Application to plant samples
The compound database used here contains 1,064 target fragments that have all been confirmed with standards, representing 336 compounds with target identification exact mass features, and confirming exact mass features (see Supplementary File 1). Using Arabidopsis as a plant model, we found 234 compounds in leaves (266 analytes, some of them generating several derivatives). We assessed the usefulness and repeatability of exact mass analysis by conducting GC-MS analyses on several Arabidopsis ecotypes (BL1, AN1, Col0, Cvi0, Oy0, Ge0, Mt0 and Sha). Results are shown in Fig. 6 as a heatmap of analytes that are significantly different between ecotypes. Hierarchical clustering shows easy discrimination of samples (without any clustering error between ecotypes), suggesting good repeatability. Many metabolites were found to be different between ecotypes, and they are here subdivided into 7 groups (Fig. 6a). For example, Cvi0 was found to be enriched in various amino acid derivatives, while Shahdara was enriched in sugars. Repeatability (both technical and biological) was assessed by calculating standard errors, expressed in % of mean value, for each genotype. For the vast majority of metabolites, there was a very good reproducibility, with a median value of SE of 9.7% only across all genotypes (Fig. 6b). Some metabolites were associated with a high variability, larger than 40%. They were all metabolites present in very low amount, and/or having very poor ionisation, and/or encountering degradation during derivatisation, such that their relative signal was extremely small, 10-5 or less (Fig. 6c).