Various embodiments illustrating a multiplexed method for high throughput screening of ions in biological samples within a single capillary when using capillary electrophoresis mass spectrometry (CE-MS) are illustrated. The method includes sequential injection of multiple sample segments in series within a single capillary, the sample segments being separated by a spacer plug of buffer, and multiplexed analysis of the sample segments simultaneously within a single capillary electrophoresis (CE) run. The method also includes application of voltage to the single capillary subsequent to sequential injection and zonal separation of polar metabolites within each sample segment by CE such that each analyte zone migrates within its characteristic electrophoretic mobility offset in time by the spacer. The incorporation of a quality control/reference sample and the use of dilution patterning with specific injection configurations also enables encoding of information temporally for enhanced data processing with quality assurance.