Biomedical Proteomics

Biomedical Proteomics at Children's Medical Research Institute (CMRI) is a collaborative research resource that combines applied proteomics with the development of Mass Spectrometry (MS)-based qualitative and quantitative methods for protein identification and characterisation. The facility supports CMRI and the Westmead Research Hub (WRH), as well as collaborations with groups and individuals from around Australia and the world by offering access to equipment and methodology as well as expertise in the assessment of feasibility and strategy development for projects and programs involving MS-based proteomics analysis.

Facility Access

If you believe an MS-based proteomics approach is suitable for your research, please discuss with your Research Project Leader who can then discuss the project feasibility, funding, expected time frame, access to Facility resources, and suitable candidates with the Facility Manager, Val Valova (

All candidates require extensive training and should have a background in, or aptitude for understanding the chemistry and physics of MS-based proteomics. They should also have a relatively long-term appointment to see the project through.


Currently the facility houses a total of eight MS systems.

Two SCIEX Triple TOF 5600 Plus 
The Triple TOF 5600 Plus is the only accurate mass MS/MS instrument with the speed and sensitivity to deliver comprehensive qualitative exploration, rapid profiling, and high-resolution quantitation in complex matrices – all in a single injection, on a single platform. Two TripleTOF 5600 Plus systems were funded by ACRF for the new ACRF-CFK. These instruments also have the capability to run metabolomics experiments, with the addition of a UPLC
Two SCIEX QTrap 5500
The 5500 QTRAP is specifically designed for label-free quantitative analysis by SRM, which cannot be performed on any other instrument available to us.  High selectivity results from monitoring one pair of precursor/fragment ions characteristic of a single peptide.  Many such "transition pairs" can be specified in any LC-MS/MS run, allowing many proteins to be quantified in parallel. The two instruments were funded by ACRF and Ramaciotti Foundations to equip the new ACRF-CFK. These instruments also have the capability to run metabolomics experiments, with the addition of a UPLC
The instrument is ideal for identification of bands/spots cut from gels.  MALDI sample plates allow for up to 384 sample identifications per semi-automated run. It enables high throughput analysis and rapid protein identification and quantification (iTRAQ).  The instrument was purchased in 2009 with funding from the Cancer Institute NSW (CI NSW) and the Ian Potter Foundation and is dedicated to cancer phosphoproteomics projects.  It has sufficient capacity to be applied to a variety of other projects requiring routine protein identification.

Thermo Elite Orbitrap
The Thermo Orbitrap LTQ is an ion trap configuration mass spectrometer. Its sensitivity in combination with a very high resolution (up to 10-fold higher than rival configurations) make it the top choice instrument for targeted phosphoproteomics research.  Its extraordinary mass accuracy allows for high-confidence identification of phosphopeptides. This item has been purchased with funding from CI NSW and since its installation in August 2009 has been successfully applied to a number of projects requiring in-depth phosphoproteomics analysis.

Two Thermo Q Exactive Plus (new)
The Thermo Q Exactive Plus hybrid quadrupole-Orbitrap mass spectrometer, equipped with a Thermo Ultimate UHPLC liquid chromatography system, enables rapid and confident identification and quantification of proteins, peptides, and post-translational modifications. It significantly improves the depth of proteomics analysis, due to its compatibility with the Tandem Mass Tag (TMT) multiplexing technology, which allows for the simultaneous quantitative analysis of up to ten samples.


The Biomedical Proteomics facility is located at the Children's Medical Research Institute


Further information

For further information, please visit