DIA assay libraries enable analyses of mRNA:protein coregulation by ecological contexts
Determining the relationship between mRNA and protein abundance was an important aim of this analysis, which shapes further analytical approaches. This study found very low correlation between mRNA and proteins in kidneys of fish acclimated from FW to BW. The proteins identified as significant using the DIA assay library approach would not have been identified from transcriptomics studies since none of the corresponding mRNAs were significantly regulated. Therefore, functional analyses based on proteome dynamics during salinity stress provide additional rather than merely redundant information when compared with mRNAseq analyses (see below). In theory, lack of coregulation between the mRNA and protein levels of biological organization during salinity acclimation can be attributed to both biological and technical causes. From a technical standpoint, the dynamic range of protein quantity in a tissue sample is several orders of magnitude greater than that for mRNA (Buccitelli & Selbach, 2020). Because the protein dynamic range is so much greater, differences in protein levels can be identified more accurately. Biologically, because protein’s action and stability can be modulated by post-translational modification (PTM), cells may not need to alter mRNA levels in order to respond to a stressor (Jovanovic et al., 2015), which has indeed been suggested for salinity stress responses of euryhaline fish (Evans & Somero, 2009). Additionally, proteins typically have a significantly longer half-life than mRNA and are less prone to rapid changes, which reduces the overall variability between replicates for proteins (Schwanhäusser et al., 2011).