Project PXD002085

PRIDE Assigned Tags:
Biomedical Dataset
Dataset Belongs to:
CPTAC Consortium
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Project Peptide Table
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Summary

Title

CPTAC, TCGA Cancer Proteome Study of Colorectal Tissue: Proteome, VU, part 6

Description

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. Ninety-five TCGA tumor samples were used in this study.

Sample Processing Protocol

Analytical Sample Protocol - Alkylation: Iodoacetamide, Fractionation: Peptide IEF, Fractions: 15, Proteolysis: Trypsin, Starting Amount: 200 ug; Chromatography Protocol - Column Length: 11 cm, Column Type: C18, Gradient Length: 95 min, Injected: 1 ug, Inside Diameter: 100 um, Particle Size: 5 um; Mass Spectrometry Protocol - Dissociation: CID, Instrument: Thermo LTQ Orbitrap Velos, MS1 Resolution: 60000, Precursors: Top 8. See associated protocols and methods documents at https://cptac-data-portal.georgetown.edu.

Data Processing Protocol

Processed using the CPTAC Common Data Analysis Pipeline at NIST. Peptide identifications from MSGF+. Filtered at 1% FDR. See associated protocols and methods documents at https://cptac-data-portal.georgetown.edu.

Contact

Nathan Edwards, Georgetown University
Daniel C. Liebler, Ph.D., Vanderbilt University ( lab head )

Submission Date

20/04/2015

Publication Date

03/07/2015

Publication

    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 PubMed: 25043054

Assay

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# Accession Title Proteins Peptides Unique Peptides Spectra Identified Spectra View in Reactome
1 51379 no assay title provided (mzIdentML) 8480 31385 1888 14152 3354
2 51378 no assay title provided (mzIdentML) 8848 47192 2046 14440 3646
3 51373 no assay title provided (mzIdentML) 8298 28137 1928 14425 3149
4 51372 no assay title provided (mzIdentML) 9240 30762 1960 14629 3259
5 51371 no assay title provided (mzIdentML) 8650 27562 1889 14347 3107
6 51370 no assay title provided (mzIdentML) 8522 26474 1851 14600 2979
7 51377 no assay title provided (mzIdentML) 8780 26789 1888 14859 3113
8 51376 no assay title provided (mzIdentML) 8195 28575 1944 15036 3371
9 51375 no assay title provided (mzIdentML) 8587 31963 1977 14811 3381
10 51374 no assay title provided (mzIdentML) 8874 32007 2097 14738 3448