21Heparin and heparan sulfate (Hp/HS) are linear complex glycosaminoglycans which 22 are involved in diverse biological processes. The structural complexity brings 23 difficulties in separation, making the study of structure-function relationships 24challenging. Here we present a separation method for Hp/HS oligosaccharide 25 fractionation with cross-compatible solvent and conditions, combining size exclusion 26 chromatography (SEC), ion-pair reversed phase chromatography (IPRP), and 27 hydrophilic interaction chromatography (HILIC) as three orthogonal separation 28 methods that do not require desalting or extensive sample handling. With this 29 method, the final eluent is suitable for structure-function relationship studies, 30including tandem mass spectrometry and microarray printing. Our data indicate that 31 high resolution is achieved on both IPRP and HILIC for Hp/HS isomers. In addition, 32the fractions co-eluted in IPRP could be further separated by HILIC, with both 33 separation dimensions capable of resolving some isomeric oligosaccharides. We 34 demonstrate this method using both unpurified reaction products from isomeric 35 synthetic hexasaccharides and an octasaccharide fraction from enoxaparin, 36 identifying isomers resolved by this multi-dimensional separation method. We 37 demonstrate both structural analysis by MS, as well as functional analysis by 38 microarray printing and screening using a prototypical Hp/HS binding protein: basic-39 fibroblast growth factor (FGF2). Collectively, this method provides a strategy for 40 efficient Hp/HS structure-function characterization . 41 42 43 44 45 46 47 48 Heparin and heparan sulfate (Hp/HS) are glycosaminoglycans (GAGs), highly 49 anionic unbranched polysaccharides found on the surface of essentially all 50 mammalian cells. Hp/HS consists of a repeating disaccharide structure either -D-51 glucuronic or -L-iduronic acid (GlcA and IdoA, respectively) and -D-N-acetyl-D-52 glucosamine (GlcNAc), all connected by 1→4 linkages 1 . As a part of biosynthesis, 53 monosaccharides can be differentially N-and O-sulfated after polymerization. The 54GlcA can be epimerized to IdoA and can be 2-O-sulfated, while the GlcNAc can be 55 deacetylated (usually followed by N-sulfation) and/or O-sulfated at the 6-and/or 3-56 position. Since these modifications are incomplete and untemplated, there is 57 enormous structural heterogeneity in Hp/HS chains, including many isomeric 58 structures with widely varying and dynamic compositions 2 . Different cell types will 59 often display different HS structures, and these structures can change as part of the 60 cell's physiological response 3 . This structural diversity mediates a wide range of 61 protein-GAG interactions of varying specificity and affinity. Hp/HS has been involved 62 in a wide and growing array of physiological and pathophysiological processes, 63usually mediated through interactions between proteins and a subset of Hp/HS 64 structures 4-6 . While the importance of oligosaccharide structure has been establishe...