Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a powerful analytical technique with great application potential in biomolecular matter research. SIMS measurements performed on biological samples, due to their complex structure and the content of many atomic, small and large molecular compounds, suffer very rich and complex mass spectra of particles, which characterise the content and physio-chemical properties of examined samples. The proper description and understanding of features appearing in the spectra, and, consequently, the final data confirming or rejecting the hypothesis put forward in the experiment, largely depend on the experimenter's correct understanding of the technique itself and its limitations, knowledge of the tested material and its appropriate preparation. These issues mean that obtaining the right answer to the questions posed in the research hypothesis requires not only the correct conduct of experiments but also the appropriate processing of post-experimental data. This study aims to demonstrate the impact of various analytical and experimental procedures applied to reach proper conclusions from TOF-SIM measurements. These are different types of data normalization, the selection of a so-called Region Of Interest (ROI), the selection of representative secondary ions, and specific quantification methods including a combination of experimental parameters. All these aspects were checked and discussed based on the results of the analysis of pancreatic β cells placed in a PBS solution on silicon wafers.