CPTAC, TCGA Cancer Proteome Study of Colorectal Tissue


The goal of the CPTAC, TCGA Cancer Proteome Study of Colorectal Tissue is to analyze the proteomes of TCGA tumor samples that have been comprehensively characterized by molecular methods (Cancer Genome Atlas Network, Nature 2012).

Ninety-five TCGA tumor samples were used in this study from 90 patients, with 5 samples representing different portions from the same tumor. The samples originated from two TCGA cohorts: 64 are from Colon Adenocarcinoma (COAD) samples and 31 are from the Rectum Adenocarcinoma (READ) collection. The primary data from the liquid chromatography-tandem mass spectrometry (LC-MS/MS) global proteomic profiling of each tumor sample is associated with a data set in the table below. This work was accomplished by the Proteome Characterization Center (PCC) at Vanderbilt University led by Dr. Daniel C. Liebler. Clinical data files contain both the human readable TCGA bar codes and the UUIDs for each sample.

Complete Data Analysis from Vanderbilt University as published in Nature (Zhang, B., et al., Nature (2014) doi:10.1038/nature13438 Published online) is available here.

Data available on this study page (peptide spectrum matches and protein reports) are from the CPTAC Common Data Analysis Pipeline.

COAD tumor sample genomic data can be downloaded from here.
READ tumor sample genomic data can be downloaded from here.

Please include this attribution in publications:
“Data used in this publication were generated by the Clinical Proteomic Tumor Analysis Consortium (NCI/NIH).”

Biospecimens


Clinical Data for CPTAC, TCGA Cancer Proteome Study of Colorectal Tissue

Data Types Available for Download


(ALL): Selection of this box downloads all data in the row
(raw): The original mass spectrometry(MS) instrument files
(mzML): HUPO-PSI standard raw data files generated from the original MS instrument files
(PSM): Peptide-Spectrum Match data
(prot): Protein assembly data and protein relative abundance
(meta): Clinical data files, mapping of biospecimens to iTRAQ labels or TMT10 labels (where applicable), folder and file naming conventions
Checksum files are included in all downloads for verification.

Data Sets


DOWNLOAD

Data set name
All
raw
mzML
PSM
prot
meta
Size

VU Vanderbilt University Daniel C. Liebler, Ph.D.