Mass Spectrometry Centre

Home to expert operators of a range of advanced mass spectrometers, including some of the most powerful instruments in Australasia. Analytes can range from elements, metabolites, lipids, pharmaceuticals and peptides to intact proteins.


  • Sciex TripleTOF 6600 LC-MS/MS
  • Bruker Solarix XR 7T FT-ICR
  • Agilent 7700 ICP-MS
  • Thermo Q-Exactive LC-MS/MS
  • Agilent 5977A GC-MS
  • Agilent 5975C GC-MS
  • Thermo ISQ GC-MS
  • Thermo LTQ Ion trap LC-MS/MS
  • Agilent 6460C Triple Quadrupole
  • Bruker micrOTOF-QII LC-MS/MS
  • Agilent 5975C GC-MS (SCS)

Sciex TripleTOF 6600 LC-MS/MS

This nanoLC-MS/MS Q-TOF delivers high sensitivity, high acquisition speed and high-resolution MS and MS/MS spectra. Well suited to analysing highly complex proteomic samples, as well as simpler mixtures where accurate targeted quantitation is required.

Quantitation can be achieved by labelled (e.g. iTRAQ) label-free (e.g. SWATH/DIA) or MRM approaches.

Typical applications: Identifying and characterising proteins, and the relative quantitation of selected proteins or whole proteomes.

Specifications: Typical flowrate 300nl/min, injection volume 0.5-10ul, Resolution ~30,000 (both MS and MS/MS mode), MS/MS acquisition rate ~50Hz for IDA mode, up to 200Hz for targeted mode.

Bruker SolariX XR 7T FT-ICR

The SolariX XR 7T FT-ICR is the highest resolution mass spectrometer in New Zealand, capable of a wide array of experiments including: native mass spectrometry of large proteins and protein complexes, and 2D/3D analysis of thin tissue sections (MALDI imaging).

The ultra-high resolution, mass accuracy, and sensitivity allow accurate determination of large proteins/protein complexes, lipids, metabolites, proteins in biological tissues, or identification of low abundant species in a complex mixture.

Typical applications: Accurate MW determination of proteins or small molecules, analysis of protein complexes, gas phase experiments using dual channel emitters, MALDI imaging of biological tissues.

Specifications: MALDI or infusion ESI interface, resolution up to 1,000,000 at m/z 400, and “Coming soon”: Rapid reaction monitoring for Hydrogen/Deuterium Exchange-Mass Spectrometry to determine the solution phase structure of biomolecules.

Agilent 7700 ICP-MS

The Agilent 7700 Inductively Coupled Plasma Mass Spectrometry (ICP-MS) is suitable for trace elemental analysis of several materials, including geological, biological, metallurgic, agricultural and environmental samples.

Its main advantage is that it can rapidly analyse a large number of elements in a single analytical run. Samples can be analysed in either a liquid (solution ICP-MS) or solid form (laser ablation; LA-ICP-MS; using the ASI Resolution 193nm laser). 

The typical lower detection limits for most elements are in the parts per trillion range, however this dependent on the analysis mode and sample matrix. The ICP-MS is equipped with collision cell technology (He) for reduction and elimination of polyatomic interferences on difficult to analyse elements.

In addition to elemental analysis, the ICP-MS can be used for the determination of isotopic ratios of selected elements to a precision of ±0.2% for isotopic tracing and uranium-lead dating of minerals from rocks such as zircon.


Capillary LC-MS/MS Q-TOF. Capable of providing accurate molecular weight (+/- 0.003%) analysis of intact proteins, peptides and small molecules. LC-MS/MS analysis can be used for protein identification in moderately complex samples, or for quantitative work using MRM workflows.

Typical applications: identifying proteins from gel bands or solution digests, molecular weight profiling of pure protein solutions or simple mixtures.

Specifications: Typical flowrate 6ul/min, injection volume 1-10ul, Resolution ~10,000, MS/MS acquisition rate ~0.5-1Hz for IDA mode, up to ~10Hz for targeted mode.

Thermo Q-Exactive LC-MS/MS

The Thermo Scientific Q-Exactive hybrid quadrupole-orbitrap mass spectrometer combines high-performance quadrupole precursor selection with high-resolution, accurate-mass (HR/AM) Orbitrap detection.

High-resolution MS/MS data provides ultimate confidence for a wide range of qualitative and quantitative applications. This instrument is primarily used for non-targeted metabolomics projects, but can be used for any targeted projects.

It performs similar functions to triple quadrupole mass spectrometers, but with greater mass accuracy for more confident identification.

Typical applications: untargeted metabolomic profiling, lipid analysis, targeted small molecule analysis.

