The reach of omic analyses now includes the breadth of the cell life cycle, allowing study of processes from translation of RNA to protein, through proteome development and interactions, and metabolic activities. However, as Caprioli et al. (2018) note:
"Many published methodologies for preparing samples for proteomic analysis by mass spectrometry are entirely incompatible with the analysis of metabolites or RNA from the same sample due to the presence of specific buffer components or detergents."
The ideal, to study multiple omic systems from a single sample, is now possible using the process described in this Journal of Proteome Research paper: “An Integrated, High-Throughput Strategy for Multiomic Systems Level Analysis".
In the paper Caprioli et al. used Rapid-Digestion Trypsin/Lys-C (described on this page) in their tryptic digestion of proteomic samples.