PT  - JOURNAL ARTICLE
AU  - Jarrett D. Egertson
AU  - Dan DiPasquo
AU  - Alana Killeen
AU  - Vadim Lobanov
AU  - Sujal Patel
AU  - Parag Mallick
TI  - A theoretical framework for proteome-scale single-molecule protein identification using multi-affinity protein binding reagents
AID  - 10.1101/2021.10.11.463967
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.10.11.463967
4099  - http://biorxiv.org/content/early/2021/10/12/2021.10.11.463967.short
4100  - http://biorxiv.org/content/early/2021/10/12/2021.10.11.463967.full
AB  - 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.Competing Interest StatementJE, DD, AK, VL, SP, PM have financial interest in Nautilus Biotechnology.