Background
Cell lysis and tissue homogenization are pivotal techniques used in “-omics” studies to disrupt cell membranes or walls in order to access cellular information embedded in proteins, DNA, and RNA. However, these techniques often pose several challenges, especially when working with difficult-to-process, small, precious, and rare samples.
An essential resource in retrospective studies to discover novel biomarkers or investigate molecular mechanisms is formalin-fixed, paraffin-embedded (FFPE) tissue. However, preparing FFPE tissue samples for proteomic analysis is complicated because formalin fixation makes protein extraction difficult. Moreover, the paraffin interferes with downstream liquid chromatography-mass spectrometry (LC-MS) analysis.
The Challenge
Traditional procedures for preparing FFPE tissue samples often involve a complex and potentially dangerous xylene-based deparaffinization step. This step is multifaceted, involving deparaffinization, rehydration, and staining phases that need to be meticulously performed. The entire process requires repeated washes and cautious handling to prevent tissue damage. Notably, the deparaffinization step's high toxicity levels and the risk of sample loss often result in low reproducibility.
The Proteomics Research Infrastructure at the University of Copenhagen faced this challenge as they regularly analyze a large number of tissue samples simultaneously. Many labs use self-developed tissue homogenization protocols; however, these can be difficult to establish, and their performance is often operator-dependent, affecting reproducibility.
Struggling with cell lysis and tissue homogenization? Read: 5 Key Considerations for Achieving Efficient & Reproducible Cell Lysis and Tissue Homogenization.
The Solution
To overcome this challenge, the Proteomics Research Infrastructure adopted the BeatBox tissue homogenizer and iST proteomic sample preparation technology. This optimized solution sped up, simplified, and standardized their FFPE sample preparation process. Notably, this workflow eliminated the need for xylene-based deparaffinization, allowing for the quick and robust processing of up to 96 samples concurrently.
Dr. Michael Wierer, Director of the Proteomics Research Infrastructure at the University of Copenhagen, shared his experience with the technology, stating,
"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.”
Dr. Wierer further elaborated on the potential of BeatBox:
“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."
Application Note: See how the BeatBox FFPE workflow performed against a traditional sonification approach in its effectiveness for deep proteomic analysis of FFPE tissue in comparison with fresh frozen tissue.
Meet BeatBox: An Innovative, Easy Solution
The BeatBox is a dedicated, semi-automated instrument for fast and straightforward tissue homogenization and cell lysis of different sample types with minimal risk of cross-contamination and heat induction.
Its small footprint, quiet operation, and ease of use make BeatBox suitable for any laboratory. Flexible regarding input amounts (1-50 mg), BeatBox consistently delivers reproducible results even for challenging downstream analysis like mass spectrometry-based proteomics with scalable throughput from 1-96 samples. The instrument completes sample homogenization in as little as 10 minutes with the simple push of a button. These features make BeatBox ideal for FFPE processing in proteomics analyses.
If you’re looking for high-performance solutions and workflows that set the standard for protein analysis, let’s start a conversation today.
