Comparative analysis of three extraction method for simultaneous metabolomic and proteomic profiling

The simultaneous analysis of the proteome and metabolome in biological samples is essential for advancing systems biology, enabling a deeper understanding of molecular mechanisms governing diverse biological processes. This study compares three extraction methods: the Bligh and Dyer method, the Matyash method, and a simple methanol extraction technique. This study was conduct on lyophilized potato tuber powder, a complex matrix containing starches, proteins, and a variety of metabolites. With the use of high-resolution mass spectrometry (HRMS), specifically nanoLC-MS/MS and direct infusion Fourier transform ion cyclotron resonance mass spectrometry (DI-FT-ICR-MS), we aimed to select one of these extraction methods to understand the behaviours of several potato cultivar facing cold stress. Our findings indicate that the Matyash and methanol extraction methods provided superior performance and reproducibility for proteomic analysis, while all methods offered similar results in metabolomic profiling. Moreover, the dual-phase extraction from the Bligh and Dyer and Matyash methods revealed distinct and complementary datasets, emphasizing the importance of multi-phase approaches for comprehensive molecular characterization. Despite some redundancy observed between polar and apolar phases, the overall analysis highlights the necessity of optimal extraction techniques for future proteomic and metabolomic studies. These results enhance our understanding of the potato tuber’s biological landscape.