Day 1, Monday, October 5

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. - 8:20 a.m.

Role of Patient Advocates in Clinical Proteomics
Elda Railey
Research Advocacy Network

8:20 a.m. - 9:00 a.m.

Keynote Lecture: Title pending
James Heath, Ph.D.
Elizabeth W. Gilloon Professor of Chemistry
California Institute of Technology

9:00 a.m. - 10:40 a.m.

Theme 1: Biomarker Discovery Platforms
Chair: Steve Carr, Ph.D.
Broad Institute of MIT and Harvard

9:00 a.m. - 9:25 a.m.

Discovery and Verification of Protein Biomarkers in Cancer, Precancer and Normal Tissues
Daniel Liebler, Ph.D.
Vanderbilt University Medical Center

9:25 a.m. - 9:50 a.m.

Exploiting Cancer Biology in the Development of Mass Spectrometry-Based Proteomic Workflows
Susan Fisher, Ph.D.
University of California, San Francisco

9:50 a.m. - 10:15 a.m.

Transformation of Anecdotal Clinical Peptidomics into Activity-Based Biomarker Screens and Verification
Paul Tempst, Ph.D.
Memorial Sloan-Kettering Cancer Center

10:15 a.m. - 10:40 a.m.

A HUPO Equimolar Test Sample for Proteomics
John Bergeron, D.Phil
McGill University

10:40 a.m. - 10:50 a.m.

Break

10:50 a.m. - 12:30 p.m.

Theme 2: Platforms and Tools for PTM Studies
Chair:   Bradford W. Gibson, Ph.D.
Buck Institute for Age Research
University of California, San Francisco

10:50 a.m. - 11:15 a.m.

Affinity-Based Biomarker Discovery Workflows Targeting Cancer-Specific Posttranslationally Modified Proteins in Human  Plasma
Bradford W. Gibson, Ph.D.
Buck Institute for Age Research
University of California, San Francisco

11:15 a.m. - 11:40 a.m.

Using SILAC to Study Tyrosine Kinase Signaling in Neurons
Thomas Neubert, Ph.D.
New York University School of Medicine

11:40 a.m. - 12:05 p.m.

Modeling Phosphopeptide Gas Phase Fragmentation
William Old, Ph.D.
University of Colorado at Boulder

12:05 p.m. - 12:30 p.m.

Proteomic Phosphopeptide Chip Technology for Protein Profiling
Xiaolian Gao, Ph.D.
University of Houston

12:30 p.m. - 2:00 p.m.

Lunch and Poster Session

2:00 p.m. - 3:40 p.m.

Theme 3: Bioinformatics Resources and Tools for Proteomic Community
Chair:   Chris Kinsinger, Ph.D.
Clinical Proteomic Technologies for Cancer
National Cancer Institute, National Institutes of Health

2:00 p.m. - 2:25 p.m.

caTranche: A CPTAC Community Resource for Sharing Proteomic Data
Phil Andrews, Ph.D.
University of Michigan

2:25 p.m. - 2:50 p.m.

TagRecon Identifies Protein Mutations and Modifications
David Tabb, Ph.D.
Vanderbilt University Medical Center

2:50 p.m. - 3:15 p.m.

Analysis and Statistical Validation of Proteomic Datasets
Alexey Nesvizhskii, Ph.D.
University of Michigan

3:15 p.m. - 3:40 p.m.

Improving the Sensitivity of Peptide Identification from Tandem Mass Spectra using Meta-Search, Grid-Computing, and Machine-Learning
Nathan Edwards, Ph.D.
Georgetown University

3:40 p.m. - 4:40 p.m.

Poster Session/Break

4:40 p.m. - 5:55 p.m.

Theme 4: Advances in Proteomic Technologies
Chair: Paul Tempst, Ph.D. 
Memorial Sloan-Kettering Cancer Center

4:40 p.m. - 5:05 p.m.

High-throughput, High-sensitivity Proteomics Platform for Improved Biomarker Discovery and Verification
Richard D. Smith, Ph.D.
Pacific Northwest National Laboratory

5:05 p.m. - 5:30 p.m.

Immunosignaturing as Biomarkers of Early Chronic Disease, Including Cancer
Stephen Albert Johnston, Ph.D.
The Biodesign Institute, Arizona State University

5:30 p.m. - 5:55 p.m.

Group Quantification of Mass-Tagged Peptides Using Spectrum Clustering With PICquant and MAZIE
Dennis J. Templeton, M.D., Ph.D.
University of Virginia Health System

5:55 p.m. - 6:00 p.m.

