The long range of MeV protons in matter means that PIXE analysis of inhomogenous thick samples is subject to uncertainty if the elemental composition changes with depth. Samples which are particularly affected by this include rock and mineral samples and material of archaeological interest, such as pigments. In this study, elemental mapping of lead-tin yellow pigment grains using electron probe microanalysis (EPMA) is compared with PIXE using microfocused 2 and 3 MeV protons. It is found that, although well-defined grains can be seen using EPMA, which is sensitive only to a thin surface layer, the structure is lost using PIXE, because of Pb or Sn X-rays induced from deep within the sample. Simultaneous mapping using backscattered particles (BS) allows the grains to be seen clearly, and by taking different energy slices from the BS energy spectra the grains can be mapped at different depths below the surface. It is concluded that simultaneous BS analysis is essential when carrying out PIXE analysis of thick inhomogeneous samples to confirm that the sample is uniform at the point where the spectrum is taken. This is illustrated using a point analysis of a thin lead-tin grain overlaying a region of organic material.