Mass spectrometry Facility

The Mass Spectrometry Facility of the School of Chemistry provides analytical services for the researchers in the School of Chemistry, other researchers in the University of Sydney and users outside the University.

Mass spectrometry measures gaseous ionized samples and the methods used for ionization in the unit are EI, CI, MALDI, laser desorption, ESI and APCI.

There are three mass spectrometers in the Facility and low resolution and high resolution spectra can be obtained by most ionisation techniques.

Bookings for the Facility can be made through the online booking system:

Online Booking System (internal access only)


Bruker amaZon SL mass spectrometer (ESI, APCI, direct probe)

Bruker amaZon SL mass spectrometer (ESI, APCI, direct probe)

The amaZon is a quadrupole ion trap mass spectrometer obtained in 2015. The mass range of this instrument is m/z 50-4000 and the ion trap is ideally suited for MS/MS and MSn experiments with fast polarity switching.

The normal mode of ionization used in the amaZon is Electrospray Ionization (ESI). Samples in dilute solution are sprayed into the source and evaporation of the solvent allows gaseous ions to enter the mass spectrometer. This is a very mild (soft) form of ionization and ions in the solution phase can be converted to ions in the gas phase. Neutral molecules must be ionized by addition of a proton or a sodium ion producing positive ions or removal of a proton (or addition of a halide ion) to form negative ions.

The most suitable solvents for electrospray are methanol, acetonitrile, methanol/water, dichlomethane/methanol or dimethylformamide/methanol. Hexane or other hydrocarbons such as toluene are generally not suitable for electrospray. Where protonation of the meolcule is expected or desired, dilute solutions of acid such as acetic acid may be added to the sample solution.

This instrument also allows ionization by Atmospheric Pressure Chemical Ionization (APCI) and can be fitted with a direct probe to allow solid samples to be heated to 400 oC and the vapour formed to produce APCI like spectra.

ThermoFinniganPolarisQ GC/MS (EI, CI)


The PolarisQ is a quadrupole ion trap mass spectrometer with a mass range of m/z 10-1000. The mass spectrometer is attached to a Trace 2000 GC and also has a Direct Emission Probe Probe (DEP) with a controller assembly.

The mass spectrometer may be used to produce electron impact (EI) or chemical ionisation (CI) spectra. The ion trap is ideally suited for MS/MS and MSn experiments.

The GC/MS system may be used to determine mixed systems with molecules having molecular weights of m/z < 550. The Direct Insertion Probe may be used to obtain spectra of organic and organometallic compounds with molecular weights up to m/z 1000.

This instrument can perform automated liquid injections, manual headspace and manual SPME injections.

Bruker autoflex speed LRF MALDI-TOF mass spectrometer

Bruker autoflex speed LRF MALDI-TOF mass spectrometer

This Matrix Assisted Laser Desorption Ionization – Time of Flight (MALDI-TOF) mass spectrometer was obtained in 2015. This instrument can operate in linear or reflectron mode.

The mass range of this instrument is 1-600,000 m/z. It produces spectra with resolution of >25,000 at m/z 4000 in reflectron mode and mass accuracy of <10ppm in reflectron mode after external calibration. It is equipped with a smartBeam laser that operates at up to 2kHz and controllable to 10-100um spot size.

The mass spectrometer is equipped with a TLC-MALDI holder and flexImaging software to allow MALDI-imaging experiments to occur for TLC/tissue samples prepared elsewhere. It is capable of performing high energy MS/MS experiments using post source decay either with a collision cell or without.

This instrument also has polymerix software to aid in co-polymer interpretation and biotools for proteomic analysis.

Bruker 7T Fourier Transform Ion Cyclotron Resonance Mass Spectrometer (FTICR)

Bruker 7T Fourier Transform Ion Cyclotron Resonance Mass Spectrometer

The 7 Tesla FTICR was purchased with an ARC LIEF grant. This ion trap instrument has an actively shielded, refrigerated superconducting magnet.

The resolution of > 900,000 at m/z 400 and mass accuracy of < 1 ppm for most samples makes this an ideal instrument for high resolution and accurate mass determinations. The mass range is m/z 100-10000.

There is a dual ESI/MALDI source and also an APCI source. The ion trap cell is ideally suited to carry out MS/MS experiments, these may be accomplished by Collision-induced Dissociation or Electron Capture Dissociation of the selected trapped ions.

Sample submission information

The Mass Spectrometry Facility provides analytical services for organic compounds, biochemical compounds and organo-metallic compounds. To submit a sample, please fill out the Sample Submission Form (pdf version) and send it with the sample to Mass Spectrometry Unit, Room 246, Madsen Building, F09 The University of Sydney, NSW, 2006 by mail or by person.

To obtain a mass spectrum, the sample must first be ionized. The ionization techniques available in the Unit are EI, CI, MALDI, ESI and APCI at present. Each technique has its own advantages and limitations. Please consult the staff in the unit if you cannot decide which of the techniques would be suitable for your sample.

Samples should be submitted in a sample screw-cap vial labelled with a sample identification code. About 0.1 mg to 1 mg of solid or liquid samples is required. For normal EI or CI MS, solvent free and pure samples are preferred because solvents or impurities may suppress the peaks of interests and complicate the structure analysis. For MALDI, ESI, APCI, GC/MS or LC/MS, please specify solvent. For samples requiring GC/MS analysis, a GC trace and the column conditions should be provided, if possible.

For users from the School of Chemistry (internal users), the Sample Submission Form must be signed by a financially responsible person and the account number should be included. A University Service Requisition Form should also be attached for Sydney University users outside the school. A official order form must accompany the request for users outside the University. For the information about the costs of the services, please see the Analysis Costs or talk to the staff of the unit.

Analysis costs

The charges for services performed by the Mass Spectrometry Facility are listed below:

  School of Chemistry The University of Sydney Non-University of Sydney
ESI $15 $30 $60
APCI $15 $30 $60
EI $15 $30 $60
CI $15 $30 $60
GC/MS (El or CI) $15 $30 $60
MALDI $20 $40 $75
High Resolution (Accurate Mass) $50 $75 $100

Other services such as data interpretation, MS/MS etc. will be charged by the hour in negotiation with the Mass Spectrometry staff.

Please note:
Non-University of Sydney charges apply to all external users, whether affiliated to the School/University or not. They also apply to any contract research or consultative work performed by members of the School or University. If in doubt, it may be discussed with the staff of the Mass Spectrometry Facility.

Special rates will also apply for investigators involved in the ARC LIEF grant used to obtain the FTICR.

The costs of analysis may be discussed with the staff of the Mass Spectrometry Facility.

External invoices will include an additional 10% GST charge.

Contact details

Dr Nick Proschogo

Dr Nick Proschogo
Staff Scientist
Mass Spectrometry Facility
School of Chemistry
F09 - Madsen
The University of Sydney NSW 2006, Australia
Room 246
T (office) +61 2 9036 6495
T (lab) +61 2 9351 2738
F +61 2 9351 2738