Staff members using our proteomics facilities


Study the protein complement of cells, tissues and organisms
While the human genome has a little over 20,000 genes, the human proteome is estimated to contain over one million distinct proteoforms. Start exploring this complex and dynamic world with the assistance of our world class mass spectrometers.

Identifying and quantifying complex mixtures of proteins is a huge task. The best platform to use depends on the preferred method of quantitation. For example, Q Exactive HF and Q Exactive HF-X are popular for label free and SILAC analysis. While 6600 TripleTOFs is preferred for SWATH analysis. The Fusion Tribrid mass spectrometer is recommended for optimal TMT labeled based analysis.

Through the use of contemporary enrichment techniques, it is possible to identify and quantify tens of thousands of changes in the phosphoproteome. High throughput methods such as ‘EasyPhos’ are coupled with the latest Q Exactive platforms to create exceptional methods.

Glycomics is the characterisation of polysaccharides, typically derived from proteins. The Orbitrap Velos Pro platform is dedicated for this workflow. In glycopeptidomics, the aim is to identify both the sugar and the peptide while they are still linked together. This can be done on the Velos, or on the Fusion Lumos mass spectrometer which is equipped with Electron Transfer Dissociation and UVPD.

Top-down and intact protein analysis using either the Fusion Tribrid Mass spectrometer and/or one of the 6600 TripleToF mass spectrometers enable the characterisation of the whole protein, including any post-translational modifications. 

Protein-protein interactions and protein complex can be analysed using the latest mass spectrometry compatible cross linking methods and our Fusion Tribrid Mass spectrometer platforms.

We have a range of analysis packages for quantitative proteomics analysis, including:

  • ProteinPilot
  • PeakView/SWATH
  • Progenesis QI for Proteomics
  • Proteome Discoverer

Other types of available proteomics analysis software include:

  • Spectronaut
  • Scaffold
  • Byonic

We recommend MaxQuant as an open-source package for quantitative proteomics analysis. The software is available on a mix of high performance workstations, virtual computing resources and network licenses.

A full complement of apparatus for running 2D gels from 7cm to 24cm is available. Progenesis SameSpot software is available for the analysis of 2D gels. 


Sydney Mass Spectrometry

  • Sydney Mass Spectrometry has locations across multiple sites including the Charles Perkins Centre on the University of Sydney Camperdown campus, and the Kolling Institute on the Royal North Shore Hospital grounds. Our headquarters are in the Charles Perkins Centre.
Delivery address
Sydney Mass Spectrometry via The Hub Loading Dock, Charles Perkins Centre (D17) Orphans School Creek Lane, Camperdown University of Sydney, NSW 2006 Dock receiving time: 08:00 – 16:00, Mon - Fri.