Stable isotopically labeled amino acids are used extensively in studies of protein and amino acid metabolism at the whole-body and tissue levels. The gas chromatograph-mass spectrometer (GC-MS) is a versatile instrument to measure the isotopic enrichment of amino acids. Investigators today are faced with diverse GC-MS methods, which combine a variety of derivatives available for amino acid separation by gas chromatography (GC) with different ionization modes for mass spectrometer (MS) operation. Adding to this diversity is a variety of approaches that are used to calculate isotopic enrichments from GC-MS measurements.