Evidence of block and randomly sequenced chondroitin polysaccharides: sequential enzymatic digestion and quantification using ion trap tandem mass spectrometry.

A method for determining the sequence type of the disaccharide repeat region of cartilage samples is introduced. The samples are sequentially subjected to selective and nonselective enzymatic digestion, and the isomeric products from each step are quantified using tandem mass spectrometry. The two-step digestion/quantification protocol identifies whether the global makeup of the polymer is "alternating", "random", or "blocked" with respect to the two main components of the cartilage, 4- and 6-sulfated disaccharides. Using this procedure, the sequence type of two biologically isolated chondroitin polysaccharides was identified. The results for chondroitin sulfate A, isolated from bovine trachea, are consistent with the 4- and 6-sulfated disaccharides randomly distributed throughout the repeat region of the polysaccharide. For chondroitin sulfate C, shark cartilage, the 6-sulfated disaccharides are adjacent to each other to a larger extent than one would expect for a randomly distributed polymer, indicating that "blocks" of repeating disaccharides with the same sulfation site are present.