Dataset Information

Lung cancer and Normal Lung Tissue LC-MS/MS

ABSTRACT: 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.

INSTRUMENT(S): LTQ Orbitrap, MS:1000031

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: None Listed

PROVIDER: MSV000083969 | MassIVE | Wed Jun 12 17:29:00 BST 2019

SECONDARY ACCESSION(S): PXD000603

REPOSITORIES: MassIVE

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Proteogenomic analysis of human chromosome 9-encoded genes from human samples and lung cancer tissues.

Ahn Jung-Mo JM Kim Min-Sik MS Kim Yong-In YI Jeong Seul-Ki SK Lee Hyoung-Joo HJ Lee Sun Hee SH Paik Young-Ki YK Pandey Akhilesh A Cho Je-Yoel JY

Journal of proteome research 20131206 1

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. Approximately 74.7% of the Chr 9 genes of the human genome were identified, which included approximately 28% of missing proteins (46 of 162) on Chr 9 compared with the list of missi ...[more]

PMID: 24274035

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