Project PXD002083

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 4

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

28/07/2015

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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Showing 1 - 10 of 150 results
# Accession Title Proteins Peptides Unique Peptides Spectra Identified Spectra View in Reactome
1 50995 no assay title provided (mzIdentML) 8911 24119 1994 10820 2808
2 50996 no assay title provided (mzIdentML) 10010 25956 2196 10666 2934
3 50993 no assay title provided (mzIdentML) 10290 27700 2292 10823 3072
4 50994 no assay title provided (mzIdentML) 10417 25538 2156 10538 2841
5 51002 no assay title provided (mzIdentML) 9675 22572 1992 10598 2663
6 50999 no assay title provided (mzIdentML) 9274 23286 2027 10652 2720
7 51003 no assay title provided (mzIdentML) 8887 22901 1909 10613 2583
8 51000 no assay title provided (mzIdentML) 9930 24415 2157 10448 2877
9 50997 no assay title provided (mzIdentML) 9893 24654 2123 10413 2850
10 51001 no assay title provided (mzIdentML) 10090 24618 2174 10028 2875