Sulfation pattern within chondroitin sulfate (CS) glycosaminoglycan (GAG) chains is an important post-translational modification that regulates their interaction with proteins. In this context, development of highly efficient and reproducible analytical methods for the investigation of CS sulfation patterns is of high necessity. In this study we report a novel method for straightforward determination of N-acetylgalactosamine (GalNAc) sulfation sites in chondroitin sulfate disaccharides. Our protocol involves combining fully automated chip-based nanoelectrospray (nanoESI) for analyte infusion and ionization in negative ion mode with multistage (MSn) collision-induced dissociation (CID) high capacity ion trap (HCT) mass spectrometry for generation of sequence ions diagnostic for identification of sulfate ester group position within GalNAc residues. The feasibility of this approach is here demonstrated on chondroitin 6-O-sulfate and chondroitin 4-O-sulfate disaccharides. Fragmentation patterns obtained by MS2 and MS3 sequencing stages provided first mass spectrometric data from which sulfation site(s) within GalNAc monosaccharide ring could be unequivocally deciphered. Hence, the method allowed discriminating 4S/6S sulfation sites solely on the basis of MS and multistage MS evidence. <alternatives> [...] </alternatives>
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