MassIVE MSV000086768

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CPTAC Breast Cancer Confirmatory Study

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Description

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."

' [doi:10.25345/C5QN43] [dataset license: Custom User License]

Keywords: CPTAC

Contact

Principal Investigators:
(in alphabetical order) 		Steven A. Carr, Broad Institute of MIT and Harvard, United States
Submitting User: ccms
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Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

Distinct replicate labels are counted across all files submitted in the "Metadata" category having a "BioReplicate" or "Replicate" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

The technical replicate count is defined as the maximum number of times any one distinct combination of condition and biological replicate was analyzed across all files submitted in the "Metadata" category. In the case of fractionated experiments, only the first fraction is considered.

"N/A" means no results of this type were submitted.
Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

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Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.