Clinical Applications of Mass Spectrometry pp 423-431

Part of the Methods in Molecular Biology book series (MIMB, volume 603)

Urine Organic Acid Analysis for Inherited Metabolic Disease Using Gas Chromatography-Mass Spectrometry

  • Patricia M. Jones
  • Michael J. Bennett


Urine organic acid analysis is an essential component of the workup of the patient suspected to have an inborn error of metabolism (IEM). Urine contains several hundred different organic acids, which arise from a multitude of different sources including both normal and abnormal metabolism. They may also arise from drugs and drug metabolism or from xenobiotics and dietary supplements. In addition to the diagnosis of inborn errors of metabolism, the identification of organic acids in a urine sample has a wide range of potential applications, including toxicology and poisonings. The method described below extracts the acidic fraction from urine samples, derivatizes the extracted compounds, and identifies intermediate metabolites by GC-MS. The method utilizes electron impact ionization gas chromatography-mass spectrometry (GC-MS) with total ion collection.

Key words

Organic acids inborn errors of metabolism gas chromatography-mass spectrometry 


  1. 1.
    Chalmer, R.A., Lawson, A.M. (1982) Organic Acids in Man: The Analytical Chemistry, Biochemistry and Diagnosis of the Organic Acidurias. Chapman & Hall, London.Google Scholar
  2. 2.
    Goodman, S.I., Markey, S.P. (1981) Diagnosis of organic acidemias by gas chromatography-mass spectrometry. Laboratory and Research Methods in Biology and Medicine, Volume 6. Alan R. Liss, Inc., New York.Google Scholar
  3. 3.
    Sweetman, L. (1991) Organic acid analysis, in Techniques in Diagnostic Human Biochemical Genetics: A Laboratory Manual. (Hommes, F.A., ed), Wiley-Liss, New York, pp 143–176.Google Scholar
  4. 4.
    Hoffmann, G., Feyh, P. (2004) Organic acid analysis, in Physician’s Guide to the Laboratory Diagnosis of Metabolic Diseases, second edition (Blau, N., Duran, M., Blaskovics, M.E., Gibson, K.M., eds), Springer, New York, pp. 27–44.Google Scholar
  5. 5.
    Bennett, M. (2006) Recommendations for the measurement of urine organic acids, in Laboratory Medicine Practice Guidelines: Maternal-Fetal Risk Assessment and Reference Values in Pregnancy (Sherwin, J.E., Lockitch, G., Rosenthal, P., et al, authors) National Academy Clinical Biochemistry, Washington, DC, pp. 59–62.Google Scholar
  6. 6.
    American College of Medical Genetics. (2006) F: Clinical biochemical genetics, in Standards and Guidelines for Clinical Genetics Laboratories.
  7. 7.
    Rinaldo, P., Hahn, S., Matern, D. (2006) Inborn errors of amino acid, organic acid, and fatty acid metabolism, in Tietz Textbook of Clinical Chemistry, Fourth Edition (Burtis, C.A., Ashwood, E.R., Bruns, D.E., eds), Elsevier Saunders, St. Louis, MO, pp 2207–2247.Google Scholar
  8. 8.
    Ozand, P.T., Generoso G.G, (1991) Organic acidurias: A review. Part 2. J. Child. Neurol, 6: 288–303.CrossRefPubMedGoogle Scholar
  9. 9.
    Kumps, A., Duez, P., Mardens, Y. (2002) Metabolic, nutritional, iatrogenic, and artifactual sources of urine organic acids: A comprehensive table. Clin. Chem, 48(5): 708–717.PubMedGoogle Scholar

Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Patricia M. Jones
    • 1
  • Michael J. Bennett
    • 2
  1. 1.Department of PathologyUniversity of Texas Southwestern Medical Center and Children’s Medical CenterDallasUSA
  2. 2.Department of Pathology and Laboratory MedicineUniversity of Pennsylvania and Children’s Hospital of PhiladelphiaPhiladelphiaUSA

Personalised recommendations