You should first of all know or at least search the nature of the molecules that may contain your extract

If you're major molecule is an aromatic molecule you should try CGMS if it has another nature for that you should choose HPLC ( if you have the standard )

In your case I think it is CGMS for the operatory conditions you should see the articles that have suggested this kind of study

Good luck my dear

Thanks dear @Bennacer Amel , that's my problem, the operatory conditions I'm looking for are not mentioned in most articles

Well usually for HPLC-UV you need a clomn C18 ( 250 mm , 4.6mm 5 micro)

For the mobile phase try to read in which solvant does the molécule seperates better and UV detection you should see for instance if you did dosage with spectrophotometer UV where the detection have been made ( 250 nm , 280 nm ....ect ) in this length of detection you should do your hplc analysis ....

Especially if you are doing the analysis to identify and dose one molécule .....

For CGMS you should do several assays and see

And as an advice you better try CGMS and ask for the operator to optimize the results

Good luck

Dear @Amel thank you very much for your explanation

I agree that you need to know what types of molecules of interest you are trying to analyze / detect to choose the right method. There are many different columns available in both HPLC and GC methods depending on what you are trying to detect, and you will likely need to change the column to detect different groups of compounds. A C18 column in HPLC is a general purpose column, but some molecules will still be out of range for detection. DB-5 is the typical general purpose column in GC, but it is not good for polar small molecules or some other compounds.

If you have a list of compound types that you want to detect, sometimes you can call the technician from the company that installed either the HPLC or the GC-MS instrument and ask them to provide information for suggested columns to use based on the your analysis interest. I have done this for my GC-FID and GC-MS and the company was able to suggest a column and provide an example method with a simulated chromatogram for my compounds of interest.

In general, HPLC is going to be much more specific and exclude lots of peaks outside of those that interact well with the detector type and the column. GC-MS might provide a wider range of peaks for identification, but if you are trying to detect large molecules that do not easily volatilize (like proteins, for example), you will not have much success in analysis and may dirty or damage the injector.

So, first and foremost, determine what you are trying to analyze and then work on the methods from there. You will likely need to use many different methods and analysis to observe everything you want to analyze.

I should also mention the following website which was very helpful for me as a graduate student. https://www.chromacademy.com/

Dear Hadjouti

I agree with Kristin Nicole Johnson-Finn

You have to select protocol based on your desire target analysis and then find similar article

Thank you