Project PXD002050

Dataset Belongs to:
CPTAC Consortium
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Project Peptide Table
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Summary

Title

CPTAC proteomic analysis of TCGA colon and rectal carcinomas using standard and customized databases, 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

Peptide identification employed the RefSeq Human protein sequence database using three different database search engines: myrimatch, pepitome and MS-GF+. Spectral identification files were converted to IDPicker SQLite databases (idpDB) using IDPicker 3. The resulting files were used for final protein assembly providing the minimal list of proteins that could explain the available peptides identified. Initially, spectrum-to-peptide match stringency was set at 0.1% FDR with a minimum of 2 distinct peptides identified per protein. The dataset was limited to the 7526 protein groups identified while spectral counts were increased by relaxing the spectrum-to-peptide match FDR to 1%. Assembly at the gene level resulted in the identification of 7211 gene groups for the full dataset. Variant peptide sequences were identified by separate database searches using data from RNA-seq of the individual carcinomas using the R package customProDB. A total of 796 single amino acid variants were identified.

Contact

Robbert Slebos, Vanderbilt University
Daniel C. Liebler, Ph.D., Vanderbilt University ( lab head )

Submission Date

03/06/2015

Publication Date

13/06/2015

Publication

    Slebos RJ, Wang X, Wang X, Zhang B, Tabb DL, Liebler DC. Proteomic analysis of colon and rectal carcinoma using standard and customized databases. Sci Data. 2015 Jun 23;2:150022. eCollection 2015 PubMed: 26110064

Assay

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Showing 1 - 10 of 105 results
# Accession Title Proteins Peptides Unique Peptides Spectra Identified Spectra View in Reactome
1 49909 no assay title provided (mzIdentML) 10056 43236 2793 11779 4461
2 49908 no assay title provided (mzIdentML) 10342 46007 2805 11864 4473
3 49907 no assay title provided (mzIdentML) 10632 48433 2814 12053 4669
4 49872 no assay title provided (mzIdentML) 9559 45175 2653 11875 4436
5 49906 no assay title provided (mzIdentML) 10160 43901 2859 11832 4424
6 49873 no assay title provided (mzIdentML) 9987 45579 2743 12002 4559
7 49870 no assay title provided (mzIdentML) 9131 45630 2741 11753 4392
8 49905 no assay title provided (mzIdentML) 9725 43108 2749 11354 4294
9 49871 no assay title provided (mzIdentML) 10809 47426 2999 11461 4717
10 49904 no assay title provided (mzIdentML) 11311 44715 2773 11136 4285