Using HPLC or HPTLC, we can separate compounds but not able to identify that compounds, for identification of unknown compounds you should go for GC-MS or LC-MS.

Since you are working with an aqueous extract the best method is HPLC. Additionally, you are looking for some heavy compounds that could be determined by that method.

on the other hand, if you have a GC you must evaporate the all water in your extracts and redissolve in a solvent, but you need use a high temperature column.

You can anlayze your samples on HPLC on C18 reverse phase column and use GC-MS analysis for knowing mass of the compounds and high energy NMR for knowing the functional groups.

Dear Kathiravan 

General analysis include testing your extract with various reagents and identify them with reference literature. You must refer some pharmacognosy books for designing your experiments. Here i am attaching literature regarding analysis of phenolics.

Better go for HPTLC that's the best option available when dealing with extracts.

Using HPLC or HPTLC, we can separate compounds but not able to identify that compounds, for identification of unknown compounds you should go for GC-MS or LC-MS.

flavonoids or polyphenols or vitamins our what, spectrophotometerically or HPLC-MS analysis, pls specify

It  is  initially  better  to  fractionate the compounds through HPTLC.

You can use the microwave or ultrasonic way to get the best yield taking into account the time and power the way and temperatures when using microwave power and the best 550-watt and 70-minute time and temperature 80 degreesز

To learn chemical constituents you can use the GC - MS

Also you can find out chemical constituents if using HPLC - MS or LC - MS and after you can work isolation and purification, after that use the 1HNMR and 13CNMR

I will suggest you to employ Mass Spectrometer (MS), with any of the following:

LC, IC, or GC. However, LC-MS will be a good choice as your sample is in aqueous form. 

LC-MS would be ideal but make sure you get the correct solvent mixture for separation from your TLC before LC-MS.

I would also suggest you opt for HPLC or even better HPLC-MS. Water extracts mainly contain polar compounds. The best choice of HPLC column would be a modified C18 column (Phenomenex Aqua, Waters T3, etc) or even a C8 column. Start with a high aqueous mobile phase and slowly increase the organic portion of your eluent. An MS detector (especially a TOF or QTOF)  is the best as you can immediately determine the empirical formula, DBE count and molecular mass. Exporting your MS data to ChemSpider would enable you to get tentative structures for your compounds detected. To fully characterize your compounds you would need to purify each compound and do all the NMR experiments to elucidate the structure.

I suggest you to use LCMS/MS (QTOF type).

Another method, you can use GCMS but first you must perform derivatization using sililation