Why Are the Correlations between mRNA and Protein Levels so Low among the 275 Predicted Protein-Coding Genes on Human Chromosome 18?

J Proteome Res. 2017 Dec 1;16(12):4311-4318. doi: 10.1021/acs.jproteome.7b00348. Epub 2017 Oct 27.


In this work targeted (selected reaction monitoring, SRM, PASSEL: PASS00697) and panoramic (shotgun LC-MS/MS, PRIDE: PXD00244) mass-spectrometric methods as well as transcriptomic analysis of the same samples using RNA-Seq and PCR methods (SRA experiment IDs: SRX341198, SRX267708, SRX395473, SRX390071) were applied for quantification of chromosome 18 encoded transcripts and proteins in human liver and HepG2 cells. The obtained data was used for the estimation of quantitative mRNA-protein ratios for the 275 genes of the selected chromosome in the selected tissues. The impact of methodological limitations of existing analytical proteomic methods on gene-specific mRNA-protein ratios and possible ways of overcoming these limitations for detection of missing proteins are also discussed.

Keywords: Human Proteome Project; analytical sensitivity; human chromosome 18; limit of detection; mRNA sequencing; proteome; quantitative PCR; selected reaction monitoring; transcriptome.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosomes, Human, Pair 18 / genetics*
  • Hep G2 Cells
  • Humans
  • Liver / metabolism
  • Proteins / analysis*
  • Proteins / genetics
  • Proteomics / methods
  • RNA, Messenger / analysis*
  • Transcriptome


  • Proteins
  • RNA, Messenger