AlacatDesignerComputational Design of Peptide Concatamers for Protein Quantitation

Protein quantitation
via mass spectrometry relies on peptide proxies
for the parent protein from which abundances are estimated. Owing
to the variability in signal from individual peptides, accurate absolute
quantitation usually relies on the addition of an external standard.
Typically, this involves stable isotope-labeled peptides, delivered
singly or as a concatenated recombinant protein. Consequently, the
selection of the most appropriate surrogate peptides and the attendant
design in recombinant proteins termed QconCATs are challenges for
proteome science. QconCATs can now be built in a “a-la-carte”
assembly method using synthetic biology: ALACATs. To assist their
design, we present “AlacatDesigner”, a tool that supports
the peptide selection for recombinant protein standards based on the
user’s target protein. The user-customizable tool considers
existing databases, occurrence in the literature, potential post-translational
modifications, predicted miscleavage, predicted divergence of the
peptide and protein quantifications, and ionization potential within
the mass spectrometer. We show that peptide selections are enriched
for good proteotypic and quantotypic candidates compared to empirical
data. The software is freely available to use either via a web interface AlacatDesigner, downloaded as a Desktop application or imported as a Python package
for the command line interface or in scripts.