Multiomics Sample Preparation

Multiomic technologies and tools used to prepare samples for technologies and tools used to prepare samples for multiomic studies typically employ methods that extract nucleic acids before isolating protein. However one of the current challenges with methods where protein is precipitated last is loss of protein yield in the final extraction step. This can be sub-optimal, especially when working with small and precious samples, if the protein yield is not sufficient to perform mass spectrometry analysis. This challenge is overcome by introducing an alternative method where the protein is extracted first in higher quantities, without compromising the yield or quality or the subsequent DNA and RNA analytes. The protein-first approach addresses the longstanding challenge of optimizing recovery across all three biomolecule types simultaneously.

One approach to this type of co-purification method is utilizing two different types of magnetic beads to sequentially extract the three distinct analytes. For example, the Sequential Protein/DNA/RNA Extraction Kit follows a systematic three-step process designed to optimize recovery of each analyte. Initially, Dynabeads Sequential Protein Binding Beads are introduced to the lysed sample and incubated to facilitate protein binding, after which they are transferred to a separate tube for washing and protein processing, making them compatible with downstream western blot (WB) or MS applications without the need for further pre-prep, e.g., desalting. Subsequently, MagMAX Sequential DNA/RNA Binding Beads are added to the original tube, now depleted of proteins, to enable DNA binding and extraction using proprietary buffer formulations before transferring to a new tube for further preparation. Finally, MagMAX Sequential DNA/RNA Binding Beads are again introduced to the original tube, now depleted of both proteins and DNA, to facilitate RNA binding and extraction using specialized proprietary buffers and solutions, with subsequent transfer to a dedicated tube for final preparation. The resulting extracted proteins are suitable for WB or MS analysis, while the recovered DNA and RNA are compatible with quantitative PCR (qPCR) and next-generation sequencing (NGS) applications.

Additionally, the distinct use of a dual magnetic bead system comprised of Dynabeads magnetic beads for protein extraction and MagMAX magnetic beads for nucleic acid isolation facilitates easy integration into automated workflows. Enhance the efficiency of any multiomics workflow using the Sequential Protein/DNA/RNA Extraction Kit on Thermo Scientific KingFisher instruments. Automated protocols are available for Apex, Flex and the Duo Prime instruments.

Multiomics research has four disciplines that could be considered the key pillars. They are genomics, transcriptomics, proteomics, and metabolomics. Together they serve as a fundamental basis for multiomics studies because they reflect the central dogma of molecular biology: that DNA is transcribed into RNA, RNA is translated into protein, and proteins can then affect and influence biological and metabolic processes within cells.

Across these four pillars, Thermo Fisher Scientific offers a host of key solutions and technologies that support the research and advancement of multiomic studies.

Within multiomics research, a key distinction for any technology that extracts three different analytes from a single sample is being able to effectively do so when compared to methods that only facilitate isolation of one analyte. Comparative testing has demonstrated that the Sequential Protein/DNA/RNA Extraction Kit helps deliver yield and quality metrics comparable to standard single-analyte extraction kits currently available in the commercial market. This validation confirms that the multi-analyte approach does not compromise the recovery efficiency or integrity of individual biomolecule classes, helping provide researchers with a consolidated solution that maintains the performance standards expected from dedicated single-analyte protocols while offering the significant advantage of simultaneous multi-analyte recovery from a single sample input.