This work focuses on the application of charge transfer dissociation (CTD) to a mannuronic acid oligomerwith different extents of Na/H exchange. The goals were to determine if CTD could effectively characterize the oligomer and to investigate how Na/H exchanges impact the CTD fragmentation pathways o feven a simple oligomer like mannuronic acid. CTD provided unique and unambiguous fragments that helped determine the 1-4-linkage pattern between core mannuronic acid residues. CTD of precursors with no Na/H exchange mainly had unambiguous product ions. However, CTD of precursor ions containing two or more Na/H exchanges increased the number of possible product ion identities and yielded many isobaric product ions and, hence, more ambiguity in spectral assignments. The use of 18O labellingon the reducing terminus helped resolve some isobaric interferences between A/X, and C/Z ions but created some nominal overlap with fragment ions containing Na/H exchanges. CTD spectra demonstrated that when three or more Na/H exchanges are present in the precursor, there are at least two mainstructures of Na/H exchange sites: thefirst structure contains three Na/H exchanges on adjacent sugars closest to the non-reducing terminus and a second structure contains two adjacent Na/H exchanges on the reducing terminus. When four orfive Na/H exchanges are present, the positions of the fourth and fifth sodium ions could not be confirmed, presumably because the isolated precursors contain a distribution of structures with Na/H exchanges in different positions. In the absence of Na/H exchanges, He-CTD spectra provided rich structural information and very few ambiguous product ions. Therefore, until CTD is coupled to high-resolution mass spectrometers d which could readily resolve the ambiguity in most of the peak identities d precursors that contain the fewest possible number of Na/H exchanges willprovide the most confident peak assignments and structural characterization.