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Access to both protein and metabolite biomarker information in biospecimens from trace samples remains a significant challenge, and it is necessary to separate proteins and metabolites before analysis. In this work, the Fe3O4@SiO2@Proteins@Metal-polyphenol network (MPN) was successfully constructed and applied to separate metabolites and proteins. Tannic acid (TA) and Cu2+ were involved in the synthesis of MPN because of rapid degradation and maintaining the assay performance of proteins. There are a variety of interactions between TA and proteins, including hydrogen-bonding, hydrophobic, and ionic interactions. Moreover, benefiting from the small molecule permeability and surface adherence of MPN, proteins were encapsulated and immobilized on the surface of substrates with the growth of MPN. At the same time, endogenous metabolites remained dispersed in the supernatant. In the model sample and real biospecimen cases, the protein biomarkers (e.g., carcinoembryonic antigen and alanine aminotransferase) were encapsulated on the surface of Fe3O4@SiO2, which allowed the isolation of proteins from the original matrix, as well as release and analysis in a short time. Meanwhile, the metabolites in the produced supernatant were analyzed by LC-MS/MS. By the self-assembly and disassembly of MPN, the group differences of proteins and metabolites between physiological and pathological biospecimens are correctly characterized without multisampling. Overall, an MPN-mediated separation strategy of biomarkers was proposed, and MPN facilitated a “two birds with one stone” approach, where the proteins were encapsulated and immobilized in the precipitation while endogenous metabolites distributed in the produced supernatant, opening a new chapter in the application of MPNs.

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