Fucoidan, a macromolecule, a type of polysaccharide and contains high percentage of fucose and sulfate ester groups and other compounds in low percentage. In the last decades, a number of interesting biological activities have been studied so fucoidan has been major focus of interest for exploring new drugs against the leading human diseases. It is known in relation to biological pathways and function that it activates the pathways which mediate apoptosis. Using LC–MS and interdisciplincary approach, we developed our goal to elucidate the potential difference between the crude and pure fucoidan and the interaction of fucoidan with potential signaling molecules STAT4 and IL12RB2. Based on our analysis, we conclude that there is major difference between crude and pure fucoidan in terms of identified metabolites and their functional relevance. It leads to the conclusion that there are 18 functions which are common between crude and pure fucoidans, 47 functions pure fucoidan specific, and 84 functions crude fucoidan specific which leads to the conclusion that even the fucoidans obtained from the same organism behave functionally completely different between the processing states (with/without processing) while docking study with STAT4 and IL12RB2 display very strong binding between fucoidan and both these signaling molecules.