Studying the metabolome of specific gestational compartments is of growing interest in the context of fetus developmental disorders. However, the metabolomes of the placenta and amniotic fluid (AF) are poorly characterized. Therefore, we present the validation of a fingerprinting methodology. Using pregnant rats, we performed exhaustive and robust extractions of metabolites in the AF and lipids and more polar metabolites in the placenta. For the AF, we compared the extraction capabilities of methanol (MeOH), acetonitrile (ACN), and a mixture of both. For the placenta, we compared (i) the extraction capabilities of dichloromethane, methyl t-butyl ether (MTBE), and butanol, along with (ii) the impact of lyophilization of the placental tissue. Analyses were performed on a C18 and hydrophilic interaction liquid chromatography combined with high-resolution mass spectrometry. The efficiency and the robustness of the extractions were compared based on the number of the features or metabolites (for untargeted or targeted approach, respectively), their mean total intensity, and their coefficient of variation (% CV). The extraction capabilities of MeOH and ACN on the AF metabolome were equivalent. Lyophilization also had no significant impact and usefulness on the placental tissue metabolome profiling. Considering the placental lipidome, MTBE extraction was more informative because it allowed extraction of a slightly higher number of lipids, in higher concentration. This proof-of-concept study assessing the metabolomics and lipidomics of the AF and the placenta revealed changes in both metabolisms, at two different stages of rat gestation, and allowed a detailed prenatal metabolic fingerprinting.

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