Project PXD002081

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 2

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

14/07/2015

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 50778 no assay title provided (mzIdentML) 8815 31172 1834 11872 3343
2 50775 no assay title provided (mzIdentML) 8904 30832 1911 12028 3385
3 50776 no assay title provided (mzIdentML) 8976 28878 1854 11469 3161
4 50773 no assay title provided (mzIdentML) 9213 31995 1944 11400 3398
5 50774 no assay title provided (mzIdentML) 10080 33026 2630 11741 3866
6 50817 no assay title provided (mzIdentML) 11553 36940 2963 12244 4109
7 50771 no assay title provided (mzIdentML) 11265 38210 2975 12230 4188
8 50816 no assay title provided (mzIdentML) 11672 37776 2986 12150 4189
9 50772 no assay title provided (mzIdentML) 11612 35564 2891 12074 4015
10 50815 no assay title provided (mzIdentML) 11452 35352 2954 12147 4101