Tissue-Based Proteogenomics Reveals that Human Testis Endows Plentiful Missing Proteins

J Proteome Res. 2015 Sep 4;14(9):3583-94. doi: 10.1021/acs.jproteome.5b00435.


Investigations of missing proteins (MPs) are being endorsed by many bioanalytical strategies. We proposed that proteogenomics of testis tissue was a feasible approach to identify more MPs because testis tissues have higher gene expression levels. Here we combined proteomics and transcriptomics to survey gene expression in human testis tissues from three post-mortem individuals. Proteins were extracted and separated with glycine- and tricine-SDS-PAGE. A total of 9597 protein groups were identified; of these, 166 protein groups were listed as MPs, including 138 groups (83.1%) with transcriptional evidence. A total of 2948 proteins are designated as MPs, and 5.6% of these were identified in this study. The high incidence of MPs in testis tissue indicates that this is a rich resource for MPs. Functional category analysis revealed that the biological processes that testis MPs are mainly involved in are sexual reproduction and spermatogenesis. Some of the MPs are potentially involved in tumorgenesis in other tissues. Therefore, this proteogenomics analysis of individual testis tissues provides convincing evidence of the discovery of MPs. All mass spectrometry data from this study have been deposited in the ProteomeXchange (data set identifier PXD002179).

Keywords: Chromosome-Centric Human Proteome Project; individual; missing proteins; proteome; testis; transcriptome.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatography, Liquid
  • Electrophoresis, Polyacrylamide Gel
  • Genomics*
  • Humans
  • Male
  • Proteins / isolation & purification
  • Proteins / metabolism*
  • Proteomics*
  • Sequence Analysis, RNA
  • Tandem Mass Spectrometry
  • Testis / metabolism*
  • Transcriptome


  • Proteins