As methanol is a highly polar solvent they generally produce polar compounds peak in gas chromatography. But we found some non-polar and volatile compounds also. For GC-MS analysis, we have used a slightly polar column (Rxi-5ms, 0.25 m, 30 m long, internal diameter: 0.32 mm). Further, there is no chance of contamination from chromatographic column even after subsequent sample analysis since we are routinely analyzed our sample after a several wash of column by the GC grade ultrapure solvent/mobile phase and ensured an acceptable baseline first. Moreover, after careful and sufficient washing, we are conditioned our column following the experimental method and carefully checked baseline for its acceptance; then we run the sample for analysis. After that, we also run the blank sample to avoid any kinds of associated contaminations and false identification of compounds in the analysis. Furthermore, we reported only those compounds which are probable compounds matched from our comprehensive library (purchased with the GC-MS instrument).
What are the reasons?
Thanks in advance for your comments and explanation.
You should not use GC-MS but LC-MS for qualitative and quantitative analyses of a methanol extract which contain mostly polar compounds. Minute amount of non polar compounds may be present in a methanol extract. You have to bake the column at high temperature for a few hours or overnight to clean the GC column. We use a liquid mobile phase to wash a LC column.
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