Gas chromatography is for relatively non-polar compounds and those extracts with alcohol or hydroalcoholic ones are very polar. GC-MS analysis of polar compounds can be done if derivatised to make them non-polar – For example, fatty acids and alcohols derivatised to be made esters. If you don’t know what to expect in this hydroalcoholic extract, GC-MS is not an ideal methodology of analysis.

Your extract is a mixture of a large number of polar and non-polar compounds, it is NOT easy to detect all these compounds. It is better to fractionated using liquid- liquid extraction.

I suggest to try using MPLC chromatography.

You can do GC-MS analysis of both polar and non-polar crude extracts. In polar extract you get primary metabolites and in non- polar extract secondary metabolites.

The thing which matters in GCMS analysis is its column. So, its better use semi polar column so that you can do comprehensive profiling of metabolites

one of the important thing is that not to having any particles in your solution to be run perfectly in your GCMS.