Hi Kiran,

you can't directly analyse intact neutral lipids on the GCMS. You'll need to separate your neutral lipids from the total lipid pool (SPE), free up the fatty acids from the lipid backbone(saponification) and finally derivatising before the GC-MS analysis.

http://www.mdpi.com/2218-1989/6/4/42/htm

This paper covers PFB-derivatised fatty acids with NCI-GCMS.

Other common approaches are using meth-prep II to form FAMEs then using EI-GCMS, Methanolic HCl to form FAMEs then using EI-GCMS and TMS to fmethyl ester/trimethylsilyl derivatives of the 3-OH FAs then using GCMS.

Dear Sheik Nadeem Elahee Doomun ,

Thank you so much for your suggestions and article. Another query regarding trans-esterification methods : On what basis I should choose a one method 1.BF3-methanol, 2. Methanolic HCl, 3. (KOH or NaOH) in methanol for trans-esterification.

My answer is dependent on what specifically you wish to quantify. If you wish to quantify fatty acid composition, then Sheik's answer is very appropriate. We quantify fatty acids afer saponification by creating fatty acid methyl esters and separating by GC with an FID detector. We also introduce an internal standard (known volume and known amount of moles) of methyl pentadeconate (15:0) as an internal standard.