Deciphering the Dark Proteome: Use of the Testis and Characterization of Two Dark Proteins

J Proteome Res. 2018 Dec 7;17(12):4197-4210. doi: 10.1021/acs.jproteome.8b00387. Epub 2018 Aug 31.


For the C-HPP consortium, dark proteins include not only uPE1, but also missing proteins (MPs, PE2-4), smORFs, proteins from lncRNAs, and products from uncharacterized transcripts. Here, we investigated the expression of dark proteins in the human testis by combining public mRNA and protein expression data for several tissues and performing LC-MS/MS analysis of testis protein extracts. Most uncharacterized proteins are highly expressed in the testis. Thirty could be identified in our data set, of which two were selected for further analyses: (1) A0AOU1RQG5, a putative cancer/testis antigen specifically expressed in the testis, where it accumulates in the cytoplasm of elongated spermatids; and (2) PNMA6E, which is enriched in the testis, where it is found in the germ cell nuclei during most stages of spermatogenesis. Both proteins are coded on Chromosome X. Finally, we studied the expression of other dark proteins, uPE1 and MPs, in a series of human tissues. Most were highly expressed in the testis at both the mRNA and protein levels. The testis appears to be a relevant organ to study the dark proteome, which may have a function related to spermatogenesis and germ cell differentiation. The mass spectrometry proteomics data have been deposited with the ProteomeXchange Consortium under the data set identifier PXD009598.

Keywords: dark proteins; data mining; human proteome project; immunohistochemistry; missing proteins; testis; uPE1.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatography, Liquid
  • Data Mining
  • Humans
  • Immunohistochemistry
  • Male
  • Proteins / analysis
  • Proteome / chemistry*
  • Proteomics / methods
  • RNA, Messenger / analysis
  • Tandem Mass Spectrometry
  • Testis / chemistry*


  • Proteins
  • Proteome
  • RNA, Messenger