Single-molecule protein identification by sub-nanopore sensors

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.

Protein identification is the key step in many proteomics studies. Currently, the most popular technique for intact protein analysis is top-down mass spectrometry which recently enabled high-throughput identification of many proteins and their proteoforms. However, this approach requires large amounts of materials and is currently limited to short proteins, typically less than 30 kDa. On the other hand, nanopore sensors promise single molecule sensitivity in protein analysis, but an approach for the identification of a single protein from its blockade current (nanospectrum) has remained elusive, since the signal from the sensors relates to the amino acid sequence of the protein in a poorly understood way. In this work we describe the first algorithm for protein identification based on nanospectra associated with translocation of proteins through pores with sub-nanometer diameters. While identification accuracy currently does not allow reliable processing of complex protein samples yet, we believe, that the rapidly improving experimental protocols along with the new computational algorithms will transform into a viable protein identification approach in the near future.

Amino acid discrimination in a nanopore and the feasibility of sequencing peptides with a tandem cell and exopeptidase

Peptide sequencing in an electrolytic cell with two nanopores in tandem and exopeptidase.