Enhanced Competition at the Nano–Bio Interface Enables Comprehensive Characterization of Protein Corona Dynamics and Deep Coverage of Proteomes

Abstract

Introducing engineered nanoparticles (NPs) into a biofluid such as blood plasma leads to the formation of a selective and reproducible protein corona at the particle–protein interface, driven by the relationship between protein–NP affinity and protein abundance. This enables scalable systems that leverage protein–nano interactions to overcome current limitations of deep plasma proteomics in large cohorts. Here the importance of the protein to NP‐surface ratio (P/NP) is demonstrated and protein corona formation dynamics are modeled, which determine the competition between proteins for binding. Tuning the P/NP ratio significantly modulates the protein corona composition, enhancing depth and precision of a fully automated NP‐based deep proteomic workflow (Proteograph). By increasing the binding competition on engineered NPs, 1.2–1.7× more proteins with 1% false discovery rate are identified on the surface of each NP, and up to 3× more proteins compared to a standard plasma proteomics workflow. Moreover, the data suggest P/NP plays a significant role in determining the in vivo fate of nanomaterials in biomedical applications. Together, the study showcases the importance of P/NP as a key design element for biomaterials and nanomedicine in vivo and as a powerful tuning strategy for accurate, large‐scale NP‐based deep proteomic studies.

Nanoparticle Enrichment Mass-Spectrometry Proteomics Identifies Protein Altering Variants for Precise pQTL Mapping

“…Citrate plasma samples were obtained from 345 individuals who participated in the Qatar Metabolomics study of Diabetes (QMDiab) 21,22 . The previously unthawed samples (aliquot of 240 µL per sample) were processed using the Proteograph™ Product Suite (Seer, Inc.) 18,19 (see Methods). Briefly, samples were incubated with five proprietary physicochemically distinct nanoparticles for protein corona formation.…”

“…Proteomic Analysis. 240 µL of previously un-thawed citrate plasma were loaded onto the SP100 Automation Instrument for sample preparation with Proteograph™ Assay Kits and the Proteograph™ workflow 18,19 (Seer, Inc.) to generate purified peptides for downstream LC-MS analysis. Each plasma sample was incubated with five proprietary, physicochemically-distinct nanoparticles for protein corona formation.…”

“…Here, we examine these technology-specific challenges and propose potential solutions for effectively utilizing bottom-up MS-based proteomics in conjunction with available genetic variation information. We employ the MS-based Proteograph™ (Seer Inc.) workflow 18,19 to quantify protein and peptide intensities in blood samples from individuals of a multi-ethnic cohort. The Proteograph™ workflow uses five physicochemically distinct nanoparticles that each enrich different proteins, thereby compressing the dynamic range of proteins analyzed downstream by DIA-MS 20 .…”

Fast and Dynamic Mapping of the Protein Corona on Nanoparticle Surfaces by Photocatalytic Proximity Labeling

“…In addition to the centrifugation strategy, numerous technologies are developed recently and used to study the precise mechanism of corona formation, such as differential centrifugal sedimentation (DCS), FCS, DLS, differential dynamic microscopy (DDM), bio-layer interferometry (BLI), etc. [30][31][32][33][34][35][36][37][38] Nevertheless, it is still difficult for these technologies to resolve the detailed composition of the plasma protein corona. Notably, their pinpoint accuracy and sensitivity in detection will contribute to further enhancing the spatiotemporal resolution of nano-PPL to achieve the elaborate distinction between direct nanoparticleprotein interaction and indirect protein-protein interaction in the corona structure.…”

Proteomics to study cancer immunity and improve treatment

“…The limitation of the above-mentioned strategies is the need of a relatively high amount of sample for analysis. An alternative approach is a selective enrichment of low abundant proteins by unspecific binding to nanoparticles [ 70 ]. When combining different nanoparticles with different surface chemistry, up to 2000 proteins can be quantified from plasma samples [ 71 ].…”