PreOmics has unveiled the BeatBox-based formalin-fixed paraffin-embedded (FFPE) workflow to simplify, accelerate, and standardise FFPE sample preparation for deep, unbiased tissue proteomics.

The BeatBox workflow is said to allow high-throughput, robust, and fast processing of tissue samples by subsequent protein digestion and nanoLC-MS/MS analysis.

According to the Germany-based PreOmics, the new FFPE workflow removes the need for xylene-based deparaffinisation. It can also allow parallel processing of up to 96 samples for discovery research in one working day and for reproducible larger cohort translational and preclinical research and validation.

The workflow is intended to work with the BeatBox tissue homogeniser and the cell lyser. The system is claimed as a compact, stand-alone benchtop system for semi-automated sample homogenisation of various tissue types and cells.

It has a flexible input amount from 1-50mg to consistently provide reproducible results for LC-MS-based proteomics with scalable throughput from 1-96 samples, PreOmics said.

When working with the new FFPE protocol, the BeatBox can efficiently process FFPE samples for downstream tissue proteomics. The duo is already successful for fresh tissue and cell-line proteomics, claimed the company.

PreOmics, a spin-off from the proteomics research group of Matthias Mann at the Max-Planck Institute of Biochemistry, said that BeatBox needs no sophisticated handling or additional water conditioning, which are common in sonication devices.

BeatBox has a push-button function for FFPE or fresh frozen tissue homogenisation in around 10 minutes.

PreOmics chief marketing officer Marcello Stein said: “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.”

In a study, the BeatBox FFPE workflow was compared with a sonication approach to process FFPE along with fresh frozen mouse cardiac muscle, kidney, and liver tissue.

As per the findings, PreOmics’ FFPE workflow enhanced the proteomic depth for FFPE and fresh frozen tissue on average by 14% to 43%.

Additionally, the approach saved up to four hours of time in comparison to the sonication workflow, the company claimed.

US-based Bruker and PreOmics have a commercial agreement, under which the former will offer the BeatBox-based tissue workflows for sale with its timsTOF Pro mass spectrometer.