Applications of targeted proteomics in metabolic engineering: advances and opportunities

•Targeted proteomics is now a routine tool to verify protein expression levels.•Targeted proteomics enables multiplex quantification of selected proteins expression.•Targeted proteomics can be used to identify metabolic pathway bottleneck.•Altered native protein levels in metabolic engineering can be measured by proteomics.•Targeted proteomics supports genome-scale metabolic model and flux balance analysis. Optimization of metabolically engineered organisms requires good understanding of producing balanced level of pathway proteins. Targeted proteomics via selected-reaction monitoring (SRM) has been increasingly used in metabolic engineering studies to detect and quantify sets of proteins with high selectivity, multiplexity, and reproducibility. In combination with metabolomics and other omics tools, targeted proteomics has helped optimize the production of many bio-based chemicals in various metabolic engineering cell factories. In this review, we present recent applications of targeted proteomics in metabolic engineering studies and highlight several successful cases of targeted proteomics in boosting production of commodity and high value chemicals. Additionally, we also discuss challenges and limitations of current targeted proteomics and map opportunities for future research.