CPTAC, TCGA Cancer Proteome Study of Ovarian Tissue

Global proteome data have been acquired for 174 TCGA ovarian cancer tumor samples by 2 Proteome Characterization Centers (PCCs), Pacific Northwest National Laboratory (PNNL) and Johns Hopkins University (JHU). Both PCCs used iTRAQ (isobaric Tags for Relative and Absolute Quantification) protein quantification methods. Thirty- two of the 174 TCGA tumor samples were assayed at both sites yielding a total of 206 proteome characterizations. Glycoproteome (122 tumors) and phosphoproteome (69 tumors) analyses were also conducted, at JHU and PNNL respectively.

Information on the complete TCGA Ovarian Serous Cystadenocarcinoma (OV) cohort can be found here.
The Cancer Genome Atlas Research Network published on the Genomic characterization of the OV cohort in Nature on June 30, 2011

Genomic data for the 174 TCGA samples used in the CPTAC Proteome study can be downloaded from here.

Please include this attribution in publications:
“Data used in this publication were generated by the Clinical Proteomic Tumor Analysis Consortium (NCI/NIH).”

Biospecimens and Metadata Files

Clinical Data for CPTAC, TCGA Cancer Proteome Study of Ovarian Tissue
CPTAC, TCGA Ovarian Cancer iTRAQ Sample Mapping
Folder, File, and Sample Naming

Data Types Available for Download

(ALL): Selection of this box downloads all data in the row
(raw): The original mass spectrometry(MS) instrument files
(mzML): HUPO-PSI standard raw data files generated from the original MS instrument files
(PSM): Peptide-Spectrum Match data
(prot): Protein assembly data and protein relative abundance
(meta): Clinical data files, mapping of biospecimens to iTRAQ labels (where applicable), folder and file naming conventions
Checksum files are included in all downloads for verification.

Data Sets


Data set name

JHUZ Johns Hopkins University Hui Zhang, Ph.D.
PNNL Pacific Northwest National Laboratory Richard D. Smith, Ph.D.