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Formalin-Fixed, Paraffin-Embedded (FFPE) tissue samples are a highly valuable source for mass spectrometry-based proteomics to discover novel biomarkers, understand disease mechanisms, and monitor drug response. Compared to fresh tissue, FFPE specimens are superior in terms of tissue integrity and stability and can be stored at room temperature over long periods of time, thus reducing storage costs and facilitating sample collection over the years. Typically, only a small piece of the full FFPE tissue block is needed for proteomic analysis, and microtomes, punch biopsy needles, scalpels, or laser capture microscopes are used to create different FFPE input formats: FFPE curls/scrolls, FFPE punches, macrodissections, and microdissections, respectively.

However, scientists face several obstacles when preparing FFPE samples for LC-MS analysis. The nature of sample preservation itself makes efficient protein extraction difficult, and harsh conditions are required to reverse protein cross-links and remove the paraffin embedding that interferes with downstream LC-MS analysis. Traditional workflows often include a time-consuming xylene-based deparaffinization step that poses a health hazard due to high toxicity and results in low reproducibility.

PreOmics®’ FFPE workflow combines the BeatBox® Tissue Homogenizer and iST sample preparation technology to simplify, speed up, and standardize FFPE sample preparation for LC-MS-based proteomics. The protocol eliminates the separated sample deparaffinization step and is xylene-free. Starting from ´full´ curls or deparaffinized FFPE tissue, the workflow is scalable and enables fast and robust processing of up to 96 samples in one working day. Find out how on the following video and application note.

Click HERE for more information about the iST technology and HERE for the iST kit.

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