Abstract
Purines and pyrimidines are of interest owing to their significance in processes in living organisms. Mass spectrometry is a promising analytical tool utilized in their analysis. Two atmospheric pressure ionization (API) methods (electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI)) in both negative and positive modes applied to selected purine and pyrimidine metabolites (markers of inherited metabolic disorders) were studied. APCI is less sensitive to alkali metal cations present in a sample and offers higher response than ESI for studied compounds. Both of the techniques afford quasi‐molecular ions, but fragmentation also occurs to a certain extent. However, the application of collision‐induced dissociation of quasi‐molecular ions is essential to confirm a certain metabolite in a sample. Fragmentation of both positive and negative ions was evaluated using multi‐stage mass spectrometric experiments. Typical neutral losses correspond to molecules NH~3~, H~2~O, HCN, CO, H~2~NCN, HNCO and CO~2~. The ion [NCO]^−^ arises in the negative mode. The cleavage of the glycosidic C—N bond is characteristic for relevant metabolites. Other neutral losses (CH~2~O, C~2~H~4~O~2~ and C~3~H~6~O~3~) originate from fragmentation of the glycosidic part of the molecules. In addition to fragmentation, the formation of adducts of some ions with applied solvents (H~2~O, CH~3~OH) was observed. The composition of the solution infused into the ion source affects the appearance of the mass spectra. Tandem mass spectra allow one to distinguish compounds with the same molecular mass (uridine–pseudouridine and adenosine–2'‐deoxyguanosine). Flow injection analysis APCI‐MS/MS was tested on model samples of human urines corresponding to adenosine deaminase deficiency and xanthine oxidase deficiency. In both cases, the results showed potential diagnostic usefulness. Copyright © 2002 John Wiley & Sons, Ltd.