I would like to analyze organic acids from Synechococcus cultures using GC-MS analysis. I am currently following a protocol which uses Methanol-Chloroform-Water (MCW) for extraction and then derivatization using BSTFA. I am in the process of standardizing the protocol. Can someone let me know how much amount of biomass should I start off with. I see some papers quoting as less as 10^8 cells to 12 OD (~12X10^8 cells). Hence I am confused to the amount I should use. I understand that the abundance of organic acids are very low. But when I use high OD for extraction and dry the aqueous phase after MCW extraction procedure, I get a completely dried sample. However, when I resuspend in Methoxyamine hydrochloride (one of the first steps in derivatization method), I get a viscous and cloudy solution. I am worried my protocol is incorrect. Can someone kindly share their protocol with me or help me solve my problem.