DOI: 10.25345/c53q0p
title: MassIVE MSV000084246 - Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer
title: &lt;a href='https://pdc.esacinc.com/pdc/browse/filters/study_name:TCGA_Ovarian_JHU_Glycoproteome|TCGA_Ovarian_JHU_Proteome|TCGA_Ovarian_PNNL_Proteome|TCGA_Ovarian_PNNL_Phosphoproteome_Velos_Qexatvive' target='_blank'&gt;Explore This Study at the NCI Proteomic Data Commons&lt;/a&gt;&lt;p&gt;&lt;a href='http://www.ncbi.nlm.nih.gov/pubmed/27372738' target='_blank'&gt;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.&lt;/a&gt;&lt;/p&gt;&lt;p&gt;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.&lt;/p&gt;&lt;p&gt;Information on the complete TCGA Ovarian Serous Cystadenocarcinoma (OV) cohort can be found &lt;a href='https://gdc-portal.nci.nih.gov/projects/TCGA-OV' target='_blank'&gt;here&lt;/a&gt;.&lt;br&gt;The Cancer Genome Atlas Research Network published on the Genomic characterization of the OV cohort in &lt;a href='http://www.ncbi.nlm.nih.gov/pubmed/21720365' target='_blank'&gt;Nature&lt;/a&gt; on June 30, 2011&lt;/p&gt;&lt;p&gt;Genomic data for the 174 TCGA samples used in the CPTAC Proteome study can be downloaded from&lt;a href="https://portal.gdc.cancer.gov/legacy-archive/search/f?filters=%7B%22op%22:%22and%22,%22content%22:%5B%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.program.name%22,%22value%22:%5B%22TCGA%22%5D%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:%5B%22TCGA-OV%22%5D%7D%7D%5D%7D" target="_blank"&gt;here&lt;/a&gt;.&lt;/p&gt;&lt;p&gt;Peptide-Spectrum-Matches and Protein Reports from the CPTAC Common Data Analysis Pipeline (CDAP) can be downloaded from&lt;a href="/cptac/s/S020" target="_blank"&gt;here&lt;/a&gt;.&lt;br&gt;&lt;/p&gt;&lt;br/&gt;&lt;br/&gt; &lt;ul&gt;&lt;li&gt;Dataset imported into MassIVE from &lt;a href="https://cptac-data-portal.georgetown.edu/cptac/s/S026"&gt;https://cptac-data-portal.georgetown.edu/cptac/s/S026&lt;/a&gt; on 08/28/19&lt;/li&gt;&lt;li&gt;Dataset source: &lt;a href="https://pdc.esacinc.com/pdc/browse/filters/study_name:TCGA_Ovarian_JHU_Glycoproteome|TCGA_Ovarian_JHU_Proteome|TCGA_Ovarian_PNNL_Proteome|TCGA_Ovarian_PNNL_Phosphoproteome_Velos_Qexatvive" target="_blank"&gt;https://pdc.esacinc.com/pdc/browse/filters/study_name:TCGA_Ovarian_JHU_Glycoproteome|TCGA_Ovarian_JHU_Proteome|TCGA_Ovarian_PNNL_Proteome|TCGA_Ovarian_PNNL_Phosphoproteome_Velos_Qexatvive&lt;/a&gt;&lt;/li&gt;&lt;/ul&gt;