Day 1, Wednesday, September 8

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

Registration and Morning Break - Salon Foyer

8:00 a.m. - 8:10 a.m.

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

8:10 a.m. - 8:20 a.m.

Patient Advocates: Key Members of the Team To Advance Science
Paula Kim
Translational Research Network

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

Keynote Lecture: Biological Insights From Analysis of Receptor Tyrosine Kinase Signaling Networks
Forest M. White, Ph.D.
Massachusetts Institute of Technology

9:00 a.m. - 11:00 a.m.

Theme 1: Protein Discovery Platforms
Chair: Steven A. Carr, Ph.D.
Broad Institute

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

Discrimination of Cancer Phenotypes With a Standardized Shotgun Proteomics Analysis Platform
Daniel C. Liebler, Ph.D.
Vanderbilt University Medical Center

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

Mining the Breast Cancer Spliceosome for Subtype-Specific Biomarkers
Susan Fisher, Ph.D.
University of California, San Francisco

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

Break and Poster Session - Salon C

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

Blood-Based Aminopeptidase Activities as Biomarkers for Cancer
Paul Tempst, Ph.D.
Memorial Sloan-Kettering Cancer Center

10:35 a.m. - 11:00 a.m.

Oxidative Stress-Induced Protein Carbonylation in Breast Cancer Patient Plasma
Fred E. Regnier, Ph.D.
Purdue University

11:00 a.m. - 12:30 p.m.

Theme 2: Platforms and Tools for PTM Studies
Chair: Fred E. Regnier, Ph.D.
Purdue University

11:00 a.m. - 11:25 a.m.

Interlaboratory CPTAC Studies Targeting Posttranslationally Modified Proteins in Human Plasma Using Affinity Enrichment
Bradford W. Gibson, Ph.D.
Buck Institute for Age Research

11:25 a.m. - 11:50 a.m.

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

11:50 a.m. - 12:15 p.m.

Blind PTM Hunting Through Sequence Tagging
David L. Tabb, Ph.D.
Vanderbilt University

12:15 p.m. - 1:30 p.m.

Lunch and Poster Session - Salon C
MassQC Proteomics Tools Demonstration
(Please sign up at the registration desk.)

1:30 p.m. - 2:10 p.m.

Keynote Lecture: Functionalizing the Cancer Genome
Lynda Chin, M.D.
Dana-Farber Cancer Institute

2:10 p.m. - 3:25 p.m.

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

2:10 p.m. - 2:35 p.m.

Discovering Disease Markers Using Fractionated Samples and Pattern-Based Proteomic Analysis
Denkanikota R. Mani, Ph.D.
Broad Institute

2:35 p.m. - 3:00 p.m.

Kinetic Fragmentation Models for Spectral Library Searching and De Novo SRM Assay Design
William Old, Ph.D.
University of Colorado at Boulder

3:00 p.m. - 3:30 p.m.

Break and Poster Session - Salon C

3:30 p.m. - 3:55 p.m.

Analysis Tools for Several Platforms in Discovery and Validation of Protein Markers
Timothy Randolph, Ph.D.
Fred Hutchinson Cancer Research Center

3:55 p.m. - 4:45 p.m.

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

3:55 p.m. - 4:20 p.m.

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

4:20 p.m. - 4:45 p.m.

Quantitative Measure of Differential Peptide/Protein Expression Using Dual-Isotopic Labeling With 12C6- and 13C6-Phenylisocyanate
Dennis J. Templeton, M.D., Ph.D.
University of Virginia

4:45 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 2, Thursday, September 9

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

Registration and Morning Break - Salon Foyer

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

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

8:05 a.m. - 8:35 a.m.

Keynote Lecture: Proteomics: Foundation of Molecular Medicine - or Not?
Special Guest: Anna D. Barker, Ph.D.
Former Deputy Director
National Cancer Institute, National Institutes of Health

8:35 a.m. - 9:15 a.m.

