The total fatty acids for a biodiesel project. Thanks for your reply.
Biodiesel is already extracted commercially from algae grown in sewage ponds in NZ
http://www.scoop.co.nz/stories/SC0605/S00030.htm
The easiest method would be to extract the wet macerated mass with iso-octane a couple of times, and then derivatise a few mg of the sample in the iso-octane using 2M alcoholic KOH ( 6 mins ambient temperature with plenty of vortex mixing ), then add a drop of methyl red and neutralise with 2M HCl, Inject the iso-octane phase.
The method is very dependent on the vortex mixing and cell disruption, but is quick. Bannon and Craske reported some problems, but I've always found it to be very good. Some standard biodiesel methods use other derivatising agents.
If you want free fatty acids, you could just extract with iso octane and use diazomethane ( if you're allowed ), it's very fast and easy - especially if you use a small generator, which avoids the artifact formation issues.
There are extraction systems based on chlorinated solvent extractions, and the total lipid extraction methods, eg Bligh and Dyer. The critical aspect is how much water is with your samples. If it's dried, you can also use soxhlet extractions etc..
The most important consideration is to choose a method that will be appropriate for all the lipids you're extracting in the large scale process.
Th GC methods are discussed in the various Biodiesel specifications that are freely available on the WWW.
W.W.Christie's book "lipid analysis" is always a good place to start.
Bruce Hamilton