Formalin-fixed paraffin embedded samples represent the standard for biopsy storage. They are shelf stable at room temperature and provide excellent histological sections. However, these samples represent analytical challenges for LC-MS analysis. In traditional workflows, paraffin must be removed prior to sample preparation. Formalin crosslinking covalently links proteins together, requiring heat to unfold proteins prior to enzymatic digestion. Although this has been demonstrated, it has been historically difficult to scale to the size needed for clinical cohorts. In this work we present a workflow using the PreOmics® BeatBox®, a plate-based sample preparation approach that can be performed without xylene deparaffinization for the preparation of clinical FFPE samples.
