Modern mass spectrometry mostly invloves coupling the mass spectrometer to either an on-line or off-line separation device. The separation device ensures that not more than a limited number of compounds reach the mass spectrometer at any given time during analysis. This simplifies interpretation of data and quantification.

GC/MS, LC/MS & MALDI

Gas chromatography (GC) is used to separate volatile compounds while liquid chromatography (LC) is used for involatile compounds including polar and high molecular weight materials. A number of GC/MS and LC/MS instruments are available at the BMSF providing different levels of sensitivity and mass resolving power. Matrix assisted laser desorption/ionisation - MALDI instruments at the BMSF are used with off-line separations, simple mixtures or pure involatile samples typically of high molecular weight.

Multidimensional LC and Tandem Mass Spectrometry (LC-LC, MS/MS & MSⁿ)

For applications like proteomics, where extremely high numbers of mixture components need to resolved and identified, 2-dimensional liquid chromatographic instuments can be used (LC-LC). These separate components based on orthogonal (i.e., independent) chemical/physical properties. This helps the mass spectrometer to analyse simpler mixtures at each stage of the analysis. To better identify a particular component eluting from the LC or LC-LC instrument, most LC/MS instruments are capable of tandem mass spectrometry (MS/MS or MSⁿ). In this instrumental configuration a specific ion for one mixture component is isolated by the first MS stage and this precursor is further analysed in a second stage. The second stage is preceded by fragmentation of the precursor ion selected by the first stage. In some ion trapping mass spectrometers this last step can be repeated a number of times for MS/MS/MS ... or MSⁿ. Additional advanced modes of analysis are possible in MS/MS. The BMSF maintains a number of LC-LC and MS/MS instruments.

Prefractionation by LC or Gels

Sometimes it is advantageous to 'clean-up' a sample by prefractionation. Liquid chromatography can be used in combination with fraction collecting. Proteins in particular are amenable to separation by electrophoresis. In 1-dimensional gel separations, whole proteins are separated on the basis of molecular weight (SDS PAGE). A second dimension can be added where whole proteins are first separated on the basis of their isoelectric points (2-DE). Bands(SDS PAGE) or spots (2-DE) are stained then cut from gels and the proteins are extracted. Often the proteins are digested with a reagent or enzyme to break them into smaller units (peptides) prior to analysis by LC/MS or MALDI. The BMSF provides access to a number of LC and Gel based prefractionation devices.