Wrap-Up and Adjournment
Henry Rodriguez Ph.D., M.B.A.
National Cancer Institute, National Institutes of Health

Day 2, Tuesday, October 6

7:30 a.m. - 8:00 a.m.

Registration and Morning Break

8:00 a.m. - 8:05 a.m.

Welcome
Henry Rodriguez Ph.D., M.B.A.
Director, Clinical Proteomic Technologies for Cancer
National Cancer Institute, National Institutes of Health

8:05 a.m. - 8:45 a.m.

Keynote Lecture: Restructuring Biomarker Proteomics - Using Mass Spectrometry to Bridge Toward the Clinical Laboratory
Leigh Anderson, Ph.D.
Chief Executive Officer
Plasma Proteome Institute

8:45 a.m. - 9:25 a.m.

Special Plenary Lectures: International Perspectives in Clinical Proteomics
Chair: Daniel Liebler, Ph.D.
Vanderbilt University Medical Center

8:45 a.m. - 9:05 a.m.

Focused Integration & Valued Output: Korean Proteomics Efforts to Discover Biomarkers
Myeong-Hee Yu Ph.D.
Korea Institute of Science and Technology

9:05 a.m. - 9:25 a.m.

Drug Rescue: The Application of Quantitative Mass Spectrometric Methods to Personalized Medicine Development
K.W. Michael Siu, Ph.D.
Ontario Cancer Biomarker Network

9:25 a.m. - 11:30 a.m.

Theme 5: MS Platform Benchmarking: CPTAC Multi-Site Assessment Studies
Chair: Fred Regnier, Ph.D.
Purdue University

9:25 a.m. - 9:50 a.m.

A Multi-Site Assessment of Multiple Reaction Monitoring MS for Protein Quantitation in Human Plasma: Towards a Robust Tool for Verification of Biomarker Candidates
Steven Hall, Ph.D.
University of California, San Francisco

9:50 a.m. - 10:15 a.m.

Break

10:15 a.m. - 10:40 a.m.

Applications of the CPTAC Yeast Reference Proteome Standard
Daniel Liebler, Ph.D.
Vanderbilt University Medical Center

10:40 a.m. - 11:05 a.m.

Metrics for LC-MS/MS Performance in Proteomics
Stephen Stein Ph.D.
National Institute for Standards and Technology

11:05 a.m. - 11:30 a.m.

Repeatability and reproducibility in proteomic analyses by liquid chromatography-tandem mass spectrometry
David Tabb, Ph.D.
Vanderbilt University Medical Center

11:30 a.m. - 12:20 p.m.

Theme 6: Quantitative Proteomics
Chair: N. Leigh Anderson, Ph.D., Chief Executive Officer
Plasma Proteome Institute

11:30 a.m. - 11:55 a.m.

Measuring Cancer Biomarker Candidates by Targeted MS and Ab Enrichment
Steve Carr, Ph.D.
Broad Institute of MIT and Harvard

11:55 a.m. - 12:20 p.m.

What I've Learned from Being a Member of the Proteomics Research Group
Michael MacCoss, Ph.D.
University of Washington

12:20 p.m. - 1:30 p.m.

Lunch and Poster Session

1:30 p.m. - 2:30 p.m.

Theme 7: Special Panel on Biospecimen and Experimental Design/Statistical Considerations
Moderator: Helen Moore, Ph.D.
Office of Biorepositories and Biospecimen Research
National Cancer Institute, National Institutes of Health

1:30 p.m. - 1:45 p.m.

Design and Statistics of Marker Studies: What Can We Learn from Netflix?
David Ransohoff, M.D.
University of North Carolina at Chapel Hill

1:45 p.m. - 2:00 p.m.

The Love/Avon Army of Women: A New Model for Partnering Women and Scientists to Find the Cause and Prevention of Breast Cancer
Susan Love, M.D.
Dr. Susan Love Research Foundation

2:00 p.m. - 2:15 p.m.

Statistical Models for Longitudinal Biomarker Behavior
Steven J. Skates, Ph.D.
Harvard Medical School/Massachusetts General Hospital

2:15 p.m. - 2:30 p.m.

Using Data to Ensure Good Statistical Design
Nell Sedransk, Ph.D.
National Institute of Statistical Sciences

2:30 p.m. - 3:45 p.m.

Poster Session/Break

3:45 p.m. - 4:05 p.m.

