Determination of the molecular composition at the cellular level is important to understand the biochemical processes within the cells and thus to explore the occurrence of certain diseases. One of the promising mass spectrometry methods for 2D molecular mapping at the cellular level is MeV SIMS, spectrometry of secondary molecular ions using MeV ions that was installed in 2013 at the ion microprobe in Zagreb. Recently we have demonstrated that with the current experimental setup we can achieve 2D imaging of molecular distribution within the cell with the sub-micron later resolution. However, the full potential of the method could only be achieved by using heavier ions such as I or Au with energies up to 30 MeV, which is presently not possible in the current MeV SIMS setup due to the limitations in the required magnetic fields in the ion-optical elements. It is already known that the secondary molecular ion yield strongly depends on the electronic stopping power of the used ions which increases significantly for heavier high energy ions. High probability of these processes allow us that instead of a complex system of focusing lenses ion beam can be collimated to micron dimensions by using glass capillaries. New capillary microprobe for MeV SIMS that would be fully optimised for 2D mapping of biological samples due to its simplicity could be very interesting at accelerators facilities that do not have complex and expensive systems for ion focusing. Also, capillary microprobe mass spectrometer will be mounted in the central experimental line of the 6.0 MV tandem accelerator RBI in order to minimise the difficulties of turning ion beam to the other beam lines. In this way the setup can be obtained with the lateral resolution and secondary ion molecular yields that is superior to the existing similar setups for mass spectrometry of biological materials.