Selecting an MS Analytical Method

Guidelines on how to choose which technique to use to obtain a mass spectrum of your sample

There is no single universal mass spectral technique available that is applicable to all samples. Conversely, several different techniques may give similar results for a given sample. The mass spectral method that is selected for a specific sample is dependant on a number of factors, including the physical and chemical properties of the sample (thermal stability, etc.), the type of data required (nominal or accurate mass), and the mass range of the sample.

These parameters will influence the choice of ionization method and mass analyzer that will be required, and hence the MS technique to be employed.

Below are some guidelines for selecting the mass spectral technique for your particular sample. These are by no means definitive and if you are unsure of the method to be employed or have further questions, please seek further advice from the mass spec facility.

Selecting the type of mass spectral you want

A low resolution scan is a complete mass spectrum. It may show the molecular ion and/or fragment ions. Masses are generally accurate to within a few tenths of a mass unit (though this is not true for MALDI mass spectra). A low resolution scan is often the only mass spectrum you need. If you wish to confirm or determine the elemental composition of your compound, you will need a high resolution mass spectrum. The mass is determined to four decimal places, and a computer program calculates elemental compositions that are within experimental error of that mass. Normally, you would have only the molecular ion measured, but it is possible to measure several or all of the peaks in a spectrum. In this lab, high resolution mass spectra can only be acquired using the VG70S high resolution instrument, which is equipped with EI, CI and FAB ionization methods, and so limits this type of measurement to those samples that can be ionized by these methods.

If your compound does not fragment in the mass spectrometer and you require fragmentation for structural determination, you will need to use MS/MS analysis methods which is available with the ion-trap instrument (which is normally equipped with ESI ionization). The most common use of MS/MS is for the sequencing of peptides. If you are using isotopic labeling, you need an isotope ratio mass spectrum. Comparing the mass spectrum of your labeled and unlabeled compounds will tell you the amount of enrichment. If your sample is a mixture, and you want a mass spectrum of one or more components, you will need either GC/MS (which is equipped with EI ionization) or LC/MS (equipped with ESI). In these techniques, the effluent is directed into the mass spectrometer, where a spectrum of each component is obtained as it elutes from the column.

Selecting the Ionization method

To obtain a mass spectrum, the sample must first be ionized. The instruments in the Mass Spectrometry Laboratory are capable of all modern ionization techniques. Each has it’s own advantages. For assistance in selecting a technique, please use the chart below as a selection guide. For further advice, please contact the MSF for advice.