This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Carbohydrates of all classes consist of glycoform mixtures built on common core units. Determination of compositions and structures of such mixtures relies heavily on tandem mass spectrometric data. Native glycans are often preferred for samples available in very low quantities and for sulfated glycan classes. Negative tandem MS provides useful product ion profiles for neutral oligosaccharides and is preferred for acidic classes. In previous work from this laboratory, the influence of sialylation on product ion profiles in the negative mode was elucidated. The present work shows how the interplay of two other acidic groups, uronic acids and sulfates, determines product ion patterns for chondroitin sulfate glycosaminoglycan oligosaccharides. Unsulfated chondroitin oligosaccharides dissociate to form C-type ions almost exclusively. Sulfated forms produce only B- and Y-type ions. These observations are explained in terms of competing proton transfer reactions that occur during the collisional heating process. Mechanisms for product ion formation are proposed based on collisional breakdown diagrams of native and methyl esterified oligosaccharides.