Decide what type of spectrum you want

Low Resolution Scan

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 Da. This is not true of MALDI. See the Voyager page for MALDI mass accuracy. A low resolution scan is often the only mass spectrum you need.

High Resolution Scan

If you wish to confirm or determine the elemental composition of your compound, you will need a high resolution (EI, CI, ESI, and FAB only) 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.

MS/MS

If your compound does not fragment in the mass spectrometer and you wish to obtain fragmentation for structural determination, you need MS/MS (ESI and MALDI only). 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.

Mixture

If your sample is a mixture, and you want a mass spectrum of one or more components, you will need GC/MS (EI, CI, or FI) or LC/MS (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.