Quantification of isomers from a mixture of twelve heparin and heparan sulfate disaccharides using tandem mass spectrometry

Abstract Heparin/heparan sulfate‐like glycosaminoglycans (HSGAGs) have been implicated in clinically relevant processes such as hemostasis, infection, development, and cancer progression, through their interactions with proteins. Electrospray ionization mass spectrometry (ESI‐MS) and tandem mass spectrometry (MS n ) were combined to identify and quantify 12 HSGAG disaccharides that can be generated by enzymatic depolymerization with heparin lyases. This technique includes free amine‐containing disaccharides that had previously been observed in MS n but not quantified. Our methods use diagnostic product ions from MS n spectra of up to three isomeric disaccharides at once, and up to three sequential stages of MS n in tandem, for the quantitative analysis of the relative percentage of each of these isomers. The isomer quantification was validated using mock mixtures and showed acceptable accuracy and precision. These methods may be applied to the quantification of other isomers by MS n . While each of the 12 disaccharides alone had a linear response to an internal standard in the MS 1 spectra, the individual response factors did not remain constant when the concentrations of the other 11 disaccharides in the mixtures fluctuated, due to competition for electrospray ionization. The absolute concentration of one fluctuating isomer was determined out of a constant mixture of the other disaccharides. The rapid, accurate, and sensitive quantification of all isomeric disaccharides may contribute to the eventual sequencing of longer saccharides by MS n , enabling the elucidation of the structure‐function relationships of HSGAGs. Copyright © 2005 John Wiley & Sons, Ltd.