Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes

Research output: Contribution to journalArticle


The nematode Caenorhabditis elegans is a popular model system in genetics, not least because a majority of human disease genes are conserved in C. elegans. To generate a comprehensive inventory of its expressed proteome, we performed extensive shotgun proteomics and identified more than half of all predicted C. elegans proteins. This allowed us to confirm and extend genome annotations, characterize the role of operons in C. elegans, and semiquantitatively infer abundance levels for thousands of proteins. Furthermore, for the first time to our knowledge, we were able to compare two animal proteomes (C. elegans and Drosophila melanogaster). We found that the abundances of orthologous proteins in metazoans correlate remarkably well, better than protein abundance versus transcript abundance within each organism or transcript abundances across organisms; this suggests that changes in transcript abundance may have been partially offset during evolution by opposing changes in protein abundance.


  • Sabine P Schrimpf
  • Manuel Weiss
  • Lukas Reiter
  • Christian H. Ahrens
  • Marko Jovanovic
  • Johan Malmström
  • Erich Brunner
  • Sonali Mohanty
  • Martin J Lercher
  • Peter E Hunziker
  • Ruedi Aebersold
  • Christian von Mering
  • Michael O Hengartner
External organisations
  • ETH Zürich
Research areas and keywords


  • Animals, Caenorhabditis elegans, Caenorhabditis elegans Proteins, Drosophila Proteins, Drosophila melanogaster, Gene Duplication, Genome, Operon, Proteome, Proteomics, Sequence Homology, Amino Acid, Comparative Study, Journal Article, Research Support, Non-U.S. Gov't
Original languageEnglish
Article numbere48
JournalPLoS Biology
Issue number3
Publication statusPublished - 2009 Mar 3
Publication categoryResearch
Externally publishedYes