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).