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Dual-fraction proteomics reveals a novel class of proteins impacted by nanoparticle exposure. Background: Nanoparticles (NPs) interact with cellular proteomes, altering biological processes. Understanding these interactions requires comprehensive analyses beyond solely characterizing the NP corona. Methods: We utilized a dual-fraction mass spectrometry (MS) approach to analyze both NP-bound and unbound proteins in <i>Saccharomyces cerevisiae</i> sp. protein extracts exposed to silica nanoparticles (SiNPs). We identified unique protein signatures for each fraction and quantified protein abundance changes using spectral counts. Results: Strong correlations were observed between protein profiles in each fraction and non-exposed controls, while minimal correlation existed between the fractions themselves. Linear models demonstrated equal contributions from both fractions in predicting control sample abundance. Combining both fractions revealed a larger proteomic response to SiNP exposure compared to single-fraction analysis. We identified 302/56 proteins bound/unbound to SiNPs and an additional 196 “impacted” proteins demonstrably affected by SiNPs. Conclusion: This dual-fraction MS approach provides a more comprehensive understanding of nanoparticle interactions with cellular proteomes. It reveals a novel class of “impacted” proteins, potentially undergoing conformational changes or aggregation due to NP exposure. Further research is needed to elucidate their biological functions and the mechanisms underlying their impact.