Evaluation of automated sample preparation, retention time locked GC-MS and automated data analysis for the metabolomic study of Arabidopsis species

One of the most critical parameters in GC-MS application to metabolimic studies is the sample preparation. Often a combination of oximation and silylation is used and this method is applicable to acids (e.g. fatty acids), sterols, amines, amino acids, sugars, etc. Automation of the derivatisation process enhances repeatability and the time between sample preparation and analysis can be kept short and constant. For analysis, retention time locked (RTL) gas chromatography/mass spectrometry was used. For data analysis, AMDIS deconvolution followed by 2 multivariate statistical approaches were used and compared. Arabidopsis thaliana, a popular model organism in plant biology and genetics, was used for testing. The data analysis software allowed the detection of several features that were up- or downregulated in the different species.