Mass spectrometry (MS)-based metabolomic initiatives that use conventional separation techniques are limited by low sample throughput and complicated data processing that contribute to false discoveries. Herein, we introduce a new strategy for unambiguous identification and accurate quantification of biomarkers for inborn errors of metabolism (IEM) from dried blood spots (DBS) with quality assurance. A multiplexed separation platform based on multisegment injection-capillary electrophoresis-mass spectrometry (MSI-CE-MS) was developed to provide comparable sample throughput to flow injection analysis-tandem MS (FIA-MS/MS) but with greater selectivity as required for confirmatory testing and discovery-based metabolite profiling of volume-restricted biospecimens. Mass spectral information is encoded temporally within a separation by serial injection of three or more sample pairs, each having a unique dilution pattern, alongside a quality control (QC) that serves as a reference in every run to facilitate between-sample comparisons and/or batch correction due to system drift. Optimization of whole blood extraction conditions on DBS filter paper cut-outs was first achieved to maximize recovery of a wide range of polar metabolites from DBS extracts. An interlaboratory comparison study was also conducted using a proficiency test and retrospective neonatal DBS that demonstrated good agreement between MSI-CE-MS and validated FIA-MS/MS methods within an accredited facility. Our work demonstrated accurate identification of various IEM based on reliable measurement of a panel of primary or secondary biomarkers above an upper cutoff concentration limit for presumptive screen-positive cases without stable isotope-labeled reagents. Additionally, nontargeted metabolite profiling by MSI-CE-MS with temporal signal pattern recognition revealed new biomarkers for early detection of galactosemia, such as N-galactated amino acids, that are a novel class of pathognomonic marker due to galactose stress in affected neonates.