Project PXD002048

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 8

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

12/06/2015

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 49542 no assay title provided (mzIdentML) 11061 45735 2582 14059 4849
2 49543 no assay title provided (mzIdentML) 11142 45617 2685 14136 5067
3 49540 no assay title provided (mzIdentML) 11116 43027 2720 13972 4852
4 49541 no assay title provided (mzIdentML) 11352 49138 2587 13904 4636
5 49549 no assay title provided (mzIdentML) 11211 43228 2492 13601 4402
6 49548 no assay title provided (mzIdentML) 11299 42611 2580 14085 4686
7 49547 no assay title provided (mzIdentML) 10397 43574 2485 14675 4728
8 49546 no assay title provided (mzIdentML) 10903 44429 2701 13713 4996
9 49545 no assay title provided (mzIdentML) 11088 61011 2835 14888 5676
10 49544 no assay title provided (mzIdentML) 11603 54511 3022 14270 5537