Multiple techniques, many different biological sources, one sample preparation technique that delivers
Processing regularly large numbers of diverse clinical samples for MS-based proteotyping sample preparation brings very specific challenges that are shown here to be solved by the PreOmic’s suite of products and PreON instrumentation. Reproducibility of sample preparation while maintaining sample integrity are pre-requisites for clinical work. The additional advantages gained are the simple streamlining of workflows from many tissue types together with a three fold increase in protein identification when coupled to the adoption of the iST-Fractionation Add-on kit.
What challenges were you facing?
The ETH PHRT Swiss Multi-Omics Center receives on a regular basis larger sample cohorts of clinical biospecimen. Standard operating procedures are critical for consistent and reproducible data generation and analysis. Switching to the PreOmics' kits in combination with the PreON robot enabled us now to routinely to focus on biomedical discoveries and not technical workflows and variations.
How did PreOmics help you solve your challenges?
The PreOmics' kits have the benefit that they are compatible with a diverse range of biomedical sample types (cell pellets, tissues or FFPE specimen) that we are working with. Combining all the processing steps in a streamlined workflow allows for less hands-on time and simply save time. The PreOmics' kit format in combination with the automation makes sample handling easy, less error prone and consequently increases reproducibility. As a result, we have been able to obtain consistent very good results in digitizing clinical sample cohorts. We also utilized the recently launched iST-Fractionation Add-on kit for getting the most out of selected samples, for example for open search PTM analysis using FragPipe, and for DIA library building. The kit is easy-to-use and does not require any additional special lab equipment. Performance-wise, we have seen reproducible results and a remarkable boost in protein identifications compared to non-fractionated samples.
What was your Aha-Moment with PreOmics?
We now talk less about sample preparation and more about data analysis. Voila!
What are your plans for the future?
We are currently integrating the TMT labeling protocol with the PreON robot for the analysis of surfaceome nanoscale organization. Automated and consistent protein/peptide labeling procedures are critical for teasing out minor quantitative differences which cause eventually large biological effects.
Meet the author
Personalized Health and Related Technologies (PHRT) is a strategic focus area of the ETH Domain. Within the PHRT program, SMOC is an engine for multi-omics data generation, analysis, interpretation.
The Wollscheid laboratory at the Swiss Federal Institute of Technology/ETH Zürich develops and applies next generation technologies at the interface of biology, chemistry, medicine and bioinformatics to generate unprecedented data to establish the surfaceome proteotype and its signalling interaction networks. This digital proteotype data layer provides the basis for generating qualitative and quantitative surfaceome models explaining how molecular nanoscale organization influences cellular signalling and biological function.