Combining targeted and untargeted data acquisition to enhance quantitative plant proteomics experiments

Most quantitative proteomics experiments either target a limited number of selected proteins for quantification or quantify proteins on a broad scale in an untargeted manner. However, we recently demonstrated that experiments that have both targeted and untargeted components can be particularly advantageous. Using a combined targeted and untargeted liquid chromatography-tandem mass spectrometry data acquisition strategy termed TDA/DDA (shorthand for targeted data acquisition/data-dependent acquisition), which we applied to a model quantitative plant proteomics experiment performed on Arabidopsis, we demonstrated improved quantification of both targeted and untargeted proteins relative to purely untargeted experiments performed using conventional data-dependent acquisition (Hart-Smith et al. Front Plant Sci 8:1669, 2017). This suggests that many quantitative proteomics datasets earmarked for collection using data-dependent acquisition are likely to benefit from the use of TDA/DDA instead.

This chapter describes how TDA/DDA liquid chromatography-tandem mass spectrometry methods can be created on commonly used mass spectrometric instrument platforms. It described how, using freely available software, tandem mass spectrometry inclusion lists designed to target proteins of hypothesized interest can be generated. Best practice implementation of these inclusion lists in TDA/DDA strategies is then described. Relative to conventional data-dependent acquisition, the liquid chromatography-tandem mass spectrometry methods created using these guidelines increase the chances of quantifying targeted proteins and can produce widespread improvements in the reproducibility of untargeted protein quantification, without compromising the total numbers of proteins quantified. They are compatible with different quantitative proteomics methodologies, including metabolic labeling, chemical labeling and label-free approaches, and can be used to create tailored assay libraries to aid the interpretation of quantitative proteomics data collected using data-independent acquisition.