Identification and Targeted Quantification of Endogenous Neuropeptides in the Nematode Caenorhabditis elegans Using Mass Spectrometry

Abstract

The nematode Caenorhabditis elegans lends itself as an excellent model organism for peptidomics studies. Its ease of cultivation and quick generation time make it suitable for high-throughput studies. The nervous system, with its 302 neurons, is probably the best-known and studied endocrine tissue. Moreover, its neuropeptidergic signaling pathways display numerous similarities with those observed in other metazoans. Here, we describe two label-free approaches for neuropeptidomics in C. elegans: one for discovery purposes, and another for targeted quantification and comparisons of neuropeptide levels between different samples. Starting from a detailed peptide extraction procedure, we here outline the liquid chromatography tandem mass spectrometry (LC-MS/MS) setup and describe subsequent data analysis approaches.

Keywords: Caenorhabditis elegans; Data-dependent acquisition; FMRFamide-like peptide; LC-MS/MS; Label-free quantification; Mass spectrometry; Neuropeptide; Neuropeptide-like protein; Parallel reaction monitoring; Peptidomics; flp; nlp.