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PXD000603

PXD000603 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleLung cancer and Normal Lung Tissue LC-MS/MS
DescriptionThe 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.
HostingRepositoryPRIDE
AnnounceDate2014-07-24
AnnouncementXMLSubmission_2014-07-24_03:49:03.xml
DigitalObjectIdentifierhttp://dx.doi.org/10.6019/PXD000603
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterJe-Yoel Cho
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListdeamidated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
InstrumentLTQ Orbitrap; instrument model: LTQ Orbitrap
Dataset History
RevisionDatetimeStatusChangeLog Entry
02013-11-26 01:16:42ID requested
12014-03-18 04:50:23announced
22014-07-24 03:49:04announcedUpdated project metadata.
Publication List
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, 13(1):137-46(2014) [pubmed]
Keyword List
ProteomeXchange project tag: Chromosome-centric Human Proteome Project (C-HPP), Human Proteome Project
curator keyword: Biomedical
submitter keyword: Lung cancer, Normal Lung Tissue, LC-MS/MS
Contact List
Je-Yoel Cho
contact affiliationCollege of Veterinary Medicine
contact emailjeycho@snu.ac.kr
dataset submitter
Full Dataset Link List
Dataset FTP location
PRIDE project URI
Repository Record List
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