Lyophilization Improved Efficiency in 2‐in‐1 Metabolite and Protein Extraction for Plant Multi‐Omics

Recent advancement of integrated omics has enabled a new era characterized by the systematic identification and functional analysis of a large number of genes and molecules in an organism. For seamless integration of multi-omics data, it is ideal to use the same sample across different omics analyses, as data from the same sample yields consistent results. In this study, we developed a method for extracting metabolites and proteins from the same plant samples. Notably, lyophilized samples showed higher protein extraction efficiency compared to fresh samples, a trend that we confirmed across various plant tissues, including leaves, stems, flowers, seeds, and roots, as well as among different plant species. Furthermore, pre-extracting metabolites eliminated the need for TCA/acetone precipitation, making direct extraction of proteins using a solubilization solution both feasible and effective. The optimized method enables us to complete both metabolite and protein extraction within 2 hours while maintaining high quality and quantity. This method holds great promise for widespread applications in future integrative omics studies in plants. SUMMARY: High throughput multi-omics has advanced plant system biology to a new height. To meet the sample preparation needs, this 2-in-1 metabolite and protein extraction method was developed. The key features include: 1) metabolites and proteins can be extracted from the same sample within 2 hours, and 2) lyophilized samples have higher protein extraction efficiency than freshly frozen samples. This method facilitates an high throughput multi-omics and data integration.