PreOmics has launched a BeatBox-based formalin-fixed, paraffin wax-embedded (FFPE) workflow, which simplifies, speeds up and standardises FFPE sample preparation for deep, unbiased tissue proteomics by subsequent protein digestion and nanoLC-MS/MS analysis.
The novel BeatBox workflow – which was announced at the AACR Annual Meeting 2023 – eliminates the need for xylene-based deparaffinisation and enables fast and robust processing of up to 96 samples in parallel for discovery research, as well as for reproducible larger cohort translational and preclinical research and validation.
The BeatBox tissue homogeniser and cell lyser is a compact, affordable and stand-alone benchtop system for convenient, semi-automated sample homogenisation of various tissue types and cells. With flexible input amounts from 1-50 mg, it consistently delivers reproducible results for LC-MS-based proteomics with scalable throughput from 1-96 samples. Already successful for fresh tissue and cell-line proteomics, with the novel FFPE protocol the BeatBox can now efficiently process FFPE samples for downstream tissue proteomics. Compared to sonication devices, the BeatBox requires no complex handling or additional water conditioning. FFPE or fresh frozen tissue homogenisation takes just 10 minutes with push-button operation.
In a benchmark study, FFPE as well as fresh frozen mouse cardiac muscle, kidney, and liver tissue (provided by the Research Institute of Molecular Pathology in Vienna and the Histology Facility at Vienna BioCenter Core Facilities) was processed using the novel BeatBox FFPE workflow, as well as with a sonication approach. Peptides were analysed on a timsTOF-HT mass spectrometer (Bruker Daltonics) in DIA-PASEF mode using a 30-minute nLC gradient. The BeatBox-based FFPE workflow was shown to increase the proteomic depth for FFPE, as well as for fresh frozen tissue on average by 14% to 43%, depending on tissue type. Typical Coefficients of Variation (CV) within replicates were below 10%, emphasising the high repeatability of the homogenisation process with the compact BeatBox instrument. Furthermore, the novel approach saves up to four hours of time in comparison to the sonication workflow, enabling parallelised high-throughput processing of 96 samples within one working day.
Dr Marcello Stein, Chief Marketing Officer of PreOmics, commented: “With our novel BeatBox-based FFPE workflow, researchers finally can simplify, speed-up and standardise FFPE sample preparation without the need of xylene-based deparaffinisation to fully exploit its potential for unbiased, deep proteomics. We believe this is a leap forward for the preparation and subsequent proteomic analysis of large sample cohorts.”
Bruker Corporation and PreOmics have a commercial agreement, enabling Bruker to offer the BeatBox-based tissue workflows for sale with Bruker's timsTOF Pro mass spectrometer.
For more information please visit www.preomics.com/beatbox-tissue-homogenization-cell-lysis