CPTAC, TCGA Ovarian Cancer Proteome Study Comparison and Reference Samples (CompRef)

Comparison and Reference (CompRef) Samples, initially characterized in the System Suitability Study, were analyzed along with the TCGA Ovarian Cancer tumor samples. Pacific Northwest National Laboratory conducted iTRAQ experiments that included proteome (5 Data sets) and phosphoproteome (4 Data sets) interrogation of both the P5 (basal) and P6 (luminal) human-in-mouse xenograft breast carcinoma pooled samples. Johns Hopkins University performed 6 iTRAQ proteome experiments. The CompRef experiments were intercalated between the TCGA Ovarian Cancer experiments to monitor the consistency of laboratory protocols and mass spectrometry instrument performance.

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


P5: human-in-mouse xenograft pool breast carcinoma WHIM2 (Basal) P6: human-in-mouse xenograft pool breast carcinoma WHIM16 (Luminal)

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.