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Mixtures of standard compounds of biological interest were analyzed by capillary electrophoresis in conjunction with tandem four sector mass spectrometry (MS/MS) using an array detector. Capillary electrophoresis offers extremely high separation efficiencies while array detection allows for the simultaneous acquisition of a large fraction of a tandem mass spectrum and high utilization of the sample ions produced. Consequently, improvements in sensitivity and structural information were observed for the combined techniques in comparison to similar measurements with a four-sector and a single-point detector. Coaxial continuous-flow fast atom bombardment was used to create (M + H) precursor ions of the separated analyses and their product ion spectra were acquired from femtomole levels in electrophoretic real-time. The limit-of-detection for the acquisition of MS/MS data from electrophoretically-separated peptides was 35-100 fmol . The MS/MS data acquired at these levels showed cleavages of the peptide backbone (i.e. to give a and γ ions) and production of immonium ions from the constituent amino acids. Acquisition of the spectra via the array detector is more routine and, at the 100 femtomole level, provides more structurally informative ions and yields better ion statistics than comparable spectra acquired with a point detector.