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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:
September 2016
Data Release: Additional experiments from Breast Cancer Proteogenomics Landscape Study. Normal breast tissue samples (experiment 37), and 05TCGA_AO-A12D-01A_AN-A04A-01A_BH-A0AV-01A_Proteome_BI_20130416 iTRAQ proteome data.

August 2016
Data Release: Trapped Ion Mobility Spectrometry Study, Florida International University and Pacific Northwest National Laboratory

June 2016
Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer. Zhang H, Liu T, Zhang Z, Payne SH, Zhang B, McDermott JE et al., Cell (2016) DOI: 10.1016/j.cell.2016.05.069, Published online June 29, 2016.

May 2016
Proteogenomics Connects Somatic Mutations to Signalling in Breast Cancer. Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P et al., Nature (2016) doi:10.1038/nature18003 Published online May 25 2016.

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