Dear Kasun,

Have you tried to dissolve the sample in tetrahydrofuran and run under the following HPLC conditions:-

Mobile Phase:                      A: 0.1% Trifluoroacetic acid in Water

                                             B: 0.1% Trifluoroacetic acid in Acetonitrile

Gradient:                              (Time,%B),(0,80), (10,100), (20,100)

Flow Rate:                           1.0 mL/min

Detector:                              220 nm

Column temperature:           52 °C

Kind regards,

Ade Kujore

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Check the Agilent and Waters websites.  This analysis has been done before.

It will be easy to do Fatty Acid composition by GC as FAME (Fatty Acid Methyl Ester) analysis. A wax column can separate all the FAMEs.

I agree with Girirajan sir. GC is always the first choice for fatty acid analysis. However some of the publications for biodiesel analysis are available for HPLC analysis. 

With C18 column you can have a look at Agilent's manual for HPLC in Food Analysis. Methanol, toluene and ethyl acetate are some of the mobile phases usually used...

Dedetection VFAs could be  performed by HPLC  using the AQUASIL C18, 5 μm, 250 x 4.6 mm column; eluent: 1% acetonitrile, 99% 0.05M KH2PO4; pH = 2.8; Flow Rate (FR) = 1.25 mL/min and UV detection at 210 nm. Before performing any liquid measurements, samples subjected to filtration using a 0.22 μm membrane.