Especially in temperature programming. Recently I am screening extracts of algae and looking for pharmaceuticals, using GC-MS to analyse the sample. What is the best condition I should use?
I think you should decide your target molecules most probably volatile ones and literaature survey on work done on algal extracts
Just check for reported literature and try to start with these values and modify this to your needs.
The lowest temperature is somehow defined by your injection system, if your column is cooler your samples will be "freeze" again on the column and start later, which could make problems. Usually something around 80°C is used.
The highest temperature and a hold on the end is typically applied to free the column from bigger molecules, in your algae extract you may find di- or trisaccharides that elute quite late. If the temperature is too low and the program too fast they might not pass the column completely and will elute in the next measurements. 10 - 20 degrees below the maximal highest temperature should be enough.
Finally the ramp define the length of the program, which gives compounds more or less time to pass the column and to separate. Again, too short and big compounds have no chance, additionally you'll end up with a poor separation, making it difficult to separate and identify compounds. Too long just wastes your time (and might increase the risk of on-column degradation).
Ultimately, the compounds you are interested in should be separated from the background, you may need some fine -adjustment on the settings, maybe a lower gradient in a certain period of time and a faster gradient at the end to clean the system as described above.
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