These pages provide information on the interpretation and annotation of Mass Spectrometry results. For information on recording mass spectrometry data, please see the instrumentation pages for information about sample submission and collection of data.

The information mass spectrometry provides is very technique dependent. In general soft ionisation methods provide mass measurements for the entire molecule, with this being relatively straight forward to interpret, whereas hard ionisation methods result in fragmentation which can be more complex to analyse.

In general mass spectrometry may be able to provide information as to whether a particular molecule is present or not in a sample, however mass spectrometry alone does not usually provide information about the purity of any given sample, unless recorded through a tandem technique (ie GCMS or LCMS).

A key feature of mass spectometry is the obtaining of isotope pattern information. Many elements have multiple naturally occurring isotopes and the presence of isotopes gives rise to distinctive and predictable isotope patterns for molecules and fragments. More information can be found in the isotope patterns page.

Soft ionisation methods

Electrospray ionisation (ESI)

Electrospray ionisation is the most commonly used method for mass spectrometry analysis in the department. It is quick and easy to run with both positive and negative modes available.

Positive mode is more common and usually results in the molecule of interest being ionised as a protonated (M+H⁺), sodiated (M+Na⁺) or potassiated (M+K⁺) species. Peaks in the resulting spectrum therefore correspond to the molecular mass plus 1 for H, 23 for Na or 39 for K.

Negative mode results in the 

Atmospheric Pressure Chemical Ionisation (APCI)

APCI is an alternative ionisation technique which is routinely available and may be more suitable for some samples.

Hard ionisation methods

Electron ionisation (EI)

Electron ionisation involves the sample being ionised into the gas phase and the molecules colliding with electrons which results in the formation of positive ions through the fragmentation of the molecule, with these fragments being detected.