Applying imaging ToF-SIMS and PCA in differentiation of tissue types

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) has proven to be an extremely powerful tool for characterizing chemical distributions within biological cells and tissues. However, differentiating biological samples, e.g., cancerous cells from their normal counterparts or benign tissues from malignant tissues, presents unique challenges to ToF-SIMS. Repeatable differentiation of such samples, especially formalin-fixed paraffin-embedded (FFPE) histological specimens, could be used to improve tissue-based diagnosis and aid in prognosis decisions. In this chapter, we describe a strategy for characterizing and differentiating FFPE tissues. ToF-SIMS was used to image deparaffinized FFPE mouse embryos and differentiate tissue types. The robustness and repeatability of the method was determined by analyzing ten tissue slices from three different embryos over a period of 1 month. Using principal component analysis (PCA) to reduce the spectral data generated by ToF-SIMS, histopathologically identified tissue types of the mouse embryos can be differentiated based on the characteristic differences in their mass spectra.