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Multiomics Sample Preparation Workflow for Simultaneous Cleanup of DNA, RNA, and Proteins using ProMTag

ABSTRACT: Typical multiomics studies employ separate methods for DNA, RNA, and protein sample preparation, which is labor intensive, costly, and prone to sampling bias. We describe here a method for preparing high-quality DNA, RNA, and protein or peptides for whole genome sequencing, RNA sequencing, and whole proteome analysis from a single sample. This method utilizes a reversible protein tagging scheme to covalently link all proteins in a lysate to a bead-based matrix and nucleic acid precipitation and selective solubilization to yield separate pools of protein and nucleic acids. The proteins are then digested to generate peptides ready for mass spectrometric proteome analysis. We demonstrate the utility of this method to compare the genomes, transcriptomes, and proteomes of four triple-negative breast cancer cell lines with different degrees of malignancy. These data show the involvement of both RNA and associated proteins, and protein-only dependent pathways that distinguish these cell lines. We also demonstrate the utility of this multiomics workflow for tissue analysis using mouse brain, liver and lung tissue.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Jonathan Minden

PROVIDER: MSV000092780 | MassIVE | Tue Aug 29 10:38:00 BST 2023

SECONDARY ACCESSION(S): PXD044937

REPOSITORIES: MassIVE

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