Provided are methods for detecting a metabolic disorder in an individual using mass spectrometry. One method involves (a) contacting a sample containing (i) a metabolically indicative enzyme and (ii) a metabolic analyte, with a substrate for the enzyme to produce a reaction admixture, under conditions wherein the enzyme is capable of acting on a corresponding substrate to generate a product, and wherein a protease inhibitor is present; (b) contacting the reaction admixture with a reagent that inhibits the ability of the enzyme to act on a corresponding substrate, wherein the metabolic analyte and the product are soluble in the reagent; to produce a test sample and (c) determining the presence or amount of the metabolic analyte and the product contained in the test sample using mass spectrometry, wherein a determined presence or amount of the metabolic analyte and the product correlates with presence or absence of the metabolic disorder.