Project PXD002082

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 3

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

02/07/2015

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 50938 no assay title provided (mzIdentML) 9084 38038 2039 13895 4201
2 50892 no assay title provided (mzIdentML) 9159 38675 2128 13512 4297
3 50937 no assay title provided (mzIdentML) 8673 34739 2001 13397 3899
4 50893 no assay title provided (mzIdentML) 8504 32724 1725 12210 3160
5 50936 no assay title provided (mzIdentML) 8660 29654 1790 12205 3228
6 50890 no assay title provided (mzIdentML) 9574 31167 1940 13091 3526
7 50935 no assay title provided (mzIdentML) 8044 26788 1671 12126 2980
8 50891 no assay title provided (mzIdentML) 7398 26857 1619 11666 3034
9 50939 no assay title provided (mzIdentML) 8327 35351 1830 12336 3518
10 50898 no assay title provided (mzIdentML) 8302 34581 1865 12300 3255