Editorial: Advances in plant proteomics

Abstract

Numerous advances in protein mass spectrometry have been applied to plant systems over the past few decades (Jorrin-Novo, 2021). The intention of this Research Topic was to highlight some of these approaches in plants at a suitable level of detail to enable easy adoption by researchers.The unifying feature of submissions to the Research Topic were associated with the application of protein quantitation or quantitative proteomics. Whole sample quantification of mRNA (expression profiling) has been possible since the 1990s with the development of techniques such as DNA microarray technologies (Bumgarner, 2013), and these approaches have rapidly expanded with the advent of massively parallel sequencing technologies. By contrast, quantification of whole-proteome dynamics (e.g., cell, organ or tissue) is still not possible, even with the considerable technical advances in mass spectrometry that have occurred in the past 20 years (Timp and Timp, 2020). Nonetheless, quantitative proteomic approaches are a major driver for many plant biologists engaging with protein mass spectrometry to gain functional proteome or subproteome insights into the dynamics of protein abundance in plant systems (Mergner and Kuster, 2022).The resolving power of mass spectrometers for proteomics enabled quantitative approaches that incorporate isotopic labelling with stable heavy isotopes such as 15 N (Schulze and Usadel, 2010). Since these instruments can discriminate between heavy ( 15 N) and light ( 14 N) peptides, these metabolically labelled samples can be analysed in a single run e.g., control (light) and treatment (heavy). Such an approach considerably reduces run to run variation and enables reliable protein quantification. This Research Topic illustrates two methods that highlight the advantages of 15 N labelling for quantitative proteomics. Shrestha et al. presents a data analysis workflow outlining the steps used to extract quantitative information from a 15 N labelled analysis. Reyes et al. outlines the application of targeted proteomics or parallel reaction monitoring (PRM) to 15 N labelled samples highlighting potential advantages of combining both labelling and PRM for reliable quantification.