Patterns of lipid expression can provide insight into the origins of many pathologies, including Alzheimer’s disease, diabetes, cancer and viral pathogenesis. Currently, mass spectrometry provides the most comprehensive picture of lipid expression. Researchers at Kansas State University in Manhattan reviewed mass spectrometry for lipidomics in a chapter of the 2007 edition of Genetic Engineering Reviews.Mass spectrometry separates molecules based on their mass-to-charge ratio, so samples must be ionized. Complex lipids require such ionization methods as matrix-assisted laser desorption ionization, electrospray ionization, fast atom bombardment or atmospheric pressure chemical ionization. In electrospray ionization, the most common ionization method, droplets containing the analyte are misted into the chamber, where opposing electric fields separate them.Some laboratories have employed variations of electrospray ionization. Coordination ion spray mass spectrometry is a type of the technique that uses a metal ion, typically silver or another transition metal, to bind to nonpolar samples that are difficult to ionize. Because atmospheric pressure chemical ionization is typically better than electrospray ionization at separating steroids, some researchers have used both techniques. Compounds can be separated by liquid chromatography before ionization. Otherwise, as long as they are in liquid form, they can simply go into the mass spectrometer. For lipid analysis, the triple quadrupole — a tandem mass spectrometry instrument — is the most commonly used mass analyzer. Tandem mass spectrometers can perform a product ion scan in which analytes separated by the first spectrometer are further broken down by a second one. Precursor ion scans and neutral loss scans are other modes that are useful for lipid analysis.Matrix-assisted laser desorption ionization used with a time-of-flight analyzer can analyze lipids faster than electrospray ionization, but the technique has several drawbacks. Perhaps most notably, the method requires careful sample preparation. Additionally, the time-of-flight analyzer may be less sensitive than the quadrupole analyzer. However, matrix-assisted laser desorption ionization can be used for imaging tissues. Additionally, researchers are developing other mass spectrometry methods for imaging lipids.For quantification, mass spectrometry results must be compared with standards. However, the reviewers mention that commercially available standards for lipidomic analyses often are lacking, so laboratories must spend time making their own.The authors note that the massive amounts of lipidomic data produced by mass spectrometry will necessitate advancements in data processing and the development of accessible and comprehensive databases, as well as methods for applying lipidomic data to answering real biological questions.