Project PXD000603

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Biomedical Dataset
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Summary

Title

Lung cancer and Normal Lung Tissue LC-MS/MS

Description

The Chromosome-centric Human Proteome Project (C-HPP) was recently initiated as an international collaborative effort. Our team adopted chromosome 9 (Chr 9) and performed a bioinformatics and proteogenomic analysis to catalog Chr 9-encoded proteins from normal tissues, lung cancer cell lines and lung cancer tissues. TQ orbitrap, Orbitrap full MS scans were acquired from m/z 350 to 1500 at a resolution of 15 000 (at m/z 400). Parent ions were fragmented using the LTQ (isolation width of 2 m/z units) , with a maximum injection time of 100 ms combined with an AGC value of 1 x104 using three fragmentation modes such as collision-induced dissociation (CID) alone, the reagent ion source emission current, reagent ion electron energy, and reagent ion source chemical ionization pressure were set to 35 mA, 70 V, and 26 psi, respectively. Database : UniProt database (rel. 2012-06, 86,875 entries). Search software : MASCOT software (version 2.2.04). Database search criteria were as follows: taxonomy Homo sapiens, carboxyamidomethylated (+57 Da) at cysteine residues for fixed modifications, oxidized at methionine (+16 Da) residues for variable modi?cations, two maximum allowed missed cleavage, 10 ppm MS tolerance. Only peptides resulting from trypsin digestion were considered. PeptideProphet and ProteinProphet were used to estimate the false discovery rate (FDR). We identified proteins using two or more unique peptides with an FDR < 1% at the protein level.

Sample Processing Protocol

See details in reference(s) : 24274035

Data Processing Protocol

See details in reference(s) : 24274035

Contact

Je-Yoel Cho, Seoul National University

Submission Date

26/11/2013

Publication Date

18/03/2014

Publication

    Ahn JM, Kim MS, Kim YI, Jeong SK, Lee HJ, Lee SH, Paik YK, Pandey A, Cho JY. Proteogenomic analysis of human chromosome 9-encoded genes from human samples and lung cancer tissues. J Proteome Res. 2014 Jan 3;13(1):137-46 PubMed: 24274035

Assay

Showing 1 - 2 of 2 results
# Accession Title Proteins Peptides Unique Peptides Spectra Identified Spectra View in Reactome
1 32839 LC-MS/MS Analysis 2109 10354 2575 47536 4949
2 32840 LC-MS/MS 2622 12315 3070 44346 5649