Ovarian cancer is one of the deadliest cancers occurring in women. This is typically due to late diagnosis of the disease and difficult treatment. Infrared microspectroscopy is a complementary research method that can be helpful in the diagnosis of this disease, because it allows for the analysis of the tissues biomolecular composition. In this study, archival paraffin-embedded preparations of ovarian tissues, tumours and control, were used. However, the paraffin present in such specimens is a strong absorber of infrared radiation, which makes it impossible to reliably analyse the biomolecular composition of the sample. The solution to this problem is to deparaffinize the tissue before the analysis. However, the extend to which the paraffinization and deparaffinization processes influence the biomolecular composition of the tissues is unclear. Analysed tissues in the form of cores were placed in a paraffin micromatrix and FTIR measurements were performed. Then the samples were deparaffinized and the measurements were taken again. For both sets of samples (embedded in paraffin and deparaffinized) ratios of integrated peaks and massifs within the obtained spectra were calculated. The obtained ratios were compared for different types of diseased and healthy, control tissues. The Kruskal-Wallis test revealed statistically significant differences of the calculated ratios between most of the types of tissues. Random Forest models clearly showed that both samples in paraffin and deparaffinized retain enough information to classify the tissues reliably. The feature analysis revealed the most important feature for distinguishing between different types of samples, i.e. 1080 cm/1240 cm ratio and lipid saturation for the samples embedded in paraffin and deparaffinized respectively. The study showed that the deparaffinization process leads to changes in the biomolecular composition of the analysed tissues. Despite this, classification of the tissues based on FTIR measurements remains possible.
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