title: A proteogenomic approach for protein-level evidence of genomic variants in cancer cells.
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.
authors.affiliation: Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea.|Department of Biological Chemistry, Korea University of Science and Technology, Daejeon 34113 Republic of Korea.
authors.forename: Jeonghun
authors.initials: J
authors.lastname: Yeom
authors.affiliation: Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea.
authors.forename: Mohammad Humayun
authors.initials: MH
authors.lastname: Kabir
authors.affiliation: Genome Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea.
authors.forename: Byungho
authors.initials: B
authors.lastname: Lim
authors.affiliation: Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea.|Department of Biological Chemistry, Korea University of Science and Technology, Daejeon 34113 Republic of Korea.
authors.forename: Hee-Sung
authors.initials: HS
authors.lastname: Ahn
authors.affiliation: Genome Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea.|Department of Functional Genomics, Korea University of Science and Technology, Daejeon 34113, Republic of Korea.
authors.forename: Seon-Young
authors.initials: SY
authors.lastname: Kim
authors.affiliation: Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea.|Department of Biological Chemistry, Korea University of Science and Technology, Daejeon 34113 Republic of Korea.
authors.forename: Cheolju
authors.initials: C
authors.lastname: Lee
mesh_terms: D045744:Cell Line, Tumor; D002853:Chromatography, Liquid; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D059472:Exome; D014644:Genetic Variation; D006801:Humans; D009154:Mutation; D010455:Peptides / Q000737:chemistry; D011506:Proteins / Q000235:genetics; D000071696:Proteogenomics / Q000379:methods*; D020543:Proteome; D017423:Sequence Analysis, RNA; D013274:Stomach Neoplasms / Q000235:genetics* / Q000378:metabolism*; D053719:Tandem Mass Spectrometry; D059467:Transcriptome
chemical_list: D010455:Peptides; D011506:Proteins; D020543:Proteome