A novel method employing CE−ESMS and precursor ion scanning was developed for the selective detection of nucleotide-activated sugars. By using precursor ion scanning for fragment ions specific to the different nucleotide carriers, i.e., ions at m/z 322 for cytidine monophosphate, m/z 323, 385, and 403 for uridine diphosphate, m/z 362, 424, and 442, for guanosine diphosphate, and m/z 346, 408, and 426 for adenosine diphosphate, it was possible to selectively detect sugar nucleotides involved in the biosynthesis of glycoconjugates such as glycoproteins and lipopolysaccharides. Enhancement of sensitivity was achieved using N-(2-hydroxyethyl)piperazine-N‘-(2-ethanesulfonic acid) as a sample stacking buffer and provided detection limits between 0.2 and 3.8 pmol·mL-1. The present CE−ESMS method provided linear dynamic ranges over the concentrations 0.2−164 nM (r2 = 0.952−0.997) for different nucleotide sugar standards. The application of this method is demonstrated for the identification of intracellular pools of sugar nucleotides in wild type and isogenic mutants from the bacterial pathogen Campylobacter jejuni. By using product ion scanning (with and without front-end collision-induced dissociation), it was possible to determine the precise nature of unexpected sugar nucleotides involved in the biosynthesis of pseudaminic acid, a sialic acid-like sugar previously observed on the flagellin of some pathogenic bacteria.