We have developed a method based on capillary electrophoresis (CE) coupled to mass spectrometry (MS) that is a powerful tool for metabolome analysis. In this paper, a simple method for the simultaneous analysis of anionic metabolites such as sugar phosphates, organic acids, nucleotides and CoA compounds based on pressure-assisted capillary electrophoresis coupled to electrospray ionization mass spectrometry (PACE/ESI-MS) is described. The feature of this method is that CE polarity, where the inlet of the capillary is at the anode and the outlet at the cathode, is inverted from conventional CE analysis for anions. Moreover, an ordinary fused silica capillary was chosen instead of a specific cationic polymer-coated capillary (SMILE (+) capillary). A robust and inexpensive analytical method was established from the above-mentioned CE polarity and noncoated fused silica capillary. A trimethylamine acetate electrolyte, pH 10.0, provides a high resolution between isomers. Electrolyte flow using an air pump after electrophoresis enables the comprehensive and simultaneous analyses of sugar phosphates, organic acids, nucleotides and a CoA compound that to date have been impossible to analyze. Our method can be used as a de facto standard for metabolome analysis.