<p>Quantitative measurement of metabolites is essential to understand biological and disease processes. Absolute quantification by spiking heavy&#xa0;isotope-labeled internal standards and analyzing on mass spectrometry (MS) platform is a key method to determine the concentration of metabolites in biological samples. However, MS-based absolute quantification is often challenged by the commercial availability and high costs of isotope-labeled internal standards. Here, we establish an absolute quantification method for amine metabolites utilizing isotopic <i>N</i>,<i>N</i>-dimethyl leucine (iDiLeu) tagging on the LC-MS/MS platform. Absolute quantification of metabolites with excellent accuracy and precision can be achieved with five-plex iDiLeu labeling without the need of isotope-labeled internal standards. We demonstrated that iDiLeu labeling improved the separation and detection limits of polar metabolites. Particularly, detection limits for glycine, GABA, and serotonin have been improved by more than 20 folds, and valine by more than 2000 folds. With iDiLeu tagging, 87 amine-containing metabolites were identified and quantified in human cerebrospinal fluid (CSF) samples, revealing potential metabolic changes in Alzheimer’s disease patients.</p> Graphical Abstract <p></p>