Bacterial small RNA (sRNA) regulators have been identified in many species and play critical regulatory roles in the cell. The majority of identified sRNAs remain uncharacterized and the standard approaches for identifying sRNA targets focus on measuring transcript, not protein, abundances. Here, we introduce a quantitative, time-resolved proteomic method for elucidating sRNA function. Using bio-orthogonal non-canonical amino acid tagging (BONCAT), we measured proteome-wide effects of the expression of the Escherichia coli sRNA regulator CyaR on a time scale of minutes. We identify and confirm three new CyaR targets, expanding the known functions of CyaR to include carbon metabolism, osmoregulation and transcriptional regulation.