NeuCode Labeling in Nematodes: Proteomic and Phosphoproteomic Impact of Ascaroside Treatment in Caenorhabditis elegans

Mol Cell Proteomics. 2015 Nov;14(11):2922-35. doi: 10.1074/mcp.M115.049684. Epub 2015 Sep 21.


The nematode Caenorhabditis elegans is an important model organism for biomedical research. We previously described NeuCode stable isotope labeling by amino acids in cell culture (SILAC), a method for accurate proteome quantification with potential for multiplexing beyond the limits of traditional stable isotope labeling by amino acids in cell culture. Here we apply NeuCode SILAC to profile the proteomic and phosphoproteomic response of C. elegans to two potent members of the ascaroside family of nematode pheromones. By consuming labeled E. coli as part of their diet, C. elegans nematodes quickly and easily incorporate the NeuCode heavy lysine isotopologues by the young adult stage. Using this approach, we report, at high confidence, one of the largest proteomic and phosphoproteomic data sets to date in C. elegans: 6596 proteins at a false discovery rate ≤ 1% and 6620 phosphorylation isoforms with localization probability ≥75%. Our data reveal a post-translational signature of pheromone sensing that includes many conserved proteins implicated in longevity and response to stress.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Caenorhabditis elegans / chemistry
  • Caenorhabditis elegans / drug effects*
  • Caenorhabditis elegans / metabolism
  • Caenorhabditis elegans Proteins / chemistry*
  • Caenorhabditis elegans Proteins / isolation & purification
  • Caenorhabditis elegans Proteins / metabolism
  • Escherichia coli / chemistry
  • Food Chain
  • Glycolipids / pharmacology*
  • Isotope Labeling / methods
  • Lysine / chemistry
  • Lysine / metabolism
  • Molecular Sequence Data
  • Pheromones / chemistry*
  • Pheromones / isolation & purification
  • Pheromones / metabolism
  • Phosphoproteins / chemistry*
  • Phosphoproteins / isolation & purification
  • Phosphoproteins / metabolism
  • Phosphorylation
  • Protein Interaction Mapping
  • Protein Processing, Post-Translational*
  • Proteome / chemistry*
  • Proteome / isolation & purification
  • Proteome / metabolism
  • Proteomics / methods


  • Caenorhabditis elegans Proteins
  • Glycolipids
  • Pheromones
  • Phosphoproteins
  • Proteome
  • Lysine