Software Pipelines for Targeted and Untargeted Proteomics in Bioengineering Applications

This chapter presents concepts, guidelines, and data processing procedures for the analysis of targeted and untargeted proteomics data in bioengineering contexts. The pipelines have been successfully demonstrated in microbial systems such as Rhodotorula toruloides, Pseudomonas putida, and Aspergillus niger. The methods described in these workflows involve popular open-source software tools and downstream algorithms that enhance data annotation, quantification, and reproducibility. These procedures can be used to quantify metabolic pathway enzymes and validate engineered strains. While focused on bioengineering applications, most of these procedures apply to any proteomics study. The chapter uses published data and step-by-step guides to allow researchers unfamiliar with the approach to successfully execute the techniques.