The sample must be in a suitable solvent before you inject it to GC/MS. Polar solvent is a no-no because it is not compatible with non-polar column such as HP-5 . It will form beads of liquid at the head of column and result in bad peak shape. The good solvent to use is acetone or toluene because it will wet the column well and give you a sharp peak. Once acetone expands in the injector port, the vapor acetone has smaller volume and will contain in the injector port. If you use polar solvent such as methanol, 1 uL of liquid methanol expand in the injector port at 250 C will have a volume of 631 uL and is more than the effective volue of the liner 4 mm id of 495 uL, then the vapor will escape from the injector port instead of going to the column. Depending on the solubility or polarity of the analyte, you either evaporate sample down to near dryness and dissolve in acetone or do liquid-liquid extraction to acetone. You can mix aqeuouse sample with acetonitrile and add salt to salt out and shake. The analyte will move to acetonitrile quantitatively. Check the QuEChERS method on Google. Try to inject acetonitrile to GC if it is ok, if it is not, evaporate and exchange to acetone or toluene. Remember, if you inject dirty sample (having lots of non-volatile material in the extract), you will have issue of these stuff deposit in the liner and have to change the liner more often, and it will affect your quantification too (matrix enhance the signal of analyte vs. in the solvent).
The sample must be in a suitable solvent before you inject it to GC/MS. Polar solvent is a no-no because it is not compatible with non-polar column such as HP-5 . It will form beads of liquid at the head of column and result in bad peak shape. The good solvent to use is acetone or toluene because it will wet the column well and give you a sharp peak. Once acetone expands in the injector port, the vapor acetone has smaller volume and will contain in the injector port. If you use polar solvent such as methanol, 1 uL of liquid methanol expand in the injector port at 250 C will have a volume of 631 uL and is more than the effective volue of the liner 4 mm id of 495 uL, then the vapor will escape from the injector port instead of going to the column. Depending on the solubility or polarity of the analyte, you either evaporate sample down to near dryness and dissolve in acetone or do liquid-liquid extraction to acetone. You can mix aqeuouse sample with acetonitrile and add salt to salt out and shake. The analyte will move to acetonitrile quantitatively. Check the QuEChERS method on Google. Try to inject acetonitrile to GC if it is ok, if it is not, evaporate and exchange to acetone or toluene. Remember, if you inject dirty sample (having lots of non-volatile material in the extract), you will have issue of these stuff deposit in the liner and have to change the liner more often, and it will affect your quantification too (matrix enhance the signal of analyte vs. in the solvent).
Pay special attention to Narong Chamkasem's final sentence! It may be tempting to inject crude extracts, but in general cleaner samples will give better results, especially with mass spectrometers as the detectors. In addition to the injection-liner and column contamination issues mentioned above, crude samples will also affect the skimmers and ion-optics of the mass spectrometers. So yes, you CAN run crude extracts, but it's not often a very good idea.
:)
thank you so much Narong Chamkasem and John S Wishnok.. And really appreciated with your answers and well explaination. :)
You also may need to derivatize the analytes (with BSTFA or MSTFA for example) to make them volatile, that depends on the compounds of interest. Because if you extract with water and methanol they may not be suitable for Gc-ms analysis
Again, it boils down to what you are looking for. If you don't know where are you going, I cannot tell you how to get there. If your compound is not amendable by GC then, you would not see it anyway. If it is the unknown anaytes, you still have to identify it, provided it give you good chromatographic peak and signal by electron impact. You may need to ask a different question, e.g., Can I run crude extract by GC to determine "x" compounds?
Before you introducea crude extract into GCMS, please ensure the sample is volatile. Many times, crude extracts contain non-volatile and high molecular weight compounds and they are difficult to be analyzed by Gas phase. These compounds will not elute out of the column and can spoil it. You should cleanup the sample and can also think of derivatizing it before introduction into GC or GCMS.
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