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CPTAC Data Portal specifications


Unique identifier OMICS_08513
Name CPTAC Data Portal
Restrictions to use None
Maintained Yes


  • person_outline Than J. Edwards

Publication for CPTAC Data Portal

CPTAC Data Portal citations


Widespread Post transcriptional Attenuation of Genomic Copy Number Variation in Cancer

Cell Syst
PMCID: 5660600
PMID: 29032074
DOI: 10.1016/j.cels.2017.08.013

[…] Proteomics measurements at the protein level for the three tumour types analysed here were compiled from the CPTAC data portal () (accession date 2016/07/06) for the following publications: BRCA (), HGSC () and COREAD (). Transcriptomics RNA-seq raw counts were acquired from () (GSE62944) and processed using […]


In depth method assessments of differentially expressed protein detection for shotgun proteomics data with missing values

Sci Rep
PMCID: 5469784
PMID: 28611393
DOI: 10.1038/s41598-017-03650-8

[…] teomics Dynamic Range Standard, Sigma-Aldrich) were added to a constant yeast background (60 ng/µL). There were three replicates for every concentration. All the raw data were downloaded from https://cptac-data-portal.georgetown.edu/cptac/public?scope=Phase+I. MaxQuant (version was used for protein identification and label-free quantification. Using default settings, we searched against […]


Expression of Nestin associates with BRCA1 mutations, a basal like phenotype and aggressive breast cancer

Sci Rep
PMCID: 5430803
PMID: 28439082
DOI: 10.1038/s41598-017-00862-w

[…] ta (n = 103) were generated by the Clinical Proteomic Tumour Analysis Consortium (NCI/NIH) using iTRAQ (isobaric Tags for Relative and Absolute Quantification) protein quantification methods (https://cptac-data-portal.georgetown.edu).mRNA microarray data generated by the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) were included (n = 1992).From Gene Expression Omnibus (G […]


Integrative proteomic profiling of ovarian cancer cell lines reveals precursor cell associated proteins and functional status

Nat Commun
PMCID: 5007461
PMID: 27561551
DOI: 10.1038/ncomms12645

[…] obaric tag for relative and absolute quantification (ITRAQ)-based TCGA proteome raw files (PNNL study) generated by the Clinical Proteomic Tumor Analysis Consortium (NCI/NIH) were downloaded from the CPTAC data portal (https://cptac-data-portal.georgetown.edu/cptacPublic/) and analysed with MaxQuant. Logarithmic reporter intensities were normalized against the control reporter channel (channel 117 […]


Integrative Omics Analysis Reveals Post Transcriptionally Enhanced Protective Host Response in Colorectal Cancers with Microsatellite Instability

J Proteome Res
PMCID: 4782175
PMID: 26680540
DOI: 10.1021/acs.jproteome.5b00847

[…] -transformed spectral count data for these samples are available in Zhang et al. The primary data from LC-MS/MS and derived secondary data files can also be downloaded from the CPTAC website (https://cptac-data-portal.georgetown.edu/cptac/s/S022). We matched the proteomics and RNA-seq data with sample and gene names (HGNC name). Eighty-seven common samples and 3,764 common genes were used for the […]


Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts

J Proteome Res
PMCID: 4779376
PMID: 26653538
DOI: 10.1021/acs.jproteome.5b00859

[…] roduction, with Orbitrap measurement of fragment ions. Both [email protected] and [email protected] employed CID instead, measuring fragments in the quadrupole ion trap. All raw data files are available from https://cptac-data-portal.georgetown.edu/cptacPublic/ under the name CompRef. All files were subjected to quality assessment through the QuaMeter IDFree mode. The resulting tables are available as a Microsoft […]


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CPTAC Data Portal institution(s)
ESAC, Inc, Chinakville, MD, USA

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