Dozens of congenital metabolic diseases  also known as inborn errors of metabolism (IEM) are now detectable by newborn screening tests, especially the testing using gas chromatography–mass spectrometry. GC–MS can determine compounds in urine even in minor concentration. These compounds are normally not present but appear in individuals suffering with metabolic disorders. This is increasingly becoming a common way to diagnose IEM for earlier diagnosis and institution of treatment eventually leading to a better outcome. It is now possible to test a newborn for over 100 genetic metabolic disorders by a urine test at birth based on GC–MS.
In combination with isotopic labeling of metabolic compounds, the GC–MS is used for determining metabolic activity. Most applications are based on the use of C as the labeling and the measurement of C-C ratios with an isotope ratio mass spectrometer (IRMS); an MS with a detector designed to measure a few select ions and return values as ratios.