Proteogenomic Analysis of Human Chromosome 9‑Encoded Genes from Human Samples and Lung Cancer Tissues

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.