Multi‐omics Sample Preparation Workflow for Proteins and DNA Using the Reversible Protein Tag ProMTag

Abstract

Sample preparation is a crucial first step for both genomics and proteomics workflows. Removal of contaminants such as salts, detergents, and other biologics while maintaining high yields of the desired product is key to reproducible and informative results from these analyses. More and more frequently, these ‐omics technologies are being used in tandem to gain deeper insights into biological processes. However, multi‐omics sample preparation remains tedious and usually requires many steps in multiple different sample preparation workflows. In this study, we present a new multi‐omics workflow for the simultaneous preparation of DNA and protein samples from a single starting cell lysate. We accomplished this using the ProMTag reversible click chemistry technology that allows for reversible modification of the surface of proteins. Using ProMTag we were able to tag proteins in a cell lysate, bind them to ProMTag capture resin, and then precipitate nucleic acids so they also stay with the resin. With the nucleic acids and proteins bound to the resin, we were then able to wash away detergents, salts, and other contaminants. We then eluted the nucleic acids by resolubilizing in a nucleic acid elution buffer. We then were able to reverse the ProMTag by adding the protein elution buffer and eluted the sample in a mass spectrometry (MS) compatible buffer ready for proteomic analysis. Using this workflow we got yields >75% for protein and >90% for DNA. Gel electrophoresis showed a genomic DNA band free of degradation and the 260/280 absorption ratio indicated a pure DNA sample. Whole genome sequencing and MS proteomics analysis were performed and compared to traditional separate sample preparation workflows for DNA and proteins. This work establishes a new, high yield, reproducible workflow for the simultaneous preparation of DNA and proteins for genomics and proteomic analysis from a single starting sample.