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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:
April 2016
Data Release: Common Data Analysis Pipeline, updated Phosphoproteome reports for TCGA Breast Cancer, TCGA Ovarian Cancer, and TCGA Ovarian Cancer CompRef Samples.

March 2016
Publication: A Description of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) Common Data Analysis Pipeline, Rudnick et al., (2016) J Proteome Res. doi:10.1021/acs.jproteome.5b01091. Epub 2016 Feb 25

December 2015
Data Release: Integrated bottom-up and top-down proteomics of patient-derived breast tumor xenografts, Ntai I et al., (2015) Molecular and Cellular Proteomics, 2016 Jan;15(1):45-56.

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Study Name Description Publications