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• W4317751903 endingPage "604" @default.
• W4317751903 startingPage "594" @default.
• W4317751903 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." @default.
• W4317751903 created "2023-01-23" @default.
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• W4317751903 date "2023-01-23" @default.
• W4317751903 modified "2023-10-14" @default.
• W4317751903 title "AlacatDesigner─Computational Design of Peptide Concatamers for Protein Quantitation" @default.
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• W4317751903 doi "https://doi.org/10.1021/acs.jproteome.2c00608" @default.
• W4317751903 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/36688735" @default.
• W4317751903 hasPublicationYear "2023" @default.
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