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Mass Spectrometry Centre

Home to a range of advanced analytical instruments and expertise, including some of the most powerful mass spectrometers in Australasia.

The Mass Spectrometry Centre provides  analytical services based around a range of mass spectrometers for the Faculty of Sciences, external research groups and commercial entities.

Comparison of Mass Spectrometry instruments

Instrument Triple TOF   QStar FTMS Q-Exactive ICP-MS GC-MS 2D-GCMS GC-MS
Model 6600 Triple TOF Q-Star XL LTQ-FT Q-Exactive 7700 Series 5975C Trace Ultra ISQ 5977A
Manufacturer Sciex Applied Biosystems Thermo Thermo Agilent Agilent Thermo Agilent
m/z range 5-40,000
5 - 40,000 50 - 4,000 50 - 6,000 6 - 260 1.6 - 1050 1.2 - 1100 1.6 - 1050
Mass Accuracy 2 ppm 20 ppm 0.2 ppm 1 ppm 0.5 - 1 amu 0.5 - 0.7 amu 0.2 - 0.5 amu 0.5 - 0.7 amu
Resolution FWHM 35,000 10,000 500,000 140,000 0.5 amu Max scan rate 12,500 amu/sec Max scan rate 11,111 amu/sec Max scan rate 12,500 amu/sec
Ionisation modes                




• AP          
•  •  •         
nESI •  •           
APCI   •  •         
APPI     •  •         
ICP         •       
EI           • 
LC capability Nano/capillary LC Capillary LC Capillary LC UPLC (TLX) •  GC 2D-GC GC
MS/MS •  •  •         
•  •         
CID •  •  •         
ECD     •           
PQD     •           
Autosampler Eksigent LC Packings Surveyor PAL Yes + LC CTC Dual CTC Agilent

Protein identification

PTM Analysis

Quantitative Global proteomics (SWATH, iTRAQ, sMRH HR)

Protein MW analysis

Ion mobility separation

Protein MW analysis

Protein identification

PTM Analysis

Quantitative Global proteomics (iTRAQ)


Protein molecular weight analysis

Protein identification

PTM Analysis


Protein MW analysis

Elemental analysis Metabolites eg Fatty acids, sugars, amino acids   Metabolites eg Fatty acids, sugars, amino acids Metabolites eg Fatty acids, sugars, amino acids

Electrospray Ionisation-Mass Spectrometry (ESI-MS)

Electrospray Ionisation-Mass Spectrometry (ESI-MS) is a powerful combination of technologies that permit the detection of ionised precursor species with minimal degradation prior to mass analysis. The following four of the centres ESI-MS instruments are capable of performing MS/MS for targeted fragmentation of isolated species, thus gaining important structural information.  While sample introduction by simple infusion is an option, all four instruments are set up with dedicated LC systems to provide separation of analytes upstream of the ionisation source. These instruments are used for various analyses including metabolomic profiling, metabolite identification, quantitative proteomic profiling and protein identification.


Sciex Triple TOF 6600 LC-MS/MS Instrument


Our newest LC-MS/MS instrument, the Sciex TripleTOF 6600 has state-of-the-art features supporting Variable Window SWATH Acquisition for comprehensive proteomic analysis, and high resolution Multiple Reaction Monitoring (MRM-HR) for accurate quantitation of target peptides in highly complex samples, e.g. biofluids and tissue samples. Equipped with an Eksigent nanoflow UPLC system for maximum sensitivity, this system is unrivalled in New Zealand for identifying, characterising and quantitating proteins and peptides, especially in complex mixtures, or where sample amount is limiting. During 2015 this system will also feature the Selexion ion mobility interface to allow the separation of different classes of analytes, resolution of structural isomers, reduction of background signals to improve sensitivity, and gas phase fractionation of complex mixtures. With a dynamic range in excess of five orders of magnitude and up to 200 MS/MS events per second, this is our most powerful instrument for proteomic applications.




The Q-Star XL Quadrupole-Time-of-Flight instrument is operated solely by facility staff and offers fragmentation analysis for peptide or metabolite identification by MS/MS. It is typically set up with capillary scale reversed-phase HPLC columns for chromatographic separations. It can also be used for simple infusion experiments. The instrument offers ESI ionisation with the option of a single round of fragmentation followed by mass analysis at a resolution of approx. 10,000 with approx 10-150 ppm mass accuracy.

