PXD002613

PXD002613 is an original dataset announced via ProteomeXchange.

Title	Exome-based proteogenomics of HEK-293 human cell line: coding genomic variants identified at the level of shotgun proteome
Description	Genomic and proteomic data were integrated into the proteogenomic workflow to identify coding genomic variants of Human Embryonic Kidney 293 (HEK-293) standard cell line at the proteome level. Shotgun proteome data published by Geiger et al (2012) and obtained in this work for HEK-293 were searched against the customized genomic databased generated using exome data published by Lin et al (2014). 54 unique variants out of ~1,200 coding variants annotated in the exome were found at the proteome level. 27 of them were validated by two search engines, X!Tandem and Andromeda. 16 (60%) of those validated variants were confidently identified in both own and published proteome datasets. Some of the variants found belonged to widely known genomic polymorphisms originated from the germline, while others are more likely to result from somatic mutations. Notably, the peptide subsets identified by only one, or the other search engine were enriched by the sequences with miscleavages. This can be due to the large presence of false-positive hits in these subsets that is especially true for the subset of variant peptides. High-resolution mass-spectra of HEK-293 cell line were deposited to ProteomeXchange repository, project accession PXD002613.
HostingRepository	PRIDE
AnnounceDate	2016-07-22
AnnouncementXML	Submission_2016-07-22_09:41:35.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Irina Ilina
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2015-07-28 03:10:36	ID requested
⏵ 1	2016-07-22 09:41:36	announced

Lobas AA, Karpov DS, Kopylov AT, Solovyeva EM, Ivanov MV, Ilina IY, Lazarev VN, Kuznetsova KG, Ilgisonis EV, Zgoda VG, Gorshkov MV, Moshkovskii SA, Exome-based proteogenomics of HEK-293 human cell line: Coding genomic variants identified at the level of shotgun proteome. Proteomics, 16(14):1980-91(2016) [pubmed]

submitter keyword: Proteogenomics, HEK-293 cell line, Exome, Shotgun proteomics

Sergei Moshkovskii
contact affiliation	Laboratory of Medical Proteomics, Department of Personalized Medicine, Institute of Biomedical Chemistry
contact email	smosh@mail.ru
lab head
Irina Ilina
contact affiliation	IBMC
contact email	irinailina.ibmc@gmail.com
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2016/07/PXD002613

PRIDE project URI

• PRIDE
  1. PXD002613
     1. Label: PRIDE project
     2. Name: Exome-based proteogenomics of HEK-293 human cell line: coding genomic variants identified at the level of shotgun proteome