Single-Molecule Protein Identification by Sub-Nanopore Sensors

TL;DR

This paper investigates the use of sub-nanopore sensors for single-molecule protein identification, demonstrating potential for matching nanospectra to small protein databases, thus advancing nanopore-based proteomics.

Contribution

It introduces an algorithm for analyzing electrical signals from sub-nanopores for protein identification, bridging nanopore technology with proteomics.

Findings

Current technology can match nanospectra to small protein databases

Sub-nanopores show promise for single-molecule protein identification

Potential for bacterial proteome analysis

Abstract

Recent advances in top-down mass spectrometry enabled identification of intact proteins, but this technology still faces challenges. For example, top-down mass spectrometry suffers from a lack of sensitivity since the ion counts for a single fragmentation event are often low. In contrast, nanopore technology is exquisitely sensitive to single intact molecules, but it has only been successfully applied to DNA sequencing, so far. Here, we explore the potential of sub-nanopores for single-molecule protein identification (SMPI) and describe an algorithm for identification of the electrical current blockade signal (nanospectrum) resulting from the translocation of a denaturated, linearly charged protein through a sub-nanopore. The analysis of identification p-values suggests that the current technology is already sufficient for matching nanospectra against small protein databases, e.g., protein identification in bacterial proteomes.