We present chemical depth profiling studies on mineralogical inclusions embedded in amygdale calcium carbonate by our Laser Ablation Ionisation Mass Spectrometer designed for in situ space research. An IR femtosecond laser ablation is employed to generate ions that are recorded by a miniature time-of-flight mass spectrometer. The mass spectra were measured at several locations on the sample surface and yield chemical depth profiles along the depth length of about 30 μm. The presence of oxides and sulphides within inclusion material allows us to derive elemental abundance calibration factors (relative sensitivity coefficients, RSCs) for major and minor elements. These are obtained from the atomic intensity correlations performed on the depth profiling data. With the RSCs corrections the quantitative analysis of more complex mineralogical phases within the inclusion is conducted by correlating atomic abundance fractions in ternary diagrams, typically used in geology. The spatial resolution of the depth profiles was sufficient to study chemically distinct micrometre-sized objects, such as mineralogical grains and thin layers of minerals including micrometre-sized filamentous structures. The method presented here is well-suited for the quantitative chemical analyses of highly heterogeneous materials where the ablation condition can vary locally with the material composition making the application of standard reference materials less accurate. The presented method is developed to distinguish between abiotic and biological material while searching for micrometre-sized extinct or extent life forms on the surfaces of Solar System bodies.