CPTAC Cancer Proteome Confirmatory Colon Study

Explore This Study at the NCI Proteomic Data Commons

One hundred and four colon tumor samples were analyzed by two proteome characterization centers, Vanderbilt University (VUMC) and Pacific Northwest National Laboratory (PNNL). One hundred tumors were investigated by label-free global proteomic profiling at VUMC and 97 tumors were assayed with TMT10plex isobaric labeling quantification. Ninety-three tumor samples were analyzed by both methods.

One hundred normal colon tissue samples were evaluated in the TMT10 plex, with 96 normal samples paired with tumors samples from the same participant. The 4 remaining normal colon tissue samples from the PNNL data set pair with 4 tumor tissue samples assayed by VUMC. In total, these data include tumor and normal global proteomic profiling from 100 individuals.

In addition to the global proteome data, phosphoproteome analyses on 197 samples were performed (97 tumor and 100 normal tissue samples).

This data release includes raw mass spectrometry data files, along with peptide-spectrum match files and protein summary reports from the CPTAC Common Data Analysis Pipeline (CDAP).
Genomic data from this study are available at the Sequence Read Archive (SRA), BioProject ID: PRJNA514017

The total amount of data is 1.1 TB

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


CPTAC Colon Cancer Prospective Collection Biospecimens
CPTAC Colon Cancer Prospective Collection Clinical Data
CPTAC Colon Cancer Prospective Collection 1 Year Follow-up Clinical Data

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


Data set name

PNNL Pacific Northwest National Laboratory Richard D. Smith, Ph.D.
VU Vanderbilt University Daniel C. Liebler, Ph.D.