The following are the current CPTAC teams, representing a network of Proteome Characterization Centers (PCCs), Proteogenomic Translational Research Centers (PTRCs), and Proteogenomic Data Analysis Centers (PGDACs). Teams are listed alphabetically by institution, with their respective Principal Investigators:
Proteome Characterization Centers
PCCs use state-of-the-art, standardized mass spectrometry-based technologies to perform comprehensive proteomic characterizations on genomically-characterized biospecimens, and quantitative measurements of protein targets of biological/clinical relevance.
Broad Institute, Cambridge, MA
Principal Investigators: Steven A. Carr, Ph.D.; Michael Gillette, M.D., Ph.D.
Johns Hopkins University, Baltimore, MD
Principal Investigators: Daniel W. Chan, Ph.D.; Hui Zhang, Ph.D.; Zhen Zhang, Ph.D.
Pacific Northwest National Laboratory, Richland, WA
Principal Investigators: Tao Liu, Ph.D.; Richard D. Smith, Ph.D.
Proteogenomic Data Analysis Centers
PGDACs conduct integration, visualization and analyses using different data types (genomics, transcriptomics, and proteomics, imaging and clinical data) to improve the understanding of genome-proteome relationship and the interplay/regulation of signaling pathways involved in cancer.
Baylor College of Medicine, Houston, TX
Principal Investigator: Bing Zhang, Ph.D.
Additional area of focus: pathway and molecular network visualization.
Broad Institute, Cambridge, MA
Principal Investigators: Denkanikota R. Mani, Ph.D.; Gad Getz, Ph.D.
Additional area of focus: patient-centric protein databases and proteogenomic data analysis pipeline and visualization portal (CPTAC Firehose).
Icahn School of Medicine at Mount Sinai, New York, NY
Principal Investigators: Pei Wang, Ph.D.; Eric Schadt, Ph.D.
Additional area of focus: missing proteomics data, batch effects, and global regulatory networks.
New York University School of Medicine, New York, NY; Washington University in St. Louis, St. Louis, MO; Pacific Northwest National Laboratory, Richland, WA
Principal Investigators: David Fenyo, Ph.D.; Li Ding, Ph.D.; Samuel Payne, Ph.D.
Additional area of focus: quantitative trait loci-centered approach, outlier analysis using posttranslational modifications data, and druggability of kinase inhibitors using protein structural information.
University of Michigan, Ann Arbor, MI
Principal Investigators: Alexey I. Nesvizhskii, Ph.D.; Arul Chinnaiyan, M.D., Ph.D.
Additional area focus: quality-control scoring measures to identify genomic/transcriptomic variants expressed at protein level.
Proteogenomic Translational Research Centers
PTRCs address questions of biology in the context of a clinical trial [NCI-sponsored], using an integration of proteomics and genomics. Focus on understanding drug response and resistance to therapies.
Baylor College of Medicine, Houston, TX; Broad Institute, Cambridge, MA
Principal Investigators: Matthew Ellis, MB, BChir, BSc., PhD; Steven A. Carr, Ph.D.
Cancer focus: Breast cancer
Fred Hutchinson Cancer Research Center, Seattle, WA; University of Alabama, Birmingham, AL
Principal Investigators: Amanda Paulovich, M.D., Ph.D.; Michael Birrer, M.D., Ph.D.
Cancer focus: Epithelial ovarian cancer
Pacific Northwest National Laboratory, Richland, WA, Oregon Health & Science University, Portland, OR
Principal Investigators: Karin Rodland, Ph.D.; Brian J. Druker, M.D.
Cancer focus: Acute myeloid leukemia