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CPTAC Releases Largest-Ever Colorectal Cancer Proteome Dataset from Previously Genome Characterized Tumors

On September 4, 2013, NCI’s Clinical Proteomics Tumor Analysis Consortium (CPTAC) publicly released proteomic data produced from colorectal tumor samples previously analyzed by The Cancer Genome Atlas (TCGA).  This is the initial release of proteomic tumor data designed to complement genomic data on the same tumors. The data is publicly available at the CPTAC data portal.

This first dataset of clinical tumors released from CPTAC includes 90 colorectal tumors with 5 additional samples representing different portions of tumor from the same patient.  Professor Daniel Liebler and his team at the Vanderbilt University Medical Center analyzed the global proteome of these tumors using standardized shotgun proteomic methods on a Thermo Orbitrap mass spectrometer.

Prior to analyzing the TCGA tumors, CPTAC centers performed a number of due diligence studies to better understand the effect of pre-analytical variables on proteomic analysis, including both instrument performance and the effects of sample handling due to a variety of protocols involved in tumor acquisition for TCGA.  A breast cancer based xenograft material provided by Washington University of St. Louis was used as a comparative reference (CompRef) to ensure that all data produced was at a high and consistent level of quality across the consortium.  Additionally, the effects of optimal cutting temperature media (OCT) and ischemic time on the sample’s proteome were examined.  These initial studies provided the basis for moving forward with the analysis of genomically characterized TCGA tumor samples. Data from these initial due diligence studies is also available on the CPTAC data portal.

This release of colorectal cancer proteomic data will provide researchers the opportunity to develop novel proteogenomic integration tools and algorithms to extend our current knowledge of the biological underpinnings of cancer.  This data set stands as an invitation to data scientists currently outside of proteomics to consider the challenges of proteogenomic integration. 

Over the next several months, CPTAC will be releasing additional resources to the community including:

  • Public Assay Portal for Multiple Reaction Monitoring-Mass Spec (MRM-MS) based assays to include standard operating procedures and assay validation data
  • Additional proteomic data sets including two additional TCGA tumor types (Breast and Ovarian) in April of 2014
  • Software that will help in the analysis of proteomic and genomic findings for cancer biologist

The analysis of the colorectal cancer proteomic data and other findings will be presented on November 13, 2013 at the CPTAC First Annual Scientific Symposium.  All researchers and investigators are welcome to attend this free event.

CPTAC is composed of five proteome characterization centers (PCCs) located throughout the United States that are currently analyzing proteins from over 300 TCGA tumors selected from colorectal, breast, and ovarian cancer types.  Using mass spectrometry and array based platforms; PCC’s are developing an inventory of cancer-related proteins as well as information about post-translationally modified proteins for each patient sample.