    Clinical Proteomic Technologies for Cancer    National Cancer Institute, National Institutes of Health    J. Randy Knowlton, Ph.D.    Innovative Molecular Analysis Technologies Program    National Cancer Institute, National Institutes of Health
8:50 a.m. - 9:15 a.m.	Raising the Bar—NCI’s Antibody Characterization Pipeline Tara Hiltke, Ph.D. Clinical Proteomic Technologies for Cancer National Cancer Institute, National Institutes of Health
9:15 a.m. - 9:40 a.m.	Technology To Optimize scFvs for Targeting Therapeutics Mark Federspiel, Ph.D. Mayo Clinic
9:40 a.m. - 10:05 a.m.	Incorporating IMAT-Developed Technology Into Another NCI Program Paul Tempst, Ph.D. Memorial Sloan-Kettering Cancer Center
10:05 a.m. - 10:20 a.m.	Break
10:20 a.m. - 10:45 a.m.	An Integrated Programmatic Environment To Support Indepth Proteomics and Phosphoproteomics Profiling and Studies of Gas Phase Chemistry of Peptides and Phosphopeptides Katheryn A. Resing, Ph.D. University of Colorado at Boulder
10:45 a.m. - 11:10 a.m.	Performance and Optimization of LC-MS/MS Platforms for Proteomic Analyses: An Interlaboratory Study Daniel C. Liebler, Ph.D. Vanderbilt University Medical Center
11:10 a.m. - 11:35 a.m.	Nanoscale Detection of the Disease Proteome Nicholas J. Wang, Ph.D. Lawrence Berkeley National Laboratory
11:35 a.m. - 12 noon	Verification of Candidate Protein Biomarkers: Reproducibility of MRM-Based Assays Steven C. Hall, Ph.D. University of California, San Francisco
12 noon - 1:30 p.m.	Lunch and Poster Session
1:30 p.m. - 3:10 p.m.	Session I: CPTC Technologies Chair:    Susan Fisher, Ph.D.    University of California, San Francisco
1:30 p.m. - 1:55 p.m.	Multi-Array® Assay Platform for Cancer Biomarker Validation and Discovery John H. Kenten, Ph.D. Meso Scale Diagnostics, LLC
1:55 p.m. - 2:20 p.m.	Improving the Sensitivity of Peptide Identification With Metasearch and Machine Learning Nathan Edwards, Ph.D. Georgetown University
2:20 p.m. - 2:45 p.m.	Automated Multianalyte Profiles (MAPs) for Early Detection of Cancer-Related Proteins Ralph L. McDade, Ph.D. Rules-Based Medicine, Inc.
2:45 p.m. - 3:10 p.m.	Significance Analysis of Spectral Count Data in Label-Free Shotgun Proteomics Alexey I. Nesvizhskii, Ph.D. University of Michigan
3:10 p.m. - 3:40 p.m.	Break and Poster Session
3:40 p.m. - 5:20 p.m.	Session II: CPTC Technologies Chair:    Daniel C. Liebler, Ph.D.    Vanderbilt University Medical Center
3:40 p.m. - 4:05 p.m.	Discovery and Validation of Lung Cancer-Specific Monoclonal Antibodies Lazlo Takacs, M.D., Ph.D., Sc.D. BioSystems International
4:05 p.m. - 4:30 p.m.	Combining PCR Amplification Technology and Mass Spectrometry for Sensitive Detection of Proteins Charles Cantor SEQUENOM, Inc.
4:30 p.m. - 4:55 p.m.	Computational Reassembly of Fractionated Samples for Biomarker Discovery Using PEPPeR D.R. Mani, Ph.D. Broad Institute of MIT and Harvard
4:55 p.m. - 5:20 p.m.	High-Throughput, High-Sensitivity Proteomics Platform for Improved Biomarker Discovery and Verification Richard D. Smith, Ph.D. Pacific Northwest National Laboratory
5:20 p.m. - 5:30 p.m.	Wrap-Up and Adjournment Henry Rodriguez Ph.D., M.B.A. Director, Clinical Proteomic Technologies for Cancer National Cancer Institute, National Institutes of Health
5:30 p.m. - 8:30 p.m.	CPTC Boston Fair and Poster Session
Day 2, Wednesday, October 29, 2008
7:30 a.m. - 8:00 a.m.	Registration and Morning Break
8:00 a.m. - 8:10 a.m.	Welcome Steven A. Carr, Ph.D. Broad Institute of MIT and Harvard
8:10 a.m. - 8:50 a.m.	Keynote Presentation: Convergence of Genomic, Proteomic, and Metabolomic Technologies To Unravel the Function of Mitochondria in Human Disease: Lessons Learned and What Is Still Needed Vamsi Mootha, M.D. Harvard Medical School
8:50 a.m. - 10:05 a.m.	Session I: CPTC Next-Generation Computational Tools and Platforms Chair:    Fred E. Regnier, Ph.D.    Purdue University
8:50 a.m. - 9:15 a.m.	Characterization of Polyubiquitin Chain Structure by Middle-Down Mass Spectrometry Junmin Peng, Ph.D. Emory University School of Medicine
9:15 a.m. - 9:40 a.m.	DirecTag Infers Partial Peptide Sequences From MS/MS Scans David L. Tabb, Ph.D. Vanderbilt University School of Medicine
9:40 a.m. - 10:05 a.m.	An Immunochromatographic Array Platform for Cancer Proteomics Fred E. Regnier, Ph.D. Quadraspec, Inc.
10:05 a.m. - 10:20 a.m.	Break
10:20 a.m. - 12 noon	Session II: CPTC Next-Generation Computational Tools and Platforms Chair:    Paul Tempst, Ph.D.    Memorial Sloan-Kettering Cancer Center
10:20 a.m. - 10:45 a.m.	Comparative Proteomics for the Discovery of Ubiquitin-Ligase Proteins Timothy Randolph, Ph.D. University of Washington
10:45 a.m. - 11:10 a.m.	Isolation and Characterization of scFv Antibodies Against Cancer Antigens Using Novel Display Library Jiwu Wang Allele Biotechnology and Pharmaceuticals
11:10 a.m. - 11:35 a.m.	Enhancement of Mass Spectrometry Signal Processing Toward Improved Cancer Biomarker Discovery Dariya Malyarenko, Ph.D., M.S. College of William and Mary
11:35 a.m. - 12 noon	MAZIE: A Mass and Charge Inference Engine To Enhance Database Searching of Tandem MS Spectra Dennis J. Templeton, M.D., Ph.D. University of Virginia Health System
12 noon	Wrap-Up and Adjournment