Day 1, October 24, 2007
7:30 a.m. - 8:30 a.m.	Registration
8:30 a.m. - 9:15 a.m.	Welcome and Keynote Address
8:30 a.m. - 8:35 a.m.	Welcome Henry Rodriguez, Ph.D., M.B.A. Director, Clinical Proteomic Technologies for Cancer National Cancer Institute, NIH
8:35 a.m. - 8:45 a.m.	Special Address: Future Role of Proteomics in Molecular Oncology John E. Niederhuber, M.D. Director National Cancer Institute, NIH
8:45 a.m. - 8:50 a.m.	Perspective from a Cancer Patient Advocate Ann McNeil, R.N. NCI Consumer Advocates in Research and Related Activities Member University of Miami
8:50 a.m. - 9:00 a.m.	Overcoming Barriers in Molecular Diagnostics Anna D. Barker, Ph.D. Deputy Director National Cancer Institute, NIH
9:00 a.m. - 9:15 a.m.	Overview of Clinical Proteomic Technologies for Cancer Henry Rodriguez, Ph.D., M.B.A. Director, Clinical Proteomic Technologies for Cancer National Cancer Institute, NIH
9:15 a.m. - 3:00 p.m.	Clinical Proteomic Technology Assessment for Cancer (CPTAC) Program (Panel Session) Moderator: Steven A. Carr, Ph.D. Chair, CPTAC Program Coordinating Committee Director of Proteomics Broad Institute of MIT and Harvard
9:15 a.m. - 9:25 a.m.	Inter-Group Studies: Introduction Steven A. Carr, Ph.D. Director of Proteomics Broad Institute of MIT and Harvard
9:25 a.m. - 10:05 a.m.	Unbiased Discovery Platform Optimization: No Matrix Stephen E. Stein, Ph.D. Director, Mass Spectometry Data Center National Institute of Standards and Technology Yeast Matrix Amanda Paulovich, M.D., Ph.D. Assistant Member Fred Hutchinson Cancer Research Center
10:05 a.m. - 10:25 a.m.	Verification Platform Optimization Studies: MRM – Plasma Spiked With Proteins Steven Hall, Ph.D. Associate Professor University of California, San Francisco Steven Skates, Ph.D. Assistant Professor of Medicine Harvard Medical School Massachusetts General Hospital
10:25 a.m. - 10:40 a.m.	Morning Break and Poster Session
10:40 a.m. - 11:00 a.m.	CPTAC Team Leader Panel Discussion (Inter-Group Studies)
11:00 a.m. - 11:30 a.m.	Assessment of Serum Peptide Profiling To Detect Cancer-Specific Patterns Paul Tempst, Ph.D. Professor Molecular Biology Program Memorial Sloan-Kettering Cancer Center
11:30 a.m. - 12 noon	Targeted and Global Proteomic Strategies for Early Breast Cancer Detection Susan J. Fisher, Ph.D. Professor University of California, San Francisco
12 noon - 1:30 p.m.	Lunch and Official Poster Session
1:30 p.m. - 2:00 p.m.	Clinical Proteomic Technology Assessment for Cancer Daniel C. Liebler, Ph.D. Professor Vanderbilt University Medical Center
2:00 p.m. - 2:30 p.m.	APT: The Analytical Proteomics Team Fred E. Regnier, Ph.D. J.H. Law Distinguished Professor Purdue University
2:30 p.m. - 3:00 p.m.	Measuring Cancer Biomarker Candidates by Targeted MS and Ab Enrichment Steven A. Carr, Ph.D. Director of Proteomics Broad Institute of MIT and Harvard
3:00 p.m. - 3:30 p.m.	CPTAC Team Leader Panel Discussion (Intra-Group Studies)
3:30 p.m. - 3:45 p.m.	Coffee Break and Poster Session
3:45 p.m. - 5:15 p.m.	Lessons Learned (Team Science): Clinical Proteomic Technologies for Cancer and International Leader Panel Discussion Moderator: Susan J. Fisher, Ph.D. Steven A. Carr, Ph.D., Director of Proteomics, Broad Institute of MIT and Harvard Paul Tempst, Ph.D., Professor, Molecular Biology Program, Memorial Sloan- Kettering Cancer Center Daniel C. Liebler, Ph.D., Professor, Vanderbilt University Medical Center Fred E. Regnier, Ph.D., J.H. Law Distinguished Professor, Purdue University Henry Rodriguez, Ph.D., M.B.A., Director, Clinical Proteomic Technologies for Cancer, National Cancer Institute, NIH Fredrik Pontén, M.D., Ph.D., Director, Uppsala University Site for the Swedish Human Proteome Resource Project Myeong-Hee Yu, Ph.D., Director, Korean Functional Proteomics Program Kenneth R. Evans, Ph.D., President and CEO, Ontario Cancer Biomarker Network Steven Gutman, M.D., M.B.A., Director, Office of In Vitro Diagnostic Device Evaluation and Safety, Center for Devices and Radiological Health, FDA
