Johns Hopkins All Children's CRIB / MDC

Mass Spectrometry:

The Basics and How It Applies to Metabolomics

Mass spectrometry (MS) is an analytical technique that allows for the accurate mass measurement of gas phase ions by separation based upon the ion’s mass to charge ratio (m/z).  There is a wide variety of MS instrumentation available, each with unique resolution, mass accuracy, sensitivity, and speed characteristics.  Instrument selection depends upon one’s budget and specific measurement or research goals.  All instrument types are comprised of three basic components: an ionization source, a mass analyzer, and a detector.

An MS experiment measures the m/z of one or more ions, however some mass spectrometers have two mass analyzers, enabling what is known as a tandem MS, or MS/MS experiment.  In these instances, a single m/z called the precursor ion is isolated, and fragmented to produce what are called product ions.  The most common means of fragmenting ions is mass spectrometry is collision-induced dissociation (CID), in which the ions collide with neutral gas molecules.  The second mass analyzer in the instrument measures the m/z of the product ions, giving information as to the structure of the precursor ion.  MS and MS/MS combined can facilitate structural elucidation of unknown molecules or validate the presence of a given substance.

Discovery metabolomics primarily relies upon MS experiments, with MS/MS less commonly used for occasional verification or towards identification of unknown metabolites.  Targeted metabolomics experiments are mostly a specific type of MS/MS experiment known single reaction monitoring (SRM) or multiple reaction monitoring (MRM), where single versus multiple reflects the number of analytes (metabolites) under study.  In this type of MS/MS experiment a single m/z is isolated in the first mass analyzer, as with a standard MS/MS experiment, but a specific product ion m/z is isolated in the second mass analyzer.  This method is extremely selective, enabling the best sensitivity available by mass spectrometry.