Overview of GC-MS analysis
As an example, the chromatogram associated with an Arabidopsisleaf sample derivatised with methoxamine andN -methyl-N -(trimethylsilyl)trifluoroacetamide (MSTFA) in pyridine is shown in Fig. 1, where the signal shown in panel (a) is total ion current (TIC). Abundant compounds form peaks that can be easily seen on the chromatogram, including some amino acids (e.g. proline), organic acids (fumarate) and sugars (e.g. sucrose), as trimethlysilylated (–Si(CH3)3, abbreviated TMS) derivatives. The TIC signal does not directly reflect the quantity (in moles) in the sample since analytes do not have all the same response coefficient in the mass spectrometer. The internal standard used for semi-quantitation (i.e. relative quantification) is adonitol (ribitol), the derivative of which (ribitol 5TMS) elutes at 10.68 min. As expected, there is some overlapping between analytes (i.e. several analytes have very close retention time and co-elute). This is visible, for example, at 15.05 (panel (b) of Fig. 1) where many m/z features related to sugars are visible together with 6-phosphogluconate specific m/z features (for example at 387.14254 Da). Interestingly, a relatively close mass (387.32912 Da) can be found at a similar retention time (15.25 min) from arachidic acid 1TMS, but such a mass difference is in practice too large (nearly 0.18 Da) to allow confusion with exact mass analysis.