Defining the metabolome using GC-MS: - Impact of temperature gradient and scan rate in quadrupole systems

Quadrupole GC-MS is often used as the initial tool of analysis for metabolomic studies due to its relative ease of use and the availability of commercial mass spectral libraries. In addition, the relativley low cost of running the instrument makes the technique highly desirable. A key driver in Metabolomics is to produce a method that is high throughput without negatively impacting the integrity of the data obtained. High throughput methods are achieved through the use of faster temperautre ramps and an increased reliance on spectral deconvolution. However, the integrity of the data can be diminished if the combination of scan rate and temperature gradient are not fully optimised. Using a Shimadzu QP2010 Ultra GC-MS, the effect of scan rate and temperature gradient was examined using urine samples. Temperature gradients ranged from 5.6ºC/min to 35ºC/min and scan rates varied from 2.5 to 20 scans per second scanning the range m/z 40-600. This approach defines the necessary mass spectral scan rate required to maximise the number of metabolites in multifunctional samples with wide dynamic ranges for high throughput metabolomics analysis methods using single quadrupole GC-MS instruments. In particular, this work defines the compromise in the metabolome coverage resulting from unoptimised GC-MS methods. Significant decreases in the deconvolution capacity of the analysis occurred when the scan rate was not sufficiently fast to pull apart similar mass spectral detail. Specifically, metabolites belonging to the same chemical group (e.g. fatty acids or sugars) suffered greatly at the expense of higher throughpu