How do I separate polar(aliphatic) amino acids from a mixture of compounds present in methanol extract, my compound of interest also soluble in methanol .
Play with RP-HPLC - you can easily separate
HPLC METHOD FOR AMINO ACIDS PROFILE IN BIOLOGICAL FLUIDS AND INBORN
METABOLIC DISORDERS OF AMINOACIDOPATHIES
Indian Journal of Clinical Biochemistry, 2002, 17 (2) 7-26
Good luck
If your compound is in methanol extract, it will be difficult to use reversed-phase HPLC or SPE to grab you analyte. See if you can ionize your analyte and retain it by ion-exchange SPE. If it is acid, increase the pH of your extract 1-2 pH higher than its pKa and trap with anion-exchange SPE. If it is basic compound, lower the pH and trap by cation exchange SPE. Most of your interference should pass thru under methanol environment. You can wash the SPE with methanol for futher cleanup. At the end, to elute your analyte, by dropping the pH for acid compound or increasing pH for basic compound. You still can use methanol to elute, provided that you have the correct pH to turn off the charge of your analyte.
You can use reverse phase HPLC method or use affinity chromatography or use specific SepaK cartridges for separaation of polar amino acids by using polar solvents.
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