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CPTAC Breast Cancer Confirmatory Study

ABSTRACT:

Tissue for this CPTAC study was collected and characterized for a confirmatory cohort of 125 individuals with breast cancer. Quantitative mass-spectrometry-based proteomic, phosphoproteomic, and acetylome analyses were performed on breast tumors (125 participants) and adjacent normal breast tissue (18 participants). The analyses of this CPTAC cohort were conducted in order to more extensively characterize the proteogenomic landscape of breast cancer initially described in the publication by Mertins et al., (Nature 2016). Data were generated with TMT10plex quantification and each 10-plex experiment contained a common reference sample composed of a pooled mixture of 40 tumor samples. There are 17 global proteomic 10-plex datasets each with 25 fractions, 17 phosphoproteomic 10-plex datasets each with 13 fractions, and 17 acetylome 10-plex datasets each with 6 fractions. Raw LC-MS/MS (level 1 data) provided below are from investigators at the Proteome Characterization Center located at the Broad Institute of MIT and Harvard. Raw data were processed through the CPTAC Common Data Analysis Pipeline (CDAP) to produce peptide spectrum match reports (level 2 data) and protein summary reports (level 3 data), which are also provided below.

TMT phosphoproteome data were generated twice for plex #2 ,02CPTAC_BCProspective_Phosphoproteome_BI. The first replicate (20160928) had an uncharacteristically low phosphopeptide enrichment rate of 72%, typical values are > 90%. Hence, the IMAC flow thru was re-enriched to generate a second dataset (20170303). However, the second replicate yielded only 60% as many phosphopeptides and the phospho-enrichment rate was worse, 62%. Consequently, only the "20160928" dataset will be used in the final analyses, the second dataset (20170303) is labeled "deprecated."

Dataset imported into MassIVE from https://cptac-data-portal.georgetown.edu/study-summary/S039 on 01/25/21

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Steven A. Carr

PROVIDER: MSV000086768 | MassIVE | Tue Jan 26 10:50:00 GMT 2021

REPOSITORIES: MassIVE

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CPTAC Breast Cancer Confirmatory Study

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