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bioRxiv · 10.1101/2021.10.11.463967

A theoretical framework for proteome-scale single-molecule protein identification using multi-affinity protein binding reagents

Egertson, J. D.·DiPasquo, D.·Killeen, A.·Lobanov, V.·Patel, S.·Mallick, P.
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Abstract

The proteome is perhaps the most dynamic and valuable source of functional biological insight. Current proteomic techniques are limited in their sensitivity and throughput. A typical single experiment measures no more than 8% of the human proteome from blood or 35% from cells and tissues 1, 2. Here, we introduce a theoretical framework for a fundamentally different approach to proteomics that we call Protein Identification by Short-epitope Mapping (PrISM). PrISM utilizes multi-affinity reagents to target short linear epitopes with both a high affinity and low specificity. PrISM further employs a novel protein decoding algorithm that considers the stochasticity expected for single-molecule binding. In simulations, PrISM is able to identify more than 98% of proteins across the proteomes of a wide range of organisms. PrISM is robust to potential experimental confounders including false negative detection events and noise. Simulations of the approach with a chip containing 10 billion protein molecules show a dynamic range of 11.5 and 9.5 orders of magnitude for blood plasma and HeLa cells, respectively. If implemented experimentally, PrISM stands to rapidly quantify over 90% of the human proteome in a single experiment, potentially revolutionizing proteomics research.

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Egertson, J. D., DiPasquo, D., Killeen, A., Lobanov, V., Patel, S., Mallick, P.. 2021-10-12. A theoretical framework for proteome-scale single-molecule protein identification using multi-affinity protein binding reagents. https://doi.org/10.1101/2021.10.11.463967

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