{\it De novo} protein sequencing is essential for understanding cellular
processes that govern the function of living organisms and all
post-translational events and other sequence modifications that occur after a
protein has been constructed from its corresponding DNA code. By obtaining the
order of the amino acids that composes a given protein one can then determine
both its secondary and tertiary structures through structure prediction, which
is used to create models for protein aggregation diseases such as Alzheimer's
Disease. Mass spectrometry is the current technique of choice for {\it de novo}
sequencing. However, because some amino acids have the same mass the sequence
cannot be completely determined in many cases. Here, we propose a new technique
for {\it de novo} protein sequencing that involves translocating a polypeptide
through a synthetic nanochannel and measuring the ionic current of each amino
acid through an intersecting {\it perpendicular} nanochannel. To calculate the
transverse ionic current blockaded by a given amino acid we use a Monte Carlo
method along with Ramachandran plots to determine the available flow area,
modified by the local density of ions obtained from molecular dynamics and the
local flow velocity ratio derived from the Stokes equation. We find that the
distribution of ionic currents for each of the 20 proteinogenic amino acids
encoded by eukaryotic genes is statistically distinct, showing this technique's
potential for {\it de novo} protein sequencing.Comment: 12 pages (9 of main text, 3 of supporting information), 4 figures, 1
table in supporting informatio
