Melbourne Mass Spectrometry and Proteomics Facility


The Melbourne Mass Spectrometry and Proteomics Facility (MMSPF) located at the Bio21 Institute is one of the largest mass spectrometry facilities in Australia. The MMSPF is an open access facility that provides academic and industry researchers access to specialist mass spectrometry and proteomic equipment and expertise.  

The Facility has 15 mass spectrometer based systems and five full time Ph.D. staff dedicated to providing all experimental design, training, machine time, and informatics support required to execute any proteomics or lipidomics research project.  The facility provides all users direct access to instrumentation and trains them to perform their own proteomics or lipidomics experiments. 

Techniques such as protein identification (e.g. Gel spots, or immuno-precipitated protein), full scale proteomics (TMT, SILAC, DIA, Label free, etc), phosphoproteomics , N-Terminomics (in-vivo protease activity), protein structural characterisation (PTM's, disulphide arrangement, HDX, Crosslinking).   

The facility has the following instrumentation:
• 2 x Thermo OrbiTrap Fusion Lumos
• 2 x Thermo Q Exactive Plus Mass spectrometer
• 2 x Thermo OrbiTrap Eclipse mass spectrometer
• Thermo OrbiTrap Exploris 480
• Thermo OrbiTrap Exactive plus
• Agilent 6520 LC/ESI-TOF mass spectrometer
• Waters XS IMS QTOF Mass spectrometer
• Waters HDX Synapt system
• Bruker TIMS TOF Pro
• Shimadzu  9030 QTOF
• Shimadzu 8050 QQQ


Proteome sequencing and quantitation Gel spots Phosphoproteomics N-Terminomics Lable-free proteomic quantitation Tandem Mass Tag (TMT) based proteomics Cellular Thermal Shift Assay (CETSA) Immuno-precipitation Protein crosslinking Hydrogen Deuterium Exchange (HDX) Intact protein QC Synthetic chemical QC Peptide analysis Bioinformatics Data-dependent acquisition (DDA), Data-independent acquisition (DIA) and DIA based acquisition, SWATH-MS Electron transfer dissociation (ETD): method to fragment peptides that utilizes ion/ion chemistry Ultraviolet photodissociation (UVPD) Post-translational modifications LC/MS/MS Ion mobility Structural mass spectrometry Nano chromatography

Targeted analysis of pharmaceuticals and other small molecules

General untargetted analysis and relative quantitation of lipids from any sample Targetted analysis of LIPIDS Lipid characterisation

Single cell proteomics

All forms of proteomics data analysis: MAXQUANT - platform for mass spectrometry-based proteomics data analysis. Phosphomatics - helps researchers interrogate possible upstream kinases for phosphorylated peptides. Proteome Discoverer - small molecule structure identification software. PEAKS - proteomics software program for tandem mass spectrometry designed for peptide sequencing, protein identification and quantification. Skyline - state of the art modeling, analytics, and visualization software to produce highly accurate and visually stunning 2D and 3D products.

Analysis of metal ions bound to intact proteins

Inductively coupled plasma mass spectrometry (ICP-MS)


Shimadzu 8050 QQQ - used for targetted analysis of pharmaceuticals or small molecules (also used for proteomics)

All of the following for different proteomic experiments: Thermo OrbiTrap Fusion Lumos ETD, 2 x Thermo Q Exactive Plus mass spectrometer 2 x Thermo OrbiTrap Eclipse mass spectrometer Thermo OrbiTrap Exploris 480 Waters XS IMS QTOF mass spectrometer Waters HDX Synapt system Bruker TIMS TOF Pro Agilent 6530 QTOF Shimadzu 9030 QT

Agilent 8900 QQQ Inductively Coupled Plasma Mass Spectrometry -used for general cellular elemental (metals) analysis and metalloproteomics

Thermo OrbiTrap Fusion Lumos UVPD - Used for both untargetted and targetted analysis of Lipid samples

Access Information


A/Prof Nicholas Williamson
Facility Head


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