AlacatDesigner─Computational Design of Peptide Concatamers for Protein Quantitation

Area of Science:

• Proteomics
• Mass Spectrometry
• Synthetic Biology

Background:

• Accurate protein quantitation in mass spectrometry often requires external standards like stable isotope-labeled peptides.
• Designing effective recombinant protein standards (QconCATs) for accurate quantitation is challenging due to peptide signal variability.
• Synthetic biology enables an "a-la-carte" assembly method for QconCATs, termed ALACATs.

Purpose of the Study:

• To introduce AlacatDesigner, a software tool to aid in the design of ALACATs.
• To support users in selecting optimal peptide sequences for recombinant protein standards based on target proteins.
• To improve the accuracy and reliability of protein quantitation in mass spectrometry.

Main Methods:

• AlacatDesigner utilizes user-defined target proteins to select peptides for recombinant standards.
• The tool considers peptide occurrence in databases and literature, potential post-translational modifications, and predicted miscleavage.
• It also evaluates predicted divergence in peptide and protein quantifications and ionization potential for mass spectrometry.

Main Results:

• AlacatDesigner facilitates the selection of peptides enriched for proteotypic and quantotypic characteristics.
• The tool's peptide selections demonstrate improved suitability for quantitation compared to empirical data.
• The software is accessible as a web interface, desktop application, or Python package.

Conclusions:

• AlacatDesigner is a valuable tool for designing customized recombinant protein standards (ALACATs).
• The software enhances the selection of peptides, leading to more accurate and reliable protein quantitation.
• AlacatDesigner democratizes the design of protein quantitation standards for proteome science.