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School of Chemistry

Mass spectrometry service

The mass spectrometry laboratory boasts a range of industry-leading instrumentations, available to use for staff and students alike.

Male researcher using mass spectrometry equipment

The laboratory is housed in GE.003 in the Chemistry Building. It deals with more than 1,500 different types of samples every year and our team constantly works hard to improve the analytical techniques we use.

The laboratory is open weekdays from 8am to 4pm.

More information on instrumentation and techniques is listed below:

Mass spectrometers and techniques available

  • Waters SQD2 (Q-MS with ES+ , ES- and APCI source);
  • Waters QTOF micro (Q-TOF reflectron with ES +- ion source, accurate mass determination <5ppm RMS);
  • Waters QTOF micro with lock spray (Q-TOF reflectron with ES+- and APCI ion source, accurate mass determination <5 ppm RMS);
  • Shimadzu Axima Confidence (MALDI TOF mass spectrometer);
  • Thermo Finnigan MAT95XP (sector MS with electron/ chemical ionisation ion source, accurate mass determination);
  • Agilent 5975C Triple Axis GCMS (GC MS, electron/ chemical ionisation);
  • Hewlet Packard 5971 MSD (GCMS/ MS, electron ionisation only).


  • Agilent Technologies 1260 Infinity (HPLC, we have five of these + one 1200 series, some of them are coupled with the mass spectrometers from the list above);
  • Hewlet Packard 1100, HPLC;
  • Thermo Scientific, Trace 1310 GC;
  • Thermo Scientific, Master GC;
  • Finnigan Forms GC.

Techniques and sample preparation

Electrospray (ES)

A good general technique. Good for polar organic or organometallic molecules, salts and acids. Atmospheric pressure chemical ionisation (APCI) works better on non-polar compounds than ES.

For both ES and APCI submit about 0.1mgs of sample in the autosampler vial with the septum lid, (stores cat. no. Vial 100). Very dilute solutions are needed for these techniques. If too much sample is submitted the excess will be discarded. Only polar solvents can be used, usually methanol, acetonitrile or water. Either the positive or negative ion spectrum can be recorded, or both if you cannot decide which.

The SQD2 is normally run in ES mode and changed to APCI about once a week. Turnaround time for ES is one to two days, and up to a fortnight for APCI.

Electron impact/chemical ionisation (EI/CI)

This can be used for small organic molecules. Volatile samples can be run by GCMS and if needed later analysed on Thermo Finnigan MAT95XP using electron/chemical ionisation for determination of accurate mass.

Matrix Assisted Laser Desorption Ionisation (MALDI)

Polymers, organometallics, proteins and high mass samples. Submit 0.5mgs or more of the solid sample in any small vial. Most solvents can be used. It is important to specify the mass range of interest on the form and put the highest likely mass into the login system.

Gas Chromatography Mass Spectrometry (GCMS)

GCMS can be used for the analysis of small volatile organic compounds. Please submit 1-2mgs of sample in an auto-sampler vial with the septum lid (Vial 100). The sample will be initially attempted by GCMS, however it may be necessary for the sample to be transferred to GC to establish chromatography conditions. The source in GCMS will be periodically swapped from Electron Impact (EI ) to Chemical ionisation (CI). Turnaround time will be variable depending on the workload.

High Resolution Accurate Mass Measurements

A labour-intensive technique, so please keep these requests to a minimum. It should only be needed on novel compounds or for data reported in a paper or a thesis.

To submit a sample, use the original request form with the spectrum attached, enter the details in the login system, change the log number on the form but leave the sample attached. Turnaround time is usually less than a month. If samples are urgent, please inform a member of the MS staff.