Dataset Information
Proteogenomic characterization of human colon and rectal cancer
Ontology highlight
ABSTRACT: Zhang, B., et al., Nature (2014) doi:10.1038/nature13438 Published online Proteomes of colon and rectal tumors previously characterized by the Cancer Genome Atlas (TCGA) were analyzed along with integrated proteogenomic analyses. 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. Three protein assemblies are provided from different protein database searches. TCGA_VU_N95 TCGA_VU_N95_Custom TCGA_VU_N95-Normal_VU_N60 TCGA_Colorectal_Cancer_proBAM_PSM_genome_mapping_files COAD tumor sample genomic data can be downloaded from here. Normal colon epithelium sample mass spectrometry data can be downloaded from here.
This assembly reflects the 95 TCGA samples for 90 tumors, spanning three search engines (MS-GF+, MyriMatch, and Pepitome), employing a standard RefSeq database and NIST spectral library.
The Custom assembly represents the same samples, the sequence database has been augmented with nonsynonymous sequence variants detected by TCGA.
The third assembly contains the searches of the 95 TCGA samples employed in the first assembly alongside the 60 normal colons analyzed by Vanderbilt University as a control, employing the same three search engines, a standard RefSeq database, and a NIST spectral library.
Peptide spectrum matches from the TCGA_VU_N95_Custom IDPicker3 protein assembly were converted to protein BAM (proBAM) format for visualization, available in the metadata folder below.
READ tumor sample genomic data can be downloaded from here.
Mass spectrometry data for comparison and reference (CompRef) sample standards run with this study can be downloaded from here.
Peptide-Spectrum-Matches and Protein Reports from the CPTAC Common Data Analysis Pipeline (CDAP) can be downloaded from here.
Network analysis of this study can be viewed at the NetGestalt CRC Portal here.
This work was accomplished by the Proteome Characterization Center (PCC) at Vanderbilt University led by Dr. Daniel C. Liebler.
INSTRUMENT(S): LTQ Orbitrap Velos
ORGANISM(S): Homo Sapiens (ncbitaxon:9606)
SUBMITTER: 
Daniel C Liebler
PROVIDER: MSV000084238 | MassIVE | Mon Aug 26 14:03:00 BST 2019
SECONDARY ACCESSION(S): PXD015905
REPOSITORIES: MassIVE
Publications
Proteogenomic characterization of human colon and rectal cancer.
Nature 20140720 7518
Extensive genomic characterization of human cancers presents the problem of inference from genomic abnormalities to cancer phenotypes. To address this problem, we analysed proteomes of colon and rectal tumours characterized previously by The Cancer Genome Atlas (TCGA) and perform integrated proteogenomic analyses. Somatic variants displayed reduced protein abundance compared to germline variants. Messenger RNA transcript abundance did not reliably predict protein abundance differences between tu ...[more]
