Mass Spectrometry

Contact: Albert Ruggi


Mass Spectrometry (MS) Tips

The choice of the MS technique is of paramount importance to obtain meaningful results.

To make this choice one must consider a few parameters:  

  • The expected mass* (m/z) of the target molecule
  • The most suitable ionization method
  • The level of accuracy needed


* “Masses” of molecules in MS (the “numbers” that appear on the x-axis of a mass spectrum) are always expressed in m/z, i.e. the ratio between molecular weight and charge of the species. This means that a molecule with a 2+ charge and a molecular weight of 1000 will be observed at 500 m/z.

Here are some basic indications to choose the most suitable instrument for your measurements.

Please contact the Responsible Person for any doubts or questions.


ESI (Bruker Esquire HCT)

The routine (open access, contact the responsible for training) instrument capable of measuring masses in the range 50-3000 m/z.  ESI works only if your compound has a permanent charge (e.g. quaternary ammonium compounds, metal complexes) or if it can take a charge from protonation (positive mode), deprotonation (negative mode) or formation of adducts with charged species (usually Na+ or Cl-).


MALDI (Bruker UltrafleXtreme MALDI-TOF)

This instrument is capable of measuring molecules of high molecular weight (1000-500000 m/z) and it is the standard instrument for polymer analysis. The access to this instrument is restraint: MALDI measurements can be requested using the MS Request Form


EI (Thermo Trace DSQ II and Voyager GC-MS)

This is the routine (open access, contact the responsible for training) instrument for low molecular weight (30-500 m/z) compounds. The EI spectrometer is connected to a GC, therefore in principle it can be used only for volatile molecules. EI technique is the best choice to analyse compounds which do not form adducts or do not have a permanent charge (e.g. hydrocarbons).


FT-ICT (Bruker BioApex II 4.7T )

This instrument is equipped with an ESI ionization source and it is used to perform high resolution mass spectrometry (HR-ESI, a.k.a. exact mass) on molecules of weight in the range 200-3000 m/z. The access to this instrument is restraint: HR-ESI measurements can be requested using the form, MS Request Form


Before asking for a HR-ESI, please keep in mind the following points:

  • HR-ESI is not a “better” ESI: if your compound is not visible in ESI it will not be visible in HR-ESI! It is recommended to perform a standard ESI before applying for HR-ESI.
  • HR-ESI is typically used to characterize a compound when high accuracy (4 decimal digits) is needed, e.g. for a publication.
  • HR-ESI does not provide any information on the purity of the compound.


Please check Rules for Mass Spectrometry Service