Types of services offered:

  • Accurate intact MW measurement of proteins and unknown species.
  • Protein identification by LC-MS/MS from digested gel bands, immuno-precipitations, solution samples, tissues and biofluids. We have software licenses for Mascot, ProteinPilot and PEAKS. Multi-dimensional chromatography (eg Strong Cation Exchange (SCX) coupled with reversed phase) for the in-depth analysis of complex samples is available.
  • Relative quantitation of hundreds of proteins across multiple samples using the iTRAQ isobaric chemical tagging technique.

This instrument is charged by sample and not by hour.

The instrument is run primarily by centre staff for analysis services and is not available for self use.




The Thermo Finnigan LTQ-FT (Linear Ion Trap- Fourier Transform) mass spectrometer offers up to 10 rounds of fragmentation on any analyte using a fast scan rate in the ion trap, while the ICR cell provides resolution of up to 500,000 with sub ppm accuracy. This instrument is equipped with ESI, Nanospray, AP-MALDI, APCI and APPI ionization modes, and offers ECD (Electron Capture Dissociation) as an alternative mode of fragmentation.

  • Characterisation of purified proteins (e.g. accurate intact MW measurement, top down analysis) and unknown species by MSn with high resolution MS detection.
  • Manual and automated de novo sequencing of peptides from unsequenced organisms
  • Identification of post-translational modifications such as phosphorylation and glycosylation.
  • Multivariate analysis involving statistical comparisons of peptide and metabolite data sets in comparable sample series are performed using SIEVE
  • Use of HighChem MassFrontier v7 to assist in analysis of MSn fragmentation data
  • The LTQ-FT is well-suited to metabolite identification using high accuracy precursor analysis and MSn “ion trees”

This instrument is charged by sample and not by hour.

The instrument is run primarily by centre staff for analysis services and is not available for self use.



Our people

Please contact Martin Middleditch for more information or assistance with the TripleTOF, QSTAR or FT-ICR

Martin Middleditch is the Centre Manager and is the first contact point for any Mass Spectrometry enquiries. Martin has 18 years experience on a range of different platforms in the field of ESI-MS in areas such as drug discovery, protein characterisation, hormone profiling and quantitative proteomics. He has a special interest in applications on the TripleTOF and QSTAR XL housed in the Thomas Building.

Academics associated with this Centre

Associate Professor David Greenwood is a biochemist and works in the School of Biological Sciences.  He is responsible for the LTQ-FT.  He has had an association with mass spectrometry for his entire professional life using it as a tool in his research in a diverse range of interests from chemical ecology and protein chemistry, through to elucidating mechanisms of plant pathogen interactions.

See, Selected Publications


Thermo Q-Exactive Orbitrap LC-MS instrument


The Q-Exactive is an Orbitrap LC-MS/MS instrument capable of UHPLC and high mass resolution with accurate mass determinations. It can be used for molecular weight determination and structural elucidation, with or without UHPLC separation.

The mass spec part has a quadrupole and a collision cell, so it can do anything a triple quadrupole can do, with mass resolution up to 140,000.  It can be used to find MS2 fragments and thereby elucidate molecular structure and follow constant neutral losses of interest.  It has the low detection limits typical of most triple quadrupole instruments.


Metabolomics profiling, identification of unknown reaction products and HPLC peaks, peptide analysis, protein molecular weight determination.

The limit of Detection is in the pg/mL (parts per trillion) of sample injected, with a wide linear dynamic range of 1 – 5000.


  • The HPLC part is UHPLC capable, with pumps that can go to 1250 bar (18,300 psi) to provide the best possible chromatographic resolution. 
  • The instrument has the valving and software for on-line sample prep using a patented turboflow system.  This allows for minimal sample prep of biological samples such as plasma and blood.


A variety of unknown compounds in a number of solvents can be resolved from extracts of both animal and plant tissues including plasma, hair and placenta.


