# A quasi-digital approach to peptide sequencing using tandem cells with endo- and exo-peptidases

## TL;DR

A new quasi-digital method for sequencing peptides uses tandem cells and peptidases to identify amino acid sequences through current blockades.

## Contribution

The paper introduces a novel quasi-digital peptide sequencing method using tandem cells and peptidases to determine amino acid sequences.

## Key findings

- A double tandem cell setup with endo- and exo-peptidases can cleave peptides into fragments and detect residues via current blockades.
- Using 20 tandem cells and a simple algorithm, the method can assemble peptide sequences from lists of residue counts.
- High translocation speeds can be managed with a sufficiently long third pore, enabling detection within current CMOS circuit capabilities.

## Abstract

A method of sequencing peptides using tandem cells (RSC Adv., 2015, 5, 167-171; RSC Adv., 2015, 5, 30694-30700) and peptidases is considered. A double tandem cell (two tandem cells in tandem) has three nanopores in series, an amino-acid-specific endopeptidase attached downstream of the first pore, and an exopeptidase attached downstream of the second pore. The endopeptidase cleaves a peptide threaded through the first pore into fragments that are well separated in time. Fragments pass through the second pore and are each cleaved by the exopeptidase into a series of single residues; the latter pass through the third pore and cause distinct current blockades that can be counted. This leads to an ordered list of integers corresponding to the number of residues in each fragment. With 20 cells, one per amino acid type, and 20 peptide copies, the resulting 20 lists of integers are used by a simple algorithm to assemble the sequence. This is a quasi-digital process that uses the lengths of subsequences to sequence the peptide, it differs from conventional analog methods which seek to identify monomers in a polymer via differences in blockade levels, residence times, or transverse currents. Several implementation issues are discussed. In particular the usually intransigent problem of high translocation speeds may be resolved through the use of a sufficiently long (40-60 nm) third pore. This translates to a resolution time of ∼2 μs, which is within the range of currently available CMOS circuits.