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Study dataset

CPTAC

Ovarian HGSOC Proteogenomics

Proteomics and PTM profiles of ~83 TCGA tumors and 25 normal fallopian tubes.

Listed Apr 24, 2026

  • Proteomic
  • Genomic
  • Ovarian

Overview

Overview: A flagship proteogenomic study from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) that layered deep mass-spectrometry-based proteomics and post-translational modification (PTM) profiling on top of existing TCGA genomic data from high-grade serous ovarian carcinoma (HGSC).

Key findings:

  • Integration of proteomics with genomics revealed how copy-number alterations drive the cancer proteome, identified proteins associated with chromosomal instability, and showed which signaling pathways diverse genomic rearrangements converge on.
  • Specific protein acetylation signatures were associated with homologous recombination deficiency, suggesting a potential approach for stratifying patients for HRD-targeted therapies.

Notes

CPTAC3 ovarian dataset provides even deeper proteomics. PDC is primary archive for mass-spec files.

Inside the dataset

  • Comprehensive mass-spectrometry-based proteomics

    on 174 ovarian tumors previously characterized by TCGA, of which 169 were HGSCs — generating protein abundance measurements across the cohort.

  • Existing TCGA genomic data

    (somatic mutations, copy-number alterations, gene expression, DNA methylation) integrated with the new proteomic layer.

  • Post-translational modification profiling

    , including protein acetylation data, which revealed patterns associated with homologous recombination deficiency and potential utility for patient stratification.

  • Phosphoproteomic data

    , enabling analysis of signaling pathway activity across tumors.

  • Clinical outcome data

    (overall survival), used to identify proteins and PTM levels associated with prognosis.

Publications