Specifications: Mass resolution up to 140,000, UPLC capable of 18,000psi, TLX on-line sample prep system, fast polarity switching.

Agilent 5977A, 5975C and Thermo ISQ GC-MS

These instruments are used primarily for metabolite profiling. Various types of derivatisation are employed to enable the analysis of organic acids, amino acids, fatty acids, sugars and other volatile compounds.

Solid Phase Micro Extraction (SPME) is an option to analyse non-derivatised volatiles.

Typical applications: metabolomics profiling of extracts from biological samples, mainly with methylchlorofomate derivatisation for general work, but also TMS and methyl esterification for other classes of analyte, e.g. fatty acid methyl esters.

Data analysis is supported by access to the Wiley NIST 2017 Mass Spectral Database (>1 million EI spectra), MassHunter, Chemstation, AMDIS, NIST MS, MassOmics, R and Python.

Thermo LTQ Ion Trap LC-MS/MS

This instrument is capable of analytical or capillary-scale LC-MS/MS workflows. The linear ion trap allows for MSn experiments to be performed for structural studies.

The mass analyser offers various spectral resolution modes and acquisition speeds. ESI, APCI and APPI are ionization options.

Typical applications involve the LC-MS analysis of intact proteins, protein digests or small molecules.

Specifications: Mass Range: 50-4000 m/z, up to 10 MS/MS events per second.

Agilent 6460C Triple Quadrupole

The Agilent 6460 Triple Quadrupole LCMS combines the separation power of HPLC with the detection power (i.e. sensitivity and selectivity) of a triple quadrupole instrument for targeted analysis of small molecules in complex samples.

The Agilent Jet Stream technology uses super-heated nitrogen to improve ion generation and desolvation, which leads to greater signal and reduced noise. Fast multiple reaction monitoring (MRM) speeds allow for analysis of over 100 overlapping compounds in a given retention time window.

Triggered MRM (tMRM) combines fast and sensitive MRM quantitation with the generation of a product ion spectrum for library searching and compound screening and confirmation.

Specifications: Mass Range: 5-2,000 m/z, Mass Resolution: 0.7 amu (FWHM).

Bruker micrOTOF-QII LC-MS/MS

The Bruker micrOTOF-QII high-resolution mass spectrometer can be used for the identification of volatile small molecules, peptides and proteins.

This instrument is equipped with ESI, Nanospray and APCI ionization capabilities. Samples may be directly infused, or introduced through the Dionex HPLC or Advion Nanomate interface.

Specifications: mass resolution to 17,500, over the range 50 – 20,000 m/z, mass accuracy of within 4 ppm.

Agilent 5975C GC-MS (SCS)

The Agilent 7890A gas chromatograph at the School of Chemical Sciences (SCS), coupled with an Agilent 5975C mass spectrometer, can be used for the analysis of fatty acids, sterols, alkanes, aldehydes, amines, sugars, sugar alcohols and amino-sugars (mono, di and tri-saccharides), polycyclic aromatic hydrocarbons (PAH), volatile compounds – fragrances, odours, fuel residues, illicit drugs, phthalates, plasticisers, silicones and unknown compounds.

It is currently configured with a non-polar (5-MS) column and an EI source, with the option of other polar columns, as well as a CI source. It has an Agilent autosampler and the NIST08 mass spectral library.

Data analysis is supported by access to MassHunter, Chemstation, AMDIS, NIST MS softwares. Our services include training for students in operation and maintenance, method development and optimisation. 

How we can help you

Project Design/method development

Our experienced team members are available to discuss the options and possibilities for your project, and help to guide your analysis in the right direction.


The various instruments available in this core have individual pricing regimes. In some cases lower rates for self-service access are available.


Most of these instruments are booked through the iLab system. Users need to be a member of a lab within iLab, with access to funds, in order to lodge a request.

Sample requirements

These vary depending upon what instrument, and which type of analysis is under consideration. Please contact the relevant person listed below to be sure that you have properly addressed the specific sample preparation requirements of your project.

Training requirements

Some mass spectrometers will have a self-use option, predicated on some training being undertaken in advance.

Data Analysis

Please liaise with the relevant facility staff member to ensure that you are getting the most out of your dataset. Some data processing software is available through various virtual machines to allow remote data processing by users.  

Related instrumentation

  • BIRU operate a MALDI-TOF for Imaging MS work | Dr Gus Grey, Faculty of Medical and Health Sciences
  • ACSRC operate QQQ and Q-TOF instrumentation | Dr Frederik Pruijn, Faculty of Medical and Health Sciences
  • Engineering operate QQQ and GC-MS instrumentation | Dr Jishan Liu (QQQ) or Dr Patricia Cabedo Sanz (GC-MS) in the Faculty of Engineering

Other resources

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