Formalin-Fixed, Paraffin-Embedded (FFPE) tissue samples are a highly valuable source for proteomic analysis. They are routinely collected and stored by hospitals and readily available in biobanks worldwide for retrospective studies, such as discovering new biomarkers. However, preparing FFPE samples for proteomic analysis is very challenging as formalin fixation hinders protein extraction.
Besides, current protocols require an initial xylene-based deparaffinization step as paraffin interferes in the downstream LC-MS analysis. This process is time-consuming, low reproducible, and hazardous due to high toxicity.
An efficient and straightforward solution for processing FFPE tissues for proteomic analysis is combining PreOmics®’ BeatBox® tissue homogenizer and the iST technology. In the BeatBox® FFPE workflow, the high-toxic xylene-based deparaffinization step is eliminated, avoiding sample loss. Fast and reproducible processing of up to 96 samples can be performed in parallel from starting material to clean peptides within one working day.
"We routinely analyze a large number of tissue samples at once, and to improve our efficiency, we have successfully adapted the BeatBox technology for tissue homogenization. Our latest discovery is that the BeatBox technology can efficiently homogenize paraffin-embedded tissue scrolls. This breakthrough now allows us to process large cohorts of FFPE tissue quickly, reproducibly, and with greater precision, opening up the possibility of large-scale biobank projects. By leveraging this technology, we are excited to uncover novel deep proteomics insights in the field of pathology research."
Easy-to-use and standardized protocol for efficient protein extraction and high reproducibility
Straightforward xylene-free workflow without a separate deparaffinization step for LC-MS-based proteomics
The protein depth of FFPE samples is equivalent to that for fresh frozen tissue
Get clean peptides from up to 96 samples/day