Systematic Analyses of the Transcriptome, Translatome, and Proteome Provide a Global View and Potential Strategy for the C‑HPP

To
estimate the potential of the state-of-the-art proteomics technologies
on full coverage of the encoding gene products, the Chinese Human
Chromosome Proteome Consortium (CCPC) applied a multiomics strategy
to systematically analyze the transciptome, translatome, and proteome
of the same cultured hepatoma cells with varied metastatic potential
qualitatively and quantitatively. The results provide a global view
of gene expression profiles. The 9064 identified high confident proteins
covered 50.2% of all gene products in the translatome. Those proteins
with function of adhesion, development, reproduction, and so on are
low abundant in transcriptome and translatome but absent in proteome.
Taking the translatome as the background of protein expression, we
found that the protein abundance plays a decisive role and hydrophobicity
has a greater influence than molecular weight and isoelectric point
on protein detectability. Thus, the enrichment strategy used for low-abundant
transcription factors helped to identify missing proteins. In addition,
those peptides with single amino acid polymorphisms played a significant role for the disease research, although they might negligibly contribute to new protein identification. The proteome raw and metadata of proteome
were collected using the iProX submission system and submitted to ProteomeXchange
(PXD000529, PXD000533, and PXD000535). All detailed information in
this study can be accessed from the Chinese Chromosome-Centric Human
Proteome Database.