Pneumatically assisted electrospray was demonstrated to be a powerful ionization source for the analysis of oligosaccharides. A mass spectrometer was interfaced to an HPLC system, using this interface, to determine oligosaccharides from the enzymatic digestion of heparin separated on a reversed-phase column. To set up the technique, and particularly to clarify the ionization process, purified disaccharides, from enzymatic digestion of chondroitin sulphates, were measured. The use of a suitable counter ion in the mobile phase, tetrapropylammonium (TPA), to optimize the HPLC separation, gave, with sulphated di- and oligosaccharides, adducts [M + nTPA - (n + m)H]m-, which were unexpectedly stable to fragmentation; molecular ions [M - (n + 1)H]n-, in the presence of the counter ion, were observed only with desulphated or monosulphated disaccharides. The stability of the adducts and the use of a deuterated ion-pair reagent permitted an exact evaluation of the molecular masses of disaccharides and oligosaccharides of unknown structure. Spectra obtained in the absence of the counter ion contained singly or multiply charged molecular ions and fragmentation ions mainly from loss of the sulphate groups; under these ionization conditions the exact mass determination and interpretation of the spectra were difficult. After removal of the counter ion, tandem mass spectra could be obtained with some interesting data for the characterization of these molecules. Complete spectral analyses were performed with amounts of samples of 50 micrograms but, using microbore columns, one twentieth of this amount may give good spectra.