Sulfated motifs on heparan sulfate (HS) are involved in various extracellular processes from cell signaling to enzymatic regulation, but the structures of these motifs are obscure. We have developed a strategy to determine the structure of sulfotransferase recognition sites which constitute these motifs. Stable isotope is first introduced into specific sites on HS with HS sulfotransferases and the modified HS is then digested into oligosaccharides of differing sizes. The overlapping oligosaccharides containing the introduced stable isotope are identified by changes in the m/z profiles by mass spectrometry, and their relationships are elucidated. In this way, the HS structures in the vicinity of the sulfotransferase recognition site are quickly determined and groups on precursor structures of HS that direct the action of HS sulfotransferases are pinpointed.Heparan sulfate (HS) 1 is one major polysaccharide found on proteoglycans. HS chains are first synthesized in the Golgi apparatus as repeated units of the disaccharide of a glucuronic acid and an N-acetylated glucosamine (GlcA-GlcNAc) n (1). The glucuronic acid can be epimerized to iduronic acid (IdoA). Incomplete sulfation at the 2-O positions of the uronic acids, and the 3-O, 6-O, and N positions of the glucosamine by various sulfotransferases results in structural diversity within HS (1, 2). The sulfate groups usually cluster in small regions and form sulfated motifs.The sulfated motifs can bind to growth factors, cytokines, and morphogens as well as proteases in the extracellular matrix and regulate their activities (3); thus HS plays critical roles in organ development (4 -6), morphogenesis (7, 8), angiogenesis (2), blood coagulation (2), inflammation (1), wound healing, and cancer progression (9). These sulfated motifs also play roles in pathological processes, such as functioning as receptors for viral entry (10 -13).Although HS plays important roles in various biological processes, the structures of these biological motifs are obscure, due to the difficulties involved in obtaining homogeneous components and determining their structures. Cloning, expressing, and sequencing biopolymers have tremendously advanced our understanding of DNA and protein, but no similar methods are available for studying HS.In this report, we describe a novel strategy that permits us to quickly determine specific HS structures in the vicinity of the sulfotransferase recognition site for 3-OST-4. HS 3-OSTs are rare modification enzymes that helps to generate binding sites for proteins such as antithrombin III (2) and herpes simplex virus glycoprotein D (11). 3-OST-4 is specifically expressed in brain tissues and may play a role in neuronal development (14). The delineation of sulfated motifs on the HS chain of proteoglycans will shed light on how cells interact with extracellular proteins, respond to extracellular signals, and initiate signaling cascade beginning on the cell membrane (15). This strategy relies on introducing a stable isotope of sulfate into specific sites on the...