Targeted Proteomics

Reducing DBTL cycles required to produce target molecules

Targeted proteomics assays are applied to specific hypotheses via selected-reaction monitoring mass spectrometry methods that accurately quantify a select group of proteins.

This approach has been applied to determine pathway bottlenecks, compare enzyme homologs for a specific enzymatic step, and to track dynamic regulation of protein levels engineered microbes. 

Potential applications of targeted proteomics:
  • Identifying protein-associated bottlenecks, resulting in improved final product levels
  • Quantifying protein levels for genetic tool development studies 
  • Characterization and quantification of stable post-translational modifications for engineered microbes

This capability uses automation to reduce sample preparation variability and leverage integration with our ICE sequence/strain repository platform and Experiment Data Depot

Our targeted proteomics capability supports the Agile BioFoundry through rapid testing of engineered microbes to reduce the number of DBTL cycles required to successfully produce target molecules. 

Targeted proteomic assays are limited to quantify fewer than 75 proteins in high-throughput applications, but can accurately quantify hundreds of proteins for lower throughput experiments. The method also requires that unique peptides for a specific protein can be targeted. Each protein and peptide has different limits of detection, so sensitivity ranges will vary depending on the experiment.

Labs:
  • Lawrence Berkeley National Laboratory
  • Pacific Northwest National Laboratory