The organic compounds HCN and C 2 H 2 , present in protoplanetary disks, may react to form precursor molecules of the nucleobases, such as the pyrimidine molecule, C 4 H 4 N 2 . De-pending on the temperature in a given region of the disk, molecules are in the gas phase or condensed onto grain surfaces. The action of X-ray photons and MeV protons, emitted by the young central star, may lead to several physical and chemical processes in such prestellar environments. In this work we have experimentally investigated the ionization, dissociation and desorption processes of pyrimidine in the condensed and the gas phase stimulated by soft X-rays and protons, respectively. Pyrimidine was frozen at temperatures below 130 K and irradiated with X-rays at energies from 394 to 427 eV. In the gas phase experiment, a pyrimidine effusive jet at room temperature was bombarded with protons of 2.5 MeV. In both experiments, the time-of-flight mass-spectrometry technique was employed. Partial photodesorption ion yields as a function of the X-ray photon energy for ions such as C 3 H 2 + , HC 3 NH + and C 4 H + were determined. The experimental results were applied to conditions of the protoplanetary disk of TW Hy-dra star. Assuming three density profiles of molecular hydrogen, 1 × 10 6 , 1 × 10 7 and 1 × 10 8 cm −3 , we determined HC 3 NH + ion-production rates of the order of 10 −31 up to 10 −8 ions cm −3 s −1 . Integrating over 1 × 10 6 yr, HC 3 NH + column density values, rang-ing from 3.47 × 10 9 to 1.29 × 10 13 cm −2 , were obtained as a function of the distance from central star. The optical depth is the main variable that affects ions production. In addition, computational simulations were used to determine the kinetic energies of ions desorbed from pyrimidine ice distributed between ∼ 7 and 15 eV.