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Exome-based proteogenomics of HEK-293 human cell line: coding genomic variants identified at the level of shotgun proteome

ABSTRACT: 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.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Early Embryonic Cell, Kidney

SUBMITTER: Irina Ilina

LAB HEAD: Sergei Moshkovskii

PROVIDER: PXD002613 | Pride | 2016-07-22

REPOSITORIES: pride

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Exome-based proteogenomics of HEK-293 human cell line: Coding genomic variants identified at the level of shotgun proteome.

Lobas Anna A AA Karpov Dmitry S DS Kopylov Arthur T AT Solovyeva Elizaveta M EM Ivanov Mark V MV Ilina Irina Y IY Lazarev Vassily N VN Kuznetsova Ksenia G KG Ilgisonis Ekaterina V EV Zgoda Victor G VG Gorshkov Mikhail V MV Moshkovskii Sergei A SA

Proteomics 20160621 14

Genomic and proteomic data were integrated into the proteogenomic workflow to identify coding genomic variants of Human Embryonic Kidney 293 (HEK-293) cell line at the proteome level. Shotgun proteome data published by Geiger et al. (2012), Chick et al. (2015), and obtained in this work for HEK-293 were searched against the customized genomic database generated using exome data published by Lin et al. (2014). Overall, 112 unique variants were identified at the proteome level out of ∼1200 coding ...[more]

PMID: 27233776

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