Mass spectrometry has a range of applications, including molecular discovery, identification, characterisation and quantification. The mass spectrometry equipment the University of Queensland has on offer is located at the Centre for Microscopy and Microanalysis, the Centre for Advanced Imagery, the Institute of Molecular Bioscience, the School of Chemistry and Molecular Biosciences and the UQ Diamantina Institute.

Mass spectrometry - Centre for Microscopy and Microanalysis/Centre for Advanced Imagery


Mass Spectrometry Imaging Facility produces the spatial distribution of various analyte classes present in tissue samples. By bringing MSI together with other imaging modalities such as microscopy and MRI, a more holistic picture of biomolecular imaging can be achieved. Within the facility we have a number of MALDI-TOF/TOF systems, and an atmospheric pressure MALDI which can be coupled to QqTOF and QIT analysers. The various system configurations allow us to answer a broad range of experimental questions. HPLC-spotting robot systems are used to facilitate analyte identification by correlating MSI and LC-MALDI from serial tissue sections.


  • Bruker Autoflex Speed (MALDI-TOF/TOF)
  • 2 x Bruker Ultraflex III (MALDI-TOF/TOF)
  • Bruker MicroTOF Q II (QqTOF)
  • Bruker Amazon Speed with ETD (QIT)
  • Masstech AP-MALDI source
  • Dionex HPLC with Probot Spotting Robot
  • Dionex HPLC with Proteineer Spotting Robot
  • Agilent 3100 Offgel
  • Dionex HPLC with Thermo QqQ MS
  • 2 x Bruker Imageprep Systems
  • Basic Histology inc microtome for MSI sample prep
  • Various software available including Mascot, SCILs Lab, Flex Imaging, ClinProt Tools, Biomap


Doctor Brett Hamilton

Centre for Microscopy and Microanalysis

(07) 3365 3505

Level 7, Chemistry Building 68, St Lucia campus

Mass spectrometry - Institute of Molecular Bioscience


IMB’s Mass Spectrometry Facility is home to a suite of state-of-the-art mass spectrometry, high-performance liquid chromatography, and robotic instrumentation that have been refined and optimised to investigate biological systems in a high-throughput qualitative and quantitative manner.

The eleven available systems within the facility provide researchers with the resources to investigate a broad range of mass spectrometric applications, including molecular discovery, identification, characterisation and quantification.


  • Nano-HPLC-AB SCIEX Triple TOF 5600


Facility Manager

Alan Jones

Institute of Molecular Bioscience

(07) 3346 2996

Institute of Molecular Bioscience, IMB Building (Building 76), St Lucia campus

Mass spectrometry - School of Chemistry and Molecular Biosciences


Mass spectrometry facility for both biological and synthetic compounds, including proteomics, analysis of natural products and synthetic compounds.  Analyses include accurate mass measurement (small molecules and intact proteins), quantitation (SWATH, ITRAQ, SILAC, MRM assays); identification of proteins and other compounds; characterisation of post-translational modifications on proteins.


  • Thermo Orbitrap Elite with ETD with Dionex UltiMate 3000 RSLCnano 
  • Sciex TripleTof 5600 with Shimadzu Prominence nanoLC
  • Sciex QTRAP 5500 with Shimadzu Nexera UPLC 
  • Bruker MicrOTof-Q with Dionex UltiMate 3000 HPLC 
  • BRUKER HCT 3D Ion Trap
  • ProteinPilot v5.0 software
  • ProteomeDiscoverer v4.0 software
  • PeakView v2.1 software
  • ProSight software
  • Protein Deconvolution software
  • Agilent 1100/1200 HPLC system with UV detector and fractionator


Doctor Amanda Nouwens

School of Chemistry and Molecular Biosciences

(07) 3364 9490

Chemistry Building (Building 68), St Lucia campus

Proteomics - UQ Diamantina Institute


The facility provides specialised services for TRI researchers and external users.  The facility also faciitates training and access to specialised equipment for sample preparation, sample analysis and data analysis.


The following equipment is available to UQ users as part of the 'Core Facilities at TRI'.

  • Agilent 6520 HPLC-Chip QTOF LC-MS/MS
  • QNCC - Triple Quad Mass Spectrophotometer*
  • Agilent 3100 Offgel Electrophoresis (fractionator)
  • Agilent 1200 Standalone HPLC
  • Microplate Speedy Vac
  • Bravo Liquid Handler

(*TRI owned)


Translational Research Institute

Mass Spectrometry – Centre for Clinical Research


The Mass Spectrometry facility at UQ Centre for Clinical Research is located within the Centre for Clinical Diagnostics (CCD) and is NATA accredited for research, development and evaluation. The MS facility offers a range of services including protein identification, SWATH, quantitation of peptides and small molecules, post translational modifications, intact protein analysis, bacterial biotyping and lipidomics. 


  • SCIEX TripleTOF 5600 System
  • SCIEX QTRAP 5500 System
  • SCIEX TOF/TOF 5800 System
  • Shimadzu LCMS 8050 System
  • Agilent 6490 System
  • SelexION® Differential Ion Mobility (DMS)
  • Shimadzu Nexera UHPLC Systems
  • Eksigent NanoLC Ultra Systems
  • Eksigent MicroLC 200 System
  • Agilent 1290 Infinity
  • TriVersa Nanomate System
  • Eksigent EkSpot system
  • Agilent 1100 HPLC systems with UV detector and fractionator
  • Hamilton MicroLab® Star Robotic system
  • Agilent 3100 Offgel Electrophoresis Fractionator
  • ProteinPilot v5.0.1 Software*
  • ProteinPilot v4.5 Software (viewing)
  • Mascot Software
  • MarkerView 1.3.1 Software*
  • PeakView v2.2 Software (with SWATH acquisition softwarev2.0.1)*
  • BioPharmaView 2.1 Software
  • LipidView 1.2 Software
  • MultiQuant 3.0.3 CFR-compliant Software)*
  • LightSight v2.3 Software
  • Shimadzu LabSolutions Insight Software
  • Shimadzu LabSolutions Post Run Software

*Latest version of the Software available from August 2018


Doctor Sarah Reed

(07) 3346 5007