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CPTAC Data Portal Overview

The Clinical Proteomic Tumor Analysis Consortium (CPTAC) analyzes cancer biospecimens by mass spectrometry, characterizing and quantifying their constituent proteins, or proteome. Mass spectrometry enables highly specific identification of proteins and proteoforms, accurate relative quantitation of protein abundance in contrasting biospecimens, and the localization of post-translational protein modifications, such as phosphorylation, on a protein’s sequence.

The CPTAC Data Portal is the centralized repository for the dissemination of proteomic data collected by the Proteome Characterization Centers (PCCs) for the CPTAC program. The portal also hosts analyses of the mass spectrometry data (mapping of spectra to peptide sequences and protein identification) from the PCCs and from a CPTAC-sponsored common data analysis pipeline (CDAP). All data is freely available to the public, subject to the data use guidelines. Reference mass spectral peptide libraries resulting from these studies may be downloaded freely from

Data release and publications:
June 2015
publication, TCGA colorectal cancer: Proteomic analysis of colon and rectal carcinoma using standard and customized databases, Slebos R.J.C., et al., (2015) Scientific Data 2, Article number: 150022

April 2015
protein reports, revision 2, TCGA breast, colorectal, and ovarian cancer studies
proteome MS files, Time Course Colon Cancer study, Gajadhar et al., Cancer Res. 2015 Apr 1;75(7):1495-503
publication, The CPTAC Data Portal, Edwards et al., J Proteome Res. 2015 Apr 15

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Study Name Description Publications