I am planning some experiments to investigate how mono cultures of microbes respond to different nutrient concentrations. I want to use an -omics based approach to understand how, on a molecular level, the microbes utilise these nutrients by looking for up regulation of associated genes. With the idea looking out for upregulation in mind, I was going to go for transcriptomics. But now I am beginning to realise that regulatory changes in genes does not necessarily translate to the molecular utilisation of a nutrient by a cell. To that end, perhaps I would be better using quantitative proteomics to capture changes in the concentration of functional proteins which are actually interacting with the nutrients. However, I worry that by relying on proteomics I might miss important regulatory changes for microbe species where the proteome is less well defined.
I should say that it's an either/or situation, there is only budget for one. I'd appreciate any thoughts on the best approach. Thanks.