Yeom, Jeonghun Kabir, Mohammad Humayun Lim, Byungho Ahn, Hee-Sung Kim, Seon-Young Lee, Cheolju 2024-01-20T03:03:49Z 2024-01-20T03:03:49Z 2021-09-04 2016-10-13 2045-2322 https://pubs.kist.re.kr/handle/201004/123564 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. English NATURE PUBLISHING GROUP DIFFERENTIAL MASS-SPECTROMETRY QUANTITATIVE-ANALYSIS SOMATIC MUTATION COMPLEX PEPTIDE PROTEOMICS QUANTIFICATION STRATEGIES ALIGNMENT MIXTURES DATABASE A proteogenomic approach for protein-level evidence of genomic variants in cancer cells Article 10.1038/srep35305 1 SCIENTIFIC REPORTS, v.6 SCIENTIFIC REPORTS 6 scie scopus 000385687800001 2-s2.0-84991491893 Multidisciplinary Sciences Science & Technology - Other Topics Article DIFFERENTIAL MASS-SPECTROMETRY QUANTITATIVE-ANALYSIS SOMATIC MUTATION COMPLEX PEPTIDE PROTEOMICS QUANTIFICATION STRATEGIES ALIGNMENT MIXTURES DATABASE