Blood is a widely used biofluid in discovery metabolomic research to search for clinical metabolite biomarkers of diseases. Analyzing the entire human blood metabolome is a major analytical challenge, as blood, after being processed into serum or plasma, contains thousands of metabolites with diverse chemical and physical properties as well as a wide range of concentrations. We describe an enabling method based on high-performance chemical isotope labeling (CIL) liquid chromatography-mass spectrometry (LC-MS) for in-depth quantification of the metabolomic differences in comparative blood samples with high accuracy and precision.