I want to isolate specific compound from aqueous extract of my plant.
What else do you know about this compound? What have you already tried?
It seems to be water soluble, so it could be a sugar, acid, or base, and possibly many other things.
There are several methods in use for the same. But it depends on compound which you are going to isolate. HPTLC is one of the standard method i think.
Preparative HPLC would be the best if you are having less crowded molecules. But it is a costly affair.
Identify how the target molecule behaves in silica TLC and then carry out column chromatography in such a solvent system where in TLC the target molecule has a Rf of about 0.3 to 0.5. Then purify using recrystallisation or using Sephadex LH-20.
But, beware the water extracted compounds will be very polar and will be strongly retained by Silica, if your target molecule is very polar better opt for a reverse phase open column chromatography and RP-TLC.
Your question is not specific. So In general ways phytochemical isolation can be done by solvent fractionation, crystallisation based on solubility, column chromatography, Prep TLC, Prep.HPLC and also LC-MS.
The best way to isolate a specific compound is using column chromatography with preparative TLC or HPLC
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