Project PXD002089

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 10

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 51876 no assay title provided (mzIdentML) 9507 27581 1878 12535 3192
2 51875 no assay title provided (mzIdentML) 9493 34209 1885 12719 3366
3 51874 no assay title provided (mzIdentML) 9194 31336 1827 12721 3465
4 51873 no assay title provided (mzIdentML) 9642 28601 1906 12176 3178
5 51879 no assay title provided (mzIdentML) 9516 26953 1952 12546 3302
6 51878 no assay title provided (mzIdentML) 8041 26360 1761 12726 3122
7 51877 no assay title provided (mzIdentML) 8731 32151 1817 12758 3224
8 51872 no assay title provided (mzIdentML) 9469 32651 2038 12813 3556
9 51871 no assay title provided (mzIdentML) 9685 28829 1967 11771 3328
10 51870 no assay title provided (mzIdentML) 9498 28159 1954 11405 3192