Cross-Platform Comparison of Caenorhabditis elegans Tissue Extraction Strategies for Comprehensive Metabolome Coverage

The nematode Caenorhabditis elegans is widely used as a model organism in many areas of the life sciences. Metabolite profiling (metabolomics/metabonomics) is a powerful means of assigning phenotypes to experimentally perturbed C. elegans samples (e.g., mutants, RNAi, or chemical treatments). Tissue extraction is a key step, and high-quality and reproducible extractions are essential to the success of metabolomics studies. We have performed an extensive comparison of different tissue extraction techniques with C. elegans, comparing two different solvent systems (chloroform/methanol and aqueous methanol) and six different tissue disruption techniques (including manual grinding in a cooled mortar, homogenization, and various grinding media in both reciprocating and orbital tissue mills). All twelve combinations were then compared by GC/MS, (1)H NMR spectroscopy, and UPLC-MS, and the results were evaluated by both overall multivariate clustering approaches as well as distributions over individual metabolites/metabolite features of coefficient of variation and yield. The choice of solvent had more influence than the disruption method used, although the homogenizer results were clearly outliers. Overall, we concluded that bead-beating with 80% methanol solution was a good trade-off, although it is important to note that the definition of the apparent "best" method depended on which analytical platform was used to evaluate the results.