Mass spectrometry (MS) has emerged as one of the most valuable tools in modern biology.

In proteomics, it facilitates the measurement of protein mass and protein identity, as well as quantification with extraordinary sensitivity, speed and accuracy.

MS can also be used to analyse other molecules such as lipids, glycans and oligonucleotides for identification and often quantification. It's a core technology for "omics" research.

Contact us

Contact Dr Amanda Nouwens for more information on sample preparation, experimental design, prices, and seminar dates.

Analyses and applications


  • Protein identification from complex mixtures and purified proteins using bottom-up or top-down methods.
  • Quantitative workflows (SWATH, multiple reaction monitoring, labelled techniques).
  • Analysis of post-translational modifications (eg glycopeptides, dimethylarginine, succinylation, phosphorylation, disulphide-bond mapping, etc).
  • Intact mass analyses to determine exact protein size.
  • Native MS for protein complexes.
  • De novo sequencing of novel proteins.

Applications and projects

  • Identification of proteins (eg those not encoded by main ORFs; confirmation of recombinant protein purification; identification of proteins from co-IP experiments). 
  • Relative quantification of proteins from different growth conditions using SWATH (wildtype versus mutant yeast, normal versus Alzheimer brain, normal versus diseased patient saliva samples).
  • Identification of biomarkers in sera and saliva for human diseases.
  • Mapping post-translational modifications, including type, amino acid location/s and analysis of when proteins are modified (eg glycosylation status in yeast mutants, dimethyarginine status on hnRNP proteins, disulphide bond linkages in recombinant proteins).
  • Confirming intact protein size so as to identify PTMs or truncations on proteins. 

Our facility has enabled a large number of School researchers and collaborators to answer their biological questions.

Equipment and location


ABSciex TripleTof 5600

The TripleTof 5600 mass spectrometer is a quadrupole-hybrid time-of-flight instrument. It's a sensitive state-of-the-art instrument with high resolution, mass accuracy and fast acquisition rates (~50 MS/MS per second), suitable for discovery projects (ie what proteins are in my sample?), relative quantitation of proteins (SWATH, iTRAQ, SILAC etc), intact mass analysis (<10 ppm error) and (some) native MS. A Shimadzu Prominence 1D nano-LC system is used to provide upstream separation of samples with reversed phase chromatography. 

ABSciex QTRAP 5500

The QTRAP 5500 mass spectrometer is a quadrupole-TRAP instrument most suitable for quantification of samples and structural analyses (eg MS^3, neutral loss and precursor ion scans). It has at least 10-fold sensitivity over previous models. An Agilent 1100/1200 capLC and a Shimadzu UHPLC system are available for upstream separation of samples.

Orbitrap Elite with ETD

The Orbitrap Elite with ETD is a state-of-the-art hybrid trap mass spectrometer. Suitable for protein identification from both bottom-up and top-down methods, as well as quantification of molecules (labelled samples), intact mass analyses, and characterisation of post-translational modifications. Accurate to < 1ppm and with resolution >240,000. A Dionex nano-UPLC system is used to provide upstream separation of samples with reversed-phase chromatography.  

Associated equipment and software

  • Shimadzu Prominence nano-LC system.
  • Agilent 1100/1200 capLC system.
  • Shimadzu Prominence UHPLC system.
  • Various MS software programs (ProteinPilot, MRMPilot, MultiQuant, LipidView).
  • Speed-vacuum concentrators, freeze-driers, water-bath sonicators, offline HPLC fractionators and incubators. 


Molecular Biosciences Building (Building 76), Room 441A

Sample requirements and training

Sample requirements

Sample preparation is critical: samples need to be detergent- and salt-free.

In general, for protein identification and quantification, samples need to be enzymatically digested (eg trypsin) followed by SPE (solid phase extraction) clean-up. 

The amount required depends on sample complexity with sensitivity on the order of femtomol to attomol range. As an easy guide, a Coomassie stained gel slice should provide excellent results for gel slices, or 1-5ug of a complex mix of digested proteins in solution.

To provide greater proteome sequence coverage, we offer an offline HPLC system for upstream fractionation of complex samples prior to LC-MS/MS analysis.

For intact mass analysis, proteins need to be in a detergent-free buffer or solvent.

The amount required depends on size:

  • 5 kDa: ~25 pmol
  • 20 kDa: ~100 pmol
  • 60 kDa: ~500 pmol.


We offer twice-yearly introductory seminars on MS that cover:

  • an introduction to MS
  • sample preparation for proteomics
  • database searching.

Charges and considerations


We charge an access fee to cover consumable and maintenance costs.


Internal users

Contact us for analyses rates.

External users

Individual analyses: $320 per sample

If you submit more than 20 samples within two months, prices will convert to tier charges.

Tier charges

Tier 1 group user <400 samples or <300 hours $6400 for 1 year or $3200 for 6 months (at half the usage rate)
Tier 2 group user 401–800 samples or 300–600 hours $11,200 for 1 year or $5600 for 6 months (at half the usage rate)
Tier 3 group user 801–1600 samples or 600–1200 hours

$16,000 for 1 year or $8000 for 6 months (at half the usage rate)


  • For usage above 1600 samples (or 1200 hours annually), prices are by negotiation.
  • As some samples require long acquisition times, tiers are based on sample number and hours.


UQ users have priority of access.

You'll need to undertake the relevant building and other inductions before using equipment.