MassIVE MSV000084238

Partial Public PXD015905

Proteogenomic characterization of human colon and rectal cancer

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Description

Explore This Study at the NCI Proteomic Data Commons

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
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.

TCGA_VU_N95_Custom
The Custom assembly represents the same samples, the sequence database has been augmented with nonsynonymous sequence variants detected by TCGA.

TCGA_VU_N95-Normal_VU_N60
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.

TCGA_Colorectal_Cancer_proBAM_PSM_genome_mapping_files
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.

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

Normal colon epithelium sample mass spectrometry 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.

[doi:10.25345/C50W8H] [dataset license: Custom User License]

Keywords: CPTAC ; MassIVE.quant reviewed - Gold

Contact

Principal Investigators:
(in alphabetical order) 		Daniel C Liebler, Vanderbilt University, USA
Submitting User: cptac

Publications

Zhang B, Wang J, Wang X, Zhu J, Liu Q, Shi Z, Chambers MC, Zimmerman LJ, Shaddox KF, Kim S, Davies SR, Wang S, Wang P, Kinsinger CR, Rivers RC, Rodriguez H, Townsend RR, Ellis MJ, Carr SA, Tabb DL, Coffey RJ, Slebos RJ, Liebler DC, NCI CPTAC.
Proteogenomic characterization of human colon and rectal cancer.
Nature. 2014 Sep 18;513(7518):382-7. Epub 2014 Jul 20.

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

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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.

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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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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.

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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.