Project PXD002047

Dataset Belongs to:
CPTAC Consortium
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Project Protein Table
Project Peptide Table
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Summary

Title

CPTAC proteomic analysis of TCGA colon and rectal carcinomas using standard and customized databases, part 7

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 49400 no assay title provided (mzIdentML) 6606 27343 1317 10431 3052
2 49489 no assay title provided (mzIdentML) 8337 37409 1747 11808 3749
3 49481 no assay title provided (mzIdentML) 7148 31602 1509 11406 3287
4 49482 no assay title provided (mzIdentML) 7691 31295 1531 11236 3051
5 49483 no assay title provided (mzIdentML) 8388 30955 1669 11464 3279
6 49484 no assay title provided (mzIdentML) 8535 33133 1646 11678 3521
7 49409 no assay title provided (mzIdentML) 7812 30587 1626 11315 3531
8 49485 no assay title provided (mzIdentML) 6866 31952 1500 11312 3656
9 49486 no assay title provided (mzIdentML) 8125 39136 1745 11664 3870
10 49487 no assay title provided (mzIdentML) 7842 30661 1537 10577 3238