Systematic evaluation of extraction methods for multi-platform based metabotyping : application to the Fasciola hepatica metabolome

Combining data from multiple analytical platforms is essential for comprehensive study of the molecular phenotype (metabotype) of a given biological sample. The metabolite profiles generated are intrinsically dependent on the analytical platforms, each requiring optimization of instrumental parameters, separation conditions and sample extraction to deliver maximal biological information. An in depth evaluation of extraction protocols for characterizing the metabolome of the hepatobiliary fluke Fasciola hepatica using UPLC-MS and CE-MS is presented. The spectrometric methods were characterized by performance and metrics of merit were established including precision, mass accuracy, selectivity, sensitivity and platform stability. Although a core group of molecules was common to all methods, each platform contributed a unique set and 142 metabolites out of 14,724 features were identified. A mixture design revealed that 15:59:26 chloroform:methanol:water was globally the best composition for metabolite extraction across UPLC-MS and CE-MS platforms accommodating different columns and ionization modes. Despite the general assumption of the necessity of platform-adapted protocols for achieving effective metabotype characterization, we show that an appropriately designed single extraction procedure is able to fit the requirements of all technologies. This may constitute a paradigm shift in developing efficient protocols for high throughput metabolite profiling with more general analytical applicability