A method based upon a combination of high performance liquid chromatography (HPLC) and electrospray ionization (ESI) mass spectrometry (MS) for the analysis of phosphorylated peptides in a complex mixture of 14 phosphoenkephalins and their nonphosphorylated analogues is described. A narrow-bore column is directly connected to the ESI interface without the need of a solvent flow-splitter. A full-scan mass analysis in the positive-ion mode is used to provide the total ion current chromatogram and the molecular mass of each eluting component. Selective detection of phosphorylated peptides is achieved by selected-ion recording of the phosphate group marker ion (PO3−) in the negative-ion mode. These two scans are acquired simultaneously on a single injection of the sample. The influence of water clusters on background ion current is also discussed.