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.

To provide a detailed analysis of the molecular components and underlying mechanisms associated with ovarian cancer, we performed a comprehensive mass-spectrometry-based proteomic characterization of 174 ovarian tumors previously analyzed by The Cancer Genome Atlas (TCGA), of which 169 were high-grade serous carcinomas (HGSCs). Integrating our proteomic measurements with the genomic data yielded a number of insights into disease, such as how different copy-number alternations influence the proteome, the proteins associated with chromosomal instability, the sets of signaling pathways that diverse genome rearrangements converge on, and the ones most associated with short overall survival. Specific protein acetylations associated with homologous recombination deficiency suggest a potential means for stratifying patients for therapy. In addition to providing a valuable resource, these findings provide a view of how the somatic genome drives the cancer proteome and associations between protein and post-translational modification levels and clinical outcomes in HGSC.

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.

Peptide-Spectrum-Matches and Protein Reports from the CPTAC Common Data Analysis Pipeline (CDAP) 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 TCGA Ovarian Tumor Tissue Samples

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 or TMT10 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.