Keynote Lecture: High-Throughput, Cell-Based Studies and Protein Microarrays for Biomarker and Target Discovery
Joshua LaBaer, M.D., Ph.D.
Arizona State University

9:15 a.m. - 9:40 a.m.

Keynote Lecture: The Ovarian Cancer Genome: Implications for CPTC
Paul Spellman, Ph.D.
Lawrence Berkeley National Laboratory

9:40 a.m. - 12:30 p.m.

Theme 5: Quantitative Proteomics
Chair: N. Leigh Anderson, Ph.D.
Plasma Proteome Institute

9:40 a.m. - 10:05 a.m.

Protein Quantification by Targeted Mass Spectrometry: A Bridge From Discovery to Clinical Validation
Steven A. Carr, Ph.D.
Broad Institute

10:05 a.m. - 10:25 a.m.

Break and Poster Session - Salon C

10:25 a.m. - 10:50 a.m.

Skyline: Software for Large-Scale Targeted Proteomics Studies
Brendan X. MacLean
University of Washington

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

Quantitative Measurement of Cancer-Associated Proteins by Targeted Mass Spectrometry: Assessing Highly Multiplexed MRM for Large-Scale Proteomics
Jeff Whiteaker, Ph.D.
Fred Hutchinson Cancer Research Center

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

Complete Human Peptide and MRM Atlas
Robert Moritz, Ph.D.
Institute for Systems Biology

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

Development and Implementation of a System Suitability Standard Protocol To Assess Data Quality in LC-MRM-MS
Across Multiple MS Platforms
Steven C. Hall, Ph.D.
University of California, San Francisco

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

Variations of Tryptic Peptide Yields in the Digestion of Proteins
Stephen Stein, Ph.D.
National Institute of Standards and Technology

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

Lunch and Poster Session - Salon C
MassQC and Skyline Proteomics Tools Demonstration
(Please sign up at the registration desk.)

1:30 p.m. - 2:20 p.m.

Theme 6: Reagents Development
Chair: Mehdi Mesri, Ph.D.
Clinical Proteomic Technologies for Cancer
National Cancer Institute, National Institutes of Health

1:30 p.m. - 1:55 p.m.

Synbodies: Alternative Protein Affinity Reagents for Molecular Medicine
John C. Chaput, Ph.D.
Arizona State University

1:55 p.m. - 2:20 p.m.

Electrochemiluminescent Multiplexed Assay Platform for Cancer Biomarkers
Galina N. Nikolenko, Ph.D.
Meso Scale Diagnostics, LLC

2:20 p.m. - 4:45 p.m.

Theme 7: CPTC: Facing Clinical Application
Chair: Daniel C. Liebler, Ph.D.
Vanderbilt University Medical Center

2:20 p.m. - 2:45 p.m.

The Potential Impact of Longitudinal Biospecimens on Candidate Verification
Steven J. Skates, Ph.D.
Massachusetts General Hospital
Harvard Medical School

2:45 p.m. - 3:10 p.m.

Break and Poster Session - Salon C

3:10 p.m. - 3:35 p.m.

PLCO Biorepository Resource for Translational Research
Claire Zhu, Ph.D.
Division of Cancer Prevention
National Cancer Institute, National Institutes of Health

3:35 p.m. - 4:00 p.m.

Lessons From the NHLBI Clinical Proteomics Program
Pothur Srinivas, Ph.D., M.P.H.
Division of Cardiovascular Diseases
National Heart, Lung, and Blood Institute, National Institutes of Health

4:00 p.m. - 4:25 p.m.

Drug Development by the NCI Cancer Therapy Evaluation Program
James Zwiebel, M.D.
Investigational Drug Branch
National Cancer Institute, National Institutes of Health

4:25 p.m. - 4:45 p.m.

Emerging Technologies for Cancer Assessment and Treatment: Where FDA Regulatory Science Fits In
Vicki Seyfert-Margolis, Ph.D.
U.S. Food and Drug Administration

4:45 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