Our people

Please contact Margaret Coe for more information or assistance with the Q-Exactive LC-MS

Margaret Coe works as a Laboratory Technician in the School of Biological Sciences.  With more than 30 years of experience in chromatography and mass spectrometry, Margaret is happy to help with your LC-MS research needs.  Prior to joining SBS in 2013, Margaret worked for Thermo Fisher Scientific as the LC-MS Product Specialist.  Before that, Margaret was the Chromatography laboratory head for DB Breweries.  She started in her native Canada in the Research department of Dow Chemical, and published 13 papers whilst there.

See, Selected Publications


Gas Chromatography Mass Spectrometry (GC-MS)

Gas Chromatography Mass Spectrometry (GC-MS) is a high throughput analysis suitable for a wide variety of organic samples.  Its main advantage is that it can analyse a sample for many different compounds in a single analytical run, and identify compounds to a high degree of certainty.  This makes it very cost-effective and ideal for analysing samples containing unknown compounds.  The coupling of column chromatography with electron ionisation in GC-MS enables separation of isomers, which is not possible on “infusion only” mass spectrometers.  Sample introduction for the machines can be by injection of analytes in organic solvent, vapour purge and trap, thermal desorption or solid-phase microextraction.  


The Agilent 5977A is the newest of the GC-MS. It is used for metabolite profiling but can be configured for other types of analysis. It has a Agilent autosampler complete with vortexer and heater. The MassHunter software is used for data analysis.

The Agilent GC-MS (SBS) is currently configured with a mid-polarity column (1701) primarily for metabolomics analysis via liquid injection.  It has a CTC PAL autosampler and the NIST05 mass spectral library.

The Thermo GC-MS (SBS) is currently configured with a mid-polarity column (1701) primarily for metabolomics analysis via liquid injection and has a programmable temperature vaporising (PTV) injector.   It has a CTC PAL autosampler and the NIST11 mass spectral library.

The Agilent GC-MS (SCS) is configured with a non-polar 5ms column for analysis of a broad range of compounds via liquid injection.  It has an Agilent autosampler and the NIST08 mass spectral library.

The Shimadzu QP2010 Plus GC-MS (SCS) is currently configured with a non-polar 5ms column for a broad range of compounds via automated solid phase microextraction (SPME).  It has a CTC PAL autosampler and the NIST08 Mass spectral library.  This GC-MS also has an olfactory sniffer option.  


  • Sample preparation including extraction and derivatisation
  • GC-MS analysis
  • Data processing techniques


Our GC-MS are capable of detecting a wide range of compounds including:

  • Amino and organic acids
  • 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
  • Phthalates, plasticisers, silicones
  • Unknown compounds

Samples that we have developed methods for include:

  • wine, juice, vinegar
  • honey
  • animal tissue extracts
  • feathers
  • body fluids: milk, plasma, urine, oil glands
  • bacterial cultures, fungal cultures, mammalian cell cultures
  • plant material

Metabolomics service

Our GC-MS services include metabolomics analysis.  Metabolomics is an unbiased approach to the analysis of small molecules (metabolites) used or produced by cells.  Analysis of a metabolic profile is a snapshot of the cell metabolism at a given growth phase, environmental condition or genetic modification.  The sample preparation and derivatisation techniques we use are designed to maximise the response of a wide range of metabolites.  Our metabolomics data processing is automated.  The raw data output from the GCMS is analysed using automated mass spectral deconvolution and identification software (AMDIS) against an in-house library of derivatised metabolites.  In‑house software is used in conjunction with the AMDIS output to process data so that trace levels of metabolites normally excluded by AMDIS are reported as non-zero values. 

Additional expertise

In addition to our specialised metabolomics work we also offer general GC-MS assistance as well as staff-specific expertise:

  • GC-MS method development and optimisation
  • Solid-phase microextraction (SPME – GCMS)
  • Training for students in GC-MS operation and maintenance
  • Expertise in GC-MS analysis of amphetamine-type stimulants (ATS)
  • Expertise in analysis of chemical contamination from clandestine methamphetamine laboratories

Our people

Please contact Erica Zarate for more information or assistance with the GC-MS.

