Proteogenomic analysis of human chromosome 9-encoded genes from human samples and lung cancer tissues

Jung Mo Ahn, Min Sik Kim, Yong In Kim, Seul Ki Jeong, Hyoung Joo Lee, Sun Hee Lee, Young Ki Paik, Akhilesh Pandey, Je Yoel Cho

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Abstract

The Chromosome-centric Human Proteome Project (C-HPP) was recently initiated as an international collaborative effort. Our team adopted chromosome 9 (Chr 9) and performed a bioinformatics and proteogenomic analysis to catalog Chr 9-encoded proteins from normal tissues, lung cancer cell lines, and lung cancer tissues. Approximately 74.7% of the Chr 9 genes of the human genome were identified, which included approximately 28% of missing proteins (46 of 162) on Chr 9 compared with the list of missing proteins from the neXtProt Master Table (2013-09). In addition, we performed a comparative proteomics analysis between normal lung and lung cancer tissues. On the basis of the data analysis, 15 proteins from Chr 9 were detected only in lung cancer tissues. Finally, we conducted a proteogenomic analysis to discover Chr 9-residing single nucleotide polymorphisms (SNP) and mutations described in the COSMIC cancer mutation database. We identified 21 SNPs and four mutations containing peptides on Chr 9 from normal human cells/tissues and lung cancer cell lines, respectively. In summary, this study provides valuable information of the human proteome for the scientific community as part of C-HPP. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD000603.

Original languageEnglish
Pages (from-to)137-146
Number of pages10
JournalJournal of Proteome Research
Volume13
Issue number1
DOIs
Publication statusPublished - 2014 Jan 3

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All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Chemistry(all)

Cite this

Ahn, J. M., Kim, M. S., Kim, Y. I., Jeong, S. K., Lee, H. J., Lee, S. H., Paik, Y. K., Pandey, A., & Cho, J. Y. (2014). Proteogenomic analysis of human chromosome 9-encoded genes from human samples and lung cancer tissues. Journal of Proteome Research, 13(1), 137-146. https://doi.org/10.1021/pr400792p