5:00 p.m. - 5:15 p.m.	Summary and Action Items of Day 1 Steven A. Carr, Ph.D. Director of Proteomics Broad Institute of MIT and Harvard Henry Rodriguez, Ph.D., M.B.A. Director, Clinical Proteomic Technologies for Cancer National Cancer Institute, NIH
5:15 p.m.	Meeting Adjournment
7:00 p.m. - 9:00 p.m.	CPTAC Program Coordinating Committee Dinner
Day 2, October 25, 2007
7:30 a.m. - 8:20 a.m.	Registration
8:20 a.m. - 8:25 a.m.	Welcome — Review of the Agenda Henry Rodriguez, Ph.D., M.B.A. Director, Clinical Proteomic Technologies for Cancer National Cancer Institute, NIH
8:25 a.m. - 8:35 a.m.	Proteomic Reagents and Resource Core Henry Rodriguez, Ph.D., M.B.A. Director, Clinical Proteomic Technologies for Cancer National Cancer Institute, NIH
8:35 a.m. - 8:45 a.m.	Clinical Proteomic Technologies for Cancer Informatics Strategy Chris Kinsinger, Ph.D. Program Manager, Clinical Proteomic Technologies for Cancer National Cancer Institute, NIH
8:45a.m. - 1:00 p.m.	Advanced Proteomic Platforms Program and Computational Science Session Moderator: Daniel C. Liebler, Ph.D. and Chris Kinsinger, Ph.D.
8:45 a.m. - 9:00 a.m.	Proteomic Characterization of Alternative Splicing and Coding Polymorphism Using Tandem Mass Spectrometry Nathan J. Edwards, Ph.D. University of Maryland, College Park
9:00 a.m. - 9:15 a.m.	Enhancement of MS Signal Processing Toward Improved Cancer Biomarker Discovery: Progress and Plans Dariya Malyarenko, Ph.D., M.S. College of William and Mary
9:15 a.m. - 9:30 a.m.	Proteomic Phosphopeptide Chip Technology for Protein Profiling Xiaolian Gao, Ph.D. University of Houston
9:30 a.m. - 9:45 a.m.	Global Production of Cancer Biomarker-Specific Monoclonal Antibodies Barry L. Karger, Ph.D. Northeastern University
9:45 a.m. - 10:00 a.m.	Analysis and Statistical Validation of Proteomic Datasets Generated Using Tandem Mass Spectrometry Alexey I. Nesvizhskii, Ph.D. University of Michigan
10:00 a.m. - 10:15 a.m.	Peptide Detection in High-Resolution Mass Spectrometry Data Timothy W. Randolph, Ph.D. Fred Hutchinson Cancer Research Center
10:15 a.m. - 11:00 a.m.	Coffee Break and Poster Session
11:00 a.m. - 11:15 a.m.	Electrospray-Assisted Laser Desorption Ionization (ELDI) and Top-Down Mass Spectrometry for Biomarker Discovery Joseph A. Loo, Ph.D. University of California, Los Angeles
11:15 a.m. - 11:30 a.m.	A New Platform for Screening Serum for Cancer Membrane Proteins Daniel B. Martin, M.D. Institute for Systems Biology
11:30 a.m. - 11:45 a.m.	Phosphoprotein Profiling of Monoq Fractionated Melanoma Cell Line ± MAPK Inhibitor Using Negative Mode Precursor Ion Scanning and Estimating Protein Stoichiometry Using Profile Data From an LTQ/Orbitrap Katheryn A. Resing, Ph.D., M.A. University of Colorado at Boulder
11:45 a.m. - 12 noon	Redesigning the Protein Identification Pipeline: New Tools for Practical Proteomics David L. Tabb, Ph.D. Vanderbilt University
12 noon - 12:15 p.m.	A Systematic Approach for the Validation of Ubiquitinated Proteome Junmin Peng, Ph.D. Emory University
12:15 p.m. - 12:30 p.m.	Advances in Proteomics Measurements for Biomarker Discovery and Validation Richard D. Smith, Ph.D. Pacific Northwest National Laboratory
12:30 p.m. - 12:45 p.m.	PICquant: An Automated Platform for Quantitative Mass Spectroscopy for Biomarker Discovery Dennis J. Templeton, M.D., Ph.D. University of Virginia
12:45 p.m. - 1:00 p.m.	PEPPeR: A Platform for Pattern-Based Proteomic Biomarker Discovery D.R. Mani, Ph.D. Broad Institute of MIT and Harvard
1:00 p.m. – 1:15 p.m.	Closing Remarks, Action Items, and Adjournment Henry Rodriguez, Ph.D., M.B.A. Director, Clinical Proteomic Technologies for Cancer National Cancer Institute, NIH