We describe the recent inclusion in Geant4 of state-of-the-art proton and alpha particle shell ionisation cross sections based on the ECPSSR approach as calculated by Cohen et al., called here ANSTO ECPSSR. The new ionisation cross sections have been integrated into Geant4. We present a comparison of the fluorescence X-ray spectra generated by the ANSTO ECPSSR set of cross sections and, alternatively, the currently available sets of Geant4 PIXE cross sections. The comparisons are performed for a large set of sample materials spanning a broad range of atomic numbers. The two alternative PIXE cross sections approaches (Geant4 and ANSTO) have been compared to existing experimental measurements performed at ANSTO with gold, tantalum and cerium targets of interest for nanomedicine applications. The results show that, while the alternative approaches produce equivalent results for vacancies generated in the K and L shell, differences are evident in the case of M shell vacancies. This work represents the next step in the effort to improve the Geant4 modelling of the atomic relaxation and provide recommended approaches to the Geant4 user community. This new Geant4 development is of interest for applications spanning from life and space to environmental science.