PT  - JOURNAL ARTICLE
AU  - Daniel Hornburg
AU  - Shadi Ferdosi
AU  - Moaraj Hasan
AU  - Behzad Tangeysh
AU  - Tristan R. Brown
AU  - Tianyu Wang
AU  - Eltaher M. Elgierari
AU  - Xiaoyan Zhao
AU  - Amir Alavi
AU  - Jessica Chu
AU  - Mike Figa
AU  - Wei Tao
AU  - Jian Wang
AU  - Martin Goldberg
AU  - Hongwei Xia
AU  - Craig Stolarczyk
AU  - Serafim Batzoglou
AU  - Asim Siddiqui
AU  - Omid C. Farokhzad
TI  - Enhanced competitive protein exchange at the nano-bio interface enables ultra-deep coverage of the human plasma proteome
AID  - 10.1101/2022.01.08.475439
DP  - 2022 Jan 01
TA  - bioRxiv
PG  - 2022.01.08.475439
4099  - http://biorxiv.org/content/early/2022/01/11/2022.01.08.475439.short
4100  - http://biorxiv.org/content/early/2022/01/11/2022.01.08.475439.full
AB  - We have developed a scalable system that leverages protein-nano interactions to overcome current limitations of deep plasma proteomics in large cohorts. Introducing proprietary 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. Here we demonstrate the importance of tuning the protein to NP-surface ratio (P/NP), which determines the competition between proteins for binding. We demonstrate how optimized P/NP ratio affects protein corona composition, ultimately enhancing performance of a fully automated NP-based deep proteomic workflow (Proteograph). By limiting the available binding surface of NPs and increasing the binding competition, we identify 1.2 – 1.7x more proteins with only 1% false discovery rate on the surface of each NP, and up to 3x compared to a standard neat plasma proteomics workflow. Moreover, increased competition means proteins are more consistently identified and quantified across replicates, yielding precise quantification and improved coverage of the plasma proteome when using multiple physicochemically distinct NPs. In summary, by optimizing NPs and assay conditions, we capture a larger and more diverse set of proteins, enabling deep proteomic studies at scale.Competing Interest StatementO.C.F. has financial interest in Selecta Biosciences, Tarveda Therapeutics, and Seer. D.H., S.F., M.H., B.T., T.R.B., T.W., E.M.E., X.Z., T.W., A.A., J.C., M.F., J.W., M.G., H.X., C.S., S.B., A.S., O.C.F. have financial interest in Seer, D.H., S.F., B.T., T.R.B., T.W., E.M.E., X.Z., T.W., J.C., M.F., J.W., M.G., H.X., C.S., A.S., O.C.F. have financial interest in PrognomiQ. Only Seer, and no other companies mentioned here, was involved in the study design, data collection and analysis, and manuscript writing/editing.