Felipe,

In most methods you will be derivatizing your FA into methyl esters previous to GC. The most common methods for FA separation are polar ones, like carbowax or FFAP based ones. Depending on exactly in which kind of FA you are interested you should chose a different type: specific stationary phase, phase thickness, column length, diameter... Some columns are specifically developed to enable the separation of isomers, but this might no be relevant for you if you are just interested in the overall FA profile. And then you will have to optimize your method. I strongly suggest you to check the literature first (an example:

https://www.researchgate.net/publication/281232839_Fatty_acid_composition_in_double_and_multilayered_microcapsules_of_o-3_as_affected_by_storage_conditions_and_type_of_emulsions

Some of the brochures for commercial columns are also quite useful).

Good luck

Article Fatty acid composition in double and multilayered microcapsu...

Thank you very much Jorge. Your help is appreciated. Saludos!

DB Wax, 30 m capillary column from Agilent is also good enough .. I have a good experience with it ..

aquatic ecosystems rich in PUFA so relatively polar column is prefered.. if budget permit you can choose 60 m column for isomers .. 

Hi Felipe, I use DB-225 by J&W Scientific (Agilent) with 30 m length (a 60 m column increases your run time with only slightly improved separation), 250 µm diameter and 0.25 µm film thickness. Email me if you need references or details on GC conditions for separation of aquatic FAMEs with this column.

Thank you Patrick! I'll do.