Rusilowicz, Martin, Newman, David W, Creamer, Declan R, Johnson, James, Adair, Kareena 
ORCID: 0000-0001-9884-2094, Harman, Victoria M ORCID: 0000-0002-0990-153X, Grant, Chris M, Beynon, Robert J ORCID: 0000-0003-0857-495X and Hubbard, Simon J
(2023)
AlacatDesigner-Computational Design of Peptide Concatamers for Protein Quantitation.
JOURNAL OF PROTEOME RESEARCH, 22 (2).
pp. 594-604.
Abstract
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.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | proteomics, absolute quantitation, protein standards, QconCATs, bioinformatics, peptide surrogates, proteotypic, quantotypic |
| Divisions: | Faculty of Health and Life Sciences Faculty of Health and Life Sciences > Institute of Systems, Molecular and Integrative Biology Faculty of Health and Life Sciences > Tech, Infrastructure and Environmental Directorate |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 17 Apr 2023 09:47 |
| Last Modified: | 27 Apr 2023 09:13 |
| DOI: | 10.1021/acs.jproteome.2c00608 |
| Open Access URL: | https://doi.org/10.1021/acs.jproteome.2c00608 |
| Related URLs: | |
| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3169597 |
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