LC-MS should give you a molecular ion whose mass you can compare with values listed already in the literature. Use NMR to confirm the structures are the same.

Thank you Jack Silver for your short but problem resolving solution. Again if you would like to answer, kindly suggest your opinion about following. The alkaloids I am looking for if are not the same (or sometimes if I get something different spectra) as described in the literature then, how would I know/confirm its identity? Please answer this (foolish?) question.

The question isn't foolish, but I need more information to help you. Are we talking mass spectra, NMR, or other spectra?

Assuming mass spectra, I look at the [M+1] peak and see if molecular weight matches anything in the literature. The actual mass spectrum can vary somewhat depending in instrument conditions such as ESI voltage (also I sometimes see different fragmentation in ESI vs APCI), and some of the voltages applied to other parts of the probe (capillary, for example). If the molecular weight is the same, NMR is usually good to confirm whether it is the same molecule or a potentially new isomer.

In the poster link below, I used NMR to confirm the identity of the compounds I purified whose molecular weight matched known compounds.

http://www.isco.com/WebProductFiles/Applications/101/Poster_and_Paper_Reprints/Purification_of_Phenolic_Flavonoids.pdf

Thanks a lot Jack Silver for making me all clear about doubts.