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Eight polysaccharides preparations (STW, STA, STW-D, STA-D, STW-DS,STA-DS, STW-D-DS and STA-D-DS) were prepared from Sargassum thunbergii.The polysaccharides might contain fucan, galactofucan, glucuronomannan and fucoglucuronan.Electrospray ionization mass spectrometry (ESI-MS) showed that the desulfated polysaccharides contained similar fragment ions.ESI-MS with collision-induced dissociation tandem mass spectrometry (ESI-CID-MS/MS) suggested that fucan contained 3-1inked fucan sulfated at C-2 or C-4, while galactofucan consisted of a backbone of either alternating Gal and Fuc or alternating (Gal)n and (Fuc)n.STW and STA were degraded to elucidate the structural features of glucuronomannan and fucoglucuronan.ESI-CID-MS/MS and ESI-CID-MS/MS/MS indicated that glucuronomannan contained alternating 2-1inked Man and 4-1inked GlcA, while fucoglucuronan contained 3-1inked glucuronan branched with Fuc at C-4 or 4-1inked glucuronan branched with Fuc at C-3.Finally, the anti-complement activities of all of the polysaccharides were determined, and the crude polysaccharides showed good anti-complement activities.The molecular weight and degree of sulfation, but not the method of extraction, contributed to the activities.