An on-line liquid chromatography electrospray ionization mass spectrometry (MS) method was developed for the characterization of polymers of kappa- (extracted from Kappaphycus alvarezii), iota-, and hybrid iota-/nu-carrageenans (both extracted from Eucheuma denticulatum) enzymatically digested with specific carrageenase enzymes. Applying either CID MS/MS or in-source fragmentation mechanisms, the results demonstrated that none of the polymers of kappa- or iota-carrageenans existed with their ideal repeating units. On the polymer of kappa-carrageenan, the nonideal structures identified consisted of iota-neocarrabiose sulfate units. On the polymer of iota-carrageenan, the nonideal structures identified consisted of the following: (i) kappa-neocarrabiose sulfate units, (ii) iota-neocarrabiose sulfate units with an additional sulfate group, and (iii) iota-neocarrabiose sulfate units with an additional sulfate and a pyruvate acetal group. For both kappa- and iota-carrageenans, the nonideal structures were randomly distributed on the polymers. The method was then applied for the characterization of a hybrid polymer of iota-/nu-carrageenans, enzymatically digested with iota-carrageenase. The results did not reveal an ideal oligosaccharide of nu-carrageenan, suggesting that the iota-carrageenase enzyme could cleave only reduced "densities" of nu-carrageenan repeating units. In addition, information about the sequence of hybrid iota-/nu-carrageenans from E. denticulatum is deduced.
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