A proteogenomic approach for protein-level evidence of genomic variants in cancer cells

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Title
A proteogenomic approach for protein-level evidence of genomic variants in cancer cells
Author(s)
J Yeom; M H Kabir; Byungho Lim; H S Ahn; Seon-Young Kim; C Lee
Bibliographic Citation
Scientific Reports, vol. 6, pp. 35305-35305
Publication Year
2016
Abstract
Variations in protein coding sequence may sometimes play important roles in cancer development. However, since variants may not express into proteins due to various cellular quality control systems, it is important to get protein-level evidence of the genomic variations. We present a proteogenomic strategy getting protein-level evidence of genomic variants, which we call sequential targeted LC-MS/MS based on prediction of peptide pI and Retention time (STaLPIR). Our approach shows improved peptide identification, and has the potential for the unbiased analysis of variant sequence as well as corresponding reference sequence. Integrated analysis of DNA, mRNA and protein suggests that protein expression level of the nonsynonymous variant is regulated either before or after translation, according to influence of the variant on protein function. In conclusion, our data provides an excellent approach getting direct evidence for the expression of variant protein forms from genome sequence data.
ISSN
2045-2322
Publisher
Springer-Nature Pub Group
DOI
http://dx.doi.org/10.1038/srep35305
Type
Article
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1. Journal Articles > Journal Articles
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