We are working on the toxic principles of a poisonous plant so as to find out an antidote for that particular poisoning. So we are trying to isolate some compounds which are protein bound.
You must run an 2DE electrophoresis and then Mass spectroscopy to find all protein of the mentioned plant. then, you can compare this protein with other founded proteins in protein database.
If you find differences, then you must to focus on its purification using different methods such as FPLC, LC, High speed centrifugation and etc.
At the final step, you can evaluate its properties using zymography, peptide sequencing and ... .