Alkyl chloroformates are known for their ability to produce mixed anhydrides, and they have found use as versatile derivatization reagents for gas chromatographic (GC) separation of amino- and organic acids. Triple-quadrupole mass spectrometers are excellent detectors for high sensitive and selective analysis. Here, we describe a methyl chloroformate (MCF) GC-MS/MS method for the quantitative analysis of metabolites containing amino- and/or carboxylic groups. The method covers over 60 metabolites with quantitation limits down to the low picomole range injected on column, and any metabolite with amino- and/or carboxylic acid functional groups that yield a stable and volatile MCF derivative can be included in the method. Absolute quantitation can be achieved by including a stable isotope-coded derivatization agent (d3-MCF) and deuterated alcohol solvent (e.g., d4-methanol). As the carboxylic and amino groups are differently labeled, the former from the solvent methanol while the latter from MCF, this approach can also be used to identify a number of amino and carboxylic groups in unknown analytes in an extract.