Project PXD002049

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 9

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

13/04/2015

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 150 results
# Accession Title Proteins Peptides Unique Peptides Spectra Identified Spectra View in Reactome
1 49678 no assay title provided (mzIdentML) 11065 42733 2325 13778 4821
2 49679 no assay title provided (mzIdentML) 11206 46131 2557 14319 5219
3 49676 no assay title provided (mzIdentML) 11449 44849 2396 13936 4777
4 49677 no assay title provided (mzIdentML) 10755 43276 2278 13599 4476
5 49779 no assay title provided (mzIdentML) 11356 40840 2335 13455 4509
6 49777 no assay title provided (mzIdentML) 10965 37868 2270 13447 4337
7 49778 no assay title provided (mzIdentML) 10501 35542 2267 13173 4293
8 49775 no assay title provided (mzIdentML) 10321 37687 2189 12977 4277
9 49776 no assay title provided (mzIdentML) 10474 40032 2214 13462 4357
10 49807 no assay title provided (mzIdentML) 10919 34176 2128 11985 3902