In this chapter, we describe a method for the quantitative analysis of glycolytic intermediates using ion chromatography-mass spectrometry (IC-MS) and gas chromatography (GC)-MS as complementary methods. With IC-MS-MS, pyruvate, glucose-6-phosphate, fructuse-6-phosphate, fructose-1,6-bisphosphate, phosphoenolpyruvate, and the sum of 2-phosphoglyceraldehyde + 3-phosphoglyceraldehyde can be quantified. With GC-MS using selected ion monitoring, glyceraldehyde-3-phosphate, dihydroxyacetonephosphate, 2-phosphoglyceraldehyde, and 3-phosphoglyceraldehyde can be analyzed. The derivatization for GC-MS is performed in two steps. In the first step, the keto and the aldehyde groups are oximated. In the next step, a silylation with N-methyl-N-trimethylsilyltrifluoroacetamide (MSTFA) is performed, giving TMS-MOX derivatives of the glycolytic intermediates. The derivatives are separated on a GC column and detected with MS in SIM mode.