Role of Clinical Chemists in Translating Novel Biomarkers into Clinical Practice - AACC Perspective on Clinical Proteomics
Saeed Jortani, Ph.D.
University of Louisville

4:05 p.m. - 4:15 p.m.

Update on National Cancer Institute-FDA Interagency Oncology Task Force on Molecular Diagnostics
Zivana Tezak, Ph.D.
U.S. Food and Drug Administration

4:15 p.m. - 5:55 p.m.

Theme 8: Reagents Development
Chair:   Mehdi Mesri, Ph.D.
Clinical Proteomic Technologies for Cancer
National Cancer Institute, National Institutes of Health

4:15 p.m. - 4:40 p.m.

CPTC’s Antibody Characterization Pipeline Update
Tara Hiltke, Ph.D.
Clinical Proteomic Technologies for Cancer
National Cancer Institute, National Institutes of Health

4:40 p.m. - 5:05 p.m.

Antibody Validation By Means Of Protein Array and Immunohistochemistry
Stephen Hewitt, M.D., Ph.D.
Center for Cancer Research
National Cancer Institute, National Institutes of Health

5:05 p.m. - 5:30 p.m.

Development of Reference Materials for Proteomics
David Bunk, Ph.D.
National Institute of Standards and Technology

5:30 p.m. - 5:55 p.m.

Synbodies: An Alternative Protein Affinity Reagent
John Chaput, Ph.D.
Arizona State University

5:55 p.m. - 6:00 p.m.

Wrap-Up and Adjournment
Henry Rodriguez Ph.D., M.B.A.
Clinical Proteomic Technologies for Cancer
National Cancer Institute, National Institutes of Health

Day 3, Wednesday, October 7

Joint CPTC/IMAT Session

7:30 a.m. - 8:00 a.m.

Registration and Morning Break

8:00 a.m. - 8:05 a.m.

Welcome and Introduction
Mark Lim, Ph.D.
Innovative Molecular Analysis Technologies (IMAT)
National Cancer Institute, National Institutes of Health

Henry Rodriguez, Ph.D., M.B.A.
Director, Clinical Proteomic Technologies for Cancer
National Cancer Institute, National Institutes of Health

8:05 a.m. - 8:45 a.m.

Keynote Lecture:
Elucidation of Tumor Biology and Assessment of Cancer Patients using Quantitative Mass Spectrometry
John Koomen, Ph.D.
Scientific Director, Proteomics Core Facility
H. Lee Moffitt Cancer Center and Research Institute

8:45 a.m. - 11:30 a.m.

CPTC and IMAT Joint Theme Session: Immunoaffinity Platforms and Protein Arrays
Co-Chairs: CPTC Representative (Susan Fisher, Ph.D.)
IMAT Representative (TBD)

8:45 a.m. - 9:10 a.m.

High-Speed Label-Free Detection by Spinning-Disk Micro-Interferometry
Fred Regnier, Ph.D.
Purdue University

9:10 a.m. - 9:35 a.m.

The Prevalence and Nature of Glycan Alterations on Specific Proteins in Pancreatic Cancer Patients Revealed Using Antibody-Lectin Sandwich Arrays
Brian Haab, Ph.D.
Van Andel Research Institute

9:35 a.m. - 10:00 a.m.

Clinically Quantifying Low-abundance Serum Proteins by LC-
MS/MS: Potential Benefits and a Case Study
Andy Hoofnagle, M.D., Ph.D.
University of Washington

10:00 a.m. - 10:15 a.m.

Break

10:15 a.m. - 10:40 a.m.

Bead Array-mass Spectrometer: Equipment and Method Development
Scott Tanner, Ph.D.
University of Toronto

10:40 a.m. - 11:05 a.m.

Multiplex Mass Spectrometric Immunoassays
Dobrin Nedelkov, Ph.D.
Intrinsic Bioprobes (SBIR)

11:05 a.m. - 11:30 a.m.

FDA Regulation of Protein-Based Diagnostic Assays
Jeffrey N. Gibbs, J.D.
Hyman, Phelps and McNamara, P.C.

11:30 a.m. - 11:45 a.m.

Diversity Training Opportunities
Mark Lim, Ph.D. (introduction)
Innovative Molecular Analysis Technologies
National Cancer Institute, National Institutes of Health

Kristina Pohaku Mitchell (M.S., Ph.D. candidate)
University of California, San Diego

11:45 a.m. - 1:00 p.m.

Lunch and Poster Session

1:00 p.m.

CPTC Meeting Adjourns