Comparative Analysis of Three Extraction Methods for Simultaneous Metabolomic and Proteomic Profiling in Potato Tubers (Solanum tuberosum)

The simultaneous analysis of the proteome and metabolome in biological samples is essential for advancing systems biology, enabling a deeper understanding of the molecular mechanisms governing diverse biological processes. This study compares three extraction methods applied for proteome and metabolome analysis of potato tubers: the Bligh and Dyer method (CHCl3), the Matyash method (MTBE), and a methanol extraction technique. This study was conducted on lyophilized potato tuber powder, a complex matrix containing starch, 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 for the comprehensive analysis of the proteome and the metabolome. Our findings show that the MTBE and MeOH extraction methods provide superior performance and reproducibility for metabolomic analysis, while all methods offer similar results in proteomics profiling. Moreover, the dual-phase extraction from the CHCl3 and MTBE methods reveals distinct and complementary data sets in water and organic phases, emphasizing the importance of multiphase 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.