Erica Zarate holds a MSc (Biological Sciences) and a PhD (Biological Sciences) in lipid and fatty acid analysis of sea urchin gonads using the GC-MS from the University of Auckland. She has been working with GC-MS since 2010 during her PhD and then as a GC-MS technician. Prior to her PhD, Erica worked as Research Technician in the Marine Lab at the University of Auckland managing the research laboratory, performing biochemical analysis and using the TLC-FID. Erica provides technical support for metabolomics analysis, sample preparation, calibration and maintenance of GC-MS and GC-MS data processing.

Academics associated with this centre

Associate Professor Silas Villlas-Boas is a biochemist with a scientific career focused primarily on microbial physiology, metabolomics and biodiscovery of bioactive metabolites. Dr Villlas-Boas research group works in close collaboration with industry developing new, cutting edge technologies relevant in industrial fermentation processes, human/animal disease development and in food processes. He had over 70 scientific publications, 9 book chapters and 3 registered patents.

See, Selected Publications


Inductively Coupled Plasma Mass Spectrometry (ICP-MS)


The University of Auckland operates an Agilent 7700 ICP-MS that can be coupled to our deep-ultraviolet (193 nm) New Wave Excimer laser ablation system or LC-MS (for compound-specific elemental analysis). The ICP-MS is equipped with collision cell technology (He) for reduction and elimination of spectral interferences on difficult to analyse elements.

Inductively Coupled Plasma Mass Spectrometry (ICP-MS) is a technique suitable for elemental analysis of a wide range of inorganic and organic materials, including geological, biological, medical, agricultural and environmental samples. Its main advantage is that it can 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 ICP-MS) with typical detection limits in the (sub)parts per trillion (solutions) or parts per billion range (solids). 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. Elements that can be analysed by ICP-MS include: Li, Be, B, Na, Mg, Al, Si, P, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Ga, Ge, As, Se, Rb, Sr, Y, Zr, Nb, Mo, Ru, Rh, Pd, Ag, Cd, In, Sn, Sb, Te, Cs, Ba, rare earth elements (actinides), Hf, Ta, W, Os, Re, Ir, Pt, Au, Hg, Tl, Pb, Bi, Th and U.

Our services include:

  • Sample preparation including mounting of solids for laser ablation ICP-MS and digestion of samples for solution ICP-MS analysis
  • Elemental analysis of a wide range of sample types either by laser ablation or solution ICP-MS

We have previously developed and applied methods that include:

  • rocks and glasses in volcanic systems
  • geochronology of minerals
  • (micro)fossil records of paleo-climatology and -oceanography
  • meteorites and the origins of the Solar System
  • kai moana (paua, cockles, mussels) and aquaculture
  • fish otoliths and life histories
  • plant and wood material
  • animal/human teeth and migration
  • provenancing of archaeological artefacts
  • anti-cancer drugs

Our people

Please contact Stuart Morrow  on extension 88760 for more information or assistance with the ICP-MS

Stuart Morrow provides technical support to the ICP-MS laboratory and has a BSc (Honours) in Biochemistry with a sub-focus in Analytical Chemistry from McMaster University, Ontario, Canada. Stuart has >8 years in practical laboratory experience in both research and manufacturing facilities including acquisition, installation and commissioning of analytical instrumentation, ICP-MS method development, operation, maintenance and troubleshooting, and sample preparation techniques (dissolution, digestion, fusion and impinging). Stuart can be contacted for information regarding commercial and routine analyses. Stuart also has expertise in a range of other analytical techniques, including GC-MS/FID, HPLC-UV/MS, TLC, and IR, FTIR, UV/VIS, fluorescence and atomic absorption spectroscopy and spectrometry.

Academics associated with this centre

Professor Joel Baker (Environment), Associate Professor Christian Hartinger (Chemical Sciences) and Dr Michael Rowe (Environment) have a combined experience of 40 years in elemental and isotopic analysis by plasma source mass spectrometry, including novel technique development and its applications in earth, ocean, space, biological, chemical, archaeological and medical sciences. Baker, Hartinger and Rowe are available to discuss facilitating collaborative projects within their areas of research expertise. These staff also have expertise in other related techniques, including electron microprobe analysis, X-ray diffraction, X-ray fluorescence spectrometry, multiple-collector ICP-MS, and stable isotope analysis. 


See, Selected Publications


Martin Middleditch is the Centre Manager for Mass Spectrometry. Please contact Martin if you require more information or assistance.