Project PXD002046

Dataset Belongs to:
CPTAC Consortium
Download Project Files
Project Protein Table
Project Peptide Table
Visualize in PRIDE Inspector
Follow the next three steps to open your selected project or assay in PRIDE Inspector:

  • 1.

    Download, uncompress and open PRIDE Inspector
  • 2.

    Click in the magnifier on the left top corner, paste the project or assay that you would like to open in the search box, and hit search
  • 3.

    Click in the corresponding "Download" button to download the files and visualize them

Summary

Title

CPTAC proteomic analysis of TCGA colon and rectal carcinomas using standard and customized databases, part 6

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

Page 1 2 3 4 5 ... 15
Page size 10 20 50 100
Showing 1 - 10 of 150 results
# Accession Title Proteins Peptides Unique Peptides Spectra Identified Spectra View in Reactome
1 49343 no assay title provided (mzIdentML) 12093 37093 2678 12396 4295
2 49342 no assay title provided (mzIdentML) 12323 37874 2836 12153 4390
3 49345 no assay title provided (mzIdentML) 12055 38439 2728 11925 4261
4 49344 no assay title provided (mzIdentML) 11761 36145 2468 11798 3905
5 49341 no assay title provided (mzIdentML) 12811 41338 2844 12230 4464
6 49340 no assay title provided (mzIdentML) 12873 37110 2885 11885 4268
7 49291 no assay title provided (mzIdentML) 12115 37551 2780 11828 4425
8 49290 no assay title provided (mzIdentML) 12557 39996 2984 12379 4807
9 49293 no assay title provided (mzIdentML) 11819 39261 2670 11914 4203
10 49292 no assay title provided (mzIdentML) 12507 36633 2724 11346 4042