Thank you for the details. So if I well understood you want to analyse fatty acids by GC from a total lipid solution and for that you want ? If it's correct, find here a commonly used protocol (check profile if you want more details):
- dry your lipid extract under nitrogen, add some ethanol in the lipid solution to avoid trace of water (inhibitor of the transesterification)
- saponification of the lipids with NaOH 5N in methanol during 10-15min at 70°C (warm bath, screw-cap glass tube) (1mL for 20mg of lipid is largely ok, more is better than less)
- transesterification of FA esters with BF3:MeOH (10-14%) 15-20min, 70°C (same volume than Na:MeOh solution
- Extract/wash your FAME with hexane or pentane/NaCL0.9%, volume depending of your lipid content
If you prefere to analyse ethyl esters, replace MeOh by EtOH.
Some one-step protocols exist and are largely discussed by adding NaOH and BF3 together but in my experience the recovery is better in 2 steps.
You can also use a direct transmethylation with sulfuric acid or HCl in methanol.
Here an article who compare the transesterification method which could interest you
Article A critical assessment of different transmethylation procedur...
You can conduct nornal transesterification reaction (50 - 65 degree centegrade over 5 to 30 minutes time) like wise people do for transesterification of oil/fat and alcohol in presence of an alkaline catalyst. But I have no idea how you would be able to separate BF3 afterwards fram the remnant. I have no idea either where this substance will be rested (i.e. in ester or glycerol phase). During propagation of the transesterification reaction, you can analyze FAMEs to get the yield. Hope, this will be informative.