Here, we seek to establish an analytical workflow, which extends this approach to the holistic analysis of calcifications present in clinical specimens, in a strategy that could be considered as a “mineralomics” type of approach. We will apply “mineralomics” in order to understand the mineral deposits in different types of breast tissue biopsies and evaluate the prospect of correlating specific minerals found in the tissue with the tumour malignancy. Additionally, calcific deposits in native and prosthetic heart valves will be characterized to increase the understanding with regard to potential differences between heart valve calcification in native and prosthetic valves.