@article {Sampath015297, author = {G. Sampath}, title = {Peptide sequencing in an electrolytic cell with two nanopores in tandem and exopeptidase}, elocation-id = {015297}, year = {2015}, doi = {10.1101/015297}, publisher = {Cold Spring Harbor Laboratory}, abstract = {A nanopore-based approach to peptide sequencing without labels or immobilization is considered. It is based on a tandem cell (RSC Adv., 2015, 5, 167-171) with the structure [cis1, upstream pore (UNP), trans1/cis2, downstream pore (DNP), trans2]. An amino or carboxyl exopeptidase attached to the downstream side of UNP cleaves successive leading residues in a peptide threading from cis1 through UNP, followed by a cleaved residue translocating to and through DNP where it is identified. A Fokker-Planck model is used to compute translocation statistics for each amino acid type. Multiple discriminators, including the current blockade level (or a variant thereof) and translocation times through trans1/cis2 and DNP, are used to identify a residue. Calculations show the 20 amino acids to be grouped by charge (positive, negative, neutral) and ordered within each group. The ordering makes error correction easier because an incorrectly called residue need only be replaced with its nearest neighbor in the order. The minimum cleaving interval required of the exopeptidase, the sample size (number of copies of the peptide to sequence or number of runs with one copy) to identify a residue with a given confidence level, and confidence levels for a given sample size are calculated. The results suggest that if the exopeptidase cleaves every residue and does so in a reasonable amount of time, peptide sequencing with acceptable (and correctable) errors may be feasible. If validated experimentally the proposed device could be an alternative to mass spectrometry and gel electrophoresis. Implementation-related issues are discussed.}, URL = {https://www.biorxiv.org/content/early/2015/02/17/015297}, eprint = {https://www.biorxiv.org/content/early/2015/02/17/015297.full.pdf}, journal = {